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

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

Micro-aerobic conditions based on membrane-covered improves the quality of compost products: Insights into fungal community evolution and dissolved organic matter characteristics

This study investigated the effects of micro-aerobic conditions on fungal community succession and dissolved organic matter transformation during dairy manure membrane-covered composting. The results showed that lignocellulose degradation in the micro-aerobic composting group (AC: oxygen concentration < 5 %) was slower than that in the static composting group (SC: oxygen concentration < 1 %), but the dissolved organic carbon in AC was greatly increased. The degree of aromatic polymerization was higher in AC than in SC. But the carboxyl carbon and alcohol/ether biodegradations were faster in SC than in AC, which promoted carbon dioxide and methane emissions, respectively. The relative abundances of pathogenic and dung saprotrophic fungi in AC were 44.6 % and 10.59 % lower than those in SC on day 30, respectively. Moreover, the relative abundance of soil saprotrophs increased by 5.18 % after micro-aerobic composting. Therefore, micro-aerobic conditions improved the quality of compost products by influencing fungal community evolution and dissolved organic matter transformation.

The regulators of soil organic carbon mineralization upon lime and/or phosphate addition vary with depth

Knowledge of the key factors regulating soil organic carbon (OC) mineralization in response to fertilizers and lime application is essential to understanding the effects of agricultural land management on soil OC preservation. Microbial community composition and OC availability to microorganisms have been proposed as the two most imperative factors controlling soil OC mineralization, although their relative importance is still under debate. Here we performed a laboratory incubation in combination with high-throughput sequencing and structural equation modeling to examine the mechanisms underlying the responses of OC mineralization in the topsoil and the subsoil of a volcanic soil (an Andosol) to the additions of lime and/or phosphate. Results showed that lime and/or phosphate additions induced distinct shifts in the microbial community composition and functional profiles in the topsoil and the subsoil. We found that OC mineralization relied on microbial community composition and functionality in the topsoil but was strongly related to the quality and quantity of the water-extractable OC (indicative of the OC availability) in the subsoil. These data suggest that the key regulator controlling the response of OC mineralization to lime and/or P additions shifts from microbial community composition to OC availability as soil depth increases in the Andosol. Our findings highlight the central role of mechanisms controlling soil OC mineralization in regulating the responses of mineralization to intensive agricultural management practices.

Green manure incorporation accelerates enzyme activity, plant growth, and changes in the fungal community of soil

Green manure can sustain agricultural production, preserve biodiversity, and mitigate soil degradation caused by long-term application of chemical fertilizers. Moreover, the application of green manure can improve soil health through increased soil biological activities. Nevertheless, little attention has been paid to the effects of leguminous and non-leguminous plants on phosphorus- and carbon-related enzyme activities and fungal community composition in soil. In this study, a pot experiment was carried out to elucidate the effects of two green manures on plant growth promoting potential, phosphorus- and carbon-related enzyme activities, and soil fungal community composition. Two green manure treatments (Brassica juncea and hairy vetch), poultry compost and control (no amendment) were applied and soil samples were collected after incorporation of green manure and after plant harvest. The results revealed that plant growth with hairy vetch was significantly higher than that with B. juncea and poultry compost, and soil enzyme activities were markedly higher with hairy vetch than with B. juncea. Both green manure amendments altered the soil fungal community composition. It is possible that the incorporation of green manure into soil and their mineralization and decomposition were controlled by the carbon: nitrogen ratio of the manures and that these manures were easily degradable by soil fungi. In particular, the incorporation of leguminous (hairy vetch) green manure with a low carbon: nitrogen ratio resulted in better plant growth through fast mineralization. Our findings suggest that green manure incorporation is an effective practice and provides substantial benefits to the soil-plant system.

Linking enhanced soil nitrogen mineralization to increased fungal decomposition capacity with Moso bamboo invasion of broadleaf forests

Plant invasion can markedly alter soil fungal communities and nitrogen (N) availability; however, the linkage between the fungal decomposition capacity and N mineralization during plant invasion remains largely unknown. Here, we examined the relationship between net mineralization rates and relevant functional genes, as well as fungal species composition and function following Moso bamboo (Phyllostachys edulis) invasion of evergreen broadleaf forests, by studying broadleaf forests (non-invaded), mixed bamboo-broadleaf forests (moderately invaded) and bamboo forests (heavily invaded). Fungal species composition and functional genes involved in organic matter decomposition (laccase and cellobiohydrolase), N mineralization (alkaline peptidases) and nitrification (ammonia monooxygenase) were determined via high-throughput sequencing and real-time PCR. Both net ammonification and nitrification rates were generally increased with bamboo invasion into the broadleaf forest, where the net ammonification rate, on average, was 10.8 times higher than the nitrification rate across the three forest types. The fungal species composition and ecological guilds were altered with bamboo invasion, as demonstrated by the increased proportion of saprotrophs but decreased proportion of symbiotrophs in the bamboo forest. The increased net ammonification rate in bamboo forest was positively correlated with both fungal species composition and functional groups, and the fungal lcc gene (for lignin breakdown) abundance explained 67% of the variation of the net ammonification rate. In addition, the gene abundance of ammonia-oxidizing bacteria (AOB) explained 62% of the variation of net nitrification rate across the three forest types. The increased soil ammonification and nitrification rates following bamboo invasion of broadleaf forests suggest that the bamboo-invasion associated increase in soil N supply provided a positive feedback that facilitated bamboo invasion into broadleaf forests.

Response of soil fungal community composition and functions on the alteration of precipitation in the grassland of Loess Plateau

A change in precipitation caused by climate change is an important factor that affects the biodiversity and ecological function of arid and semi-arid regions, but its influence on the composition and function of the soil fungi community in the grasslands of the Loess Plateau remains unclear. To fill this knowledge gap, we conducted an in-situ simulation experiment using five precipitation gradients (natural precipitation, increased and decreased by 40%, and 80%) in a natural restoration grassland for three years. The composition of soil fungal communities and their functions were analyzed using high-throughput sequencing techniques. Although the change of precipitation did not change the diversity index of soil fungi, it changed the composition and function of dominant fungal community groups. Specifically, decreased precipitation resulted in an increase in the relative abundance of Dothideomycetes and Boeremia by up to 12.17% and 9.93%, respectively, while these decreased with increased precipitation. The abundance of Basidiomycota, Glomeromycota, and Agaricomycetes abundance decreased by up to 11.27%, 6.96%, and 11.46% with decreased precipitation, but also decreased by up to 10.9%, 1.73%, and 10.51% with increased precipitation, respectively. However, the abundance of Ascomycota, Pezizomycetes, and norank_Pezizales increased by up to 22.58%, 7.45%, and 6.95% with decreased precipitation, and increased by up to 12.05%, 8.43%, and 5.81% with increased precipitation, respectively. The number of dominant fungal groups with interactive relationships weakened by 34.93% and 8.7% under decreased precipitation by 80% and increased 80%, respectively. Precipitation change had no significant effect on the proportion of saprotrophs, while a decrease of precipitation increased the endophyte-plant pathogens by up to 58.0% and decreased arbuscular mycorrhizal fungi by up to 92.6%. In brief, the dominant soil fungal communities could adapt and respond to climate change by altering the proportion of different dominant fungal groups by responding to moisture patterns with changes in the interrelationships between microbial communities and the proportional distribution of functional groups.

Rhizosphere fungal community structure succession of Xinjiang continuously cropped cotton

The large-scale long-term plantation of cotton in the Xinjiang region has been accompanied by a regular and wide outbreak of soil-borne fungal diseases such as verticillium wilt, which significantly damaged the local cotton industry. High-throughput sequencing data showed that the cotton field cultivation management measures pose a significant influence upon the original ecological soil fungal community structure. During long-term continuous cropping of cotton, a new soil fungal community structure emerges after several repeated adjustments over five years. The number of verticillium wilt pathogens in the soil increased rapidly with prolonged continuous cropping time, reaching a maximum at around the 10th y; moreover, the abundance of the verticillium wilt pathogen only serves as one of numerous essential factors for disease occurrence. The fungal community structure and the abundance of verticillium wilt pathogens in local cotton fields are gradually formed under joint effects of year-long continuous cropping and supporting cultivation management measures.

The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties

BACKGROUND

Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear.

RESULTS

We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from Bt and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content.

CONCLUSIONS

In conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both Bt and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of Bt cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.

'Concord' grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes

Leaf chlorosis in vineyards is associated with reduced crop yields and quality. While iron (Fe) is understood to play a crucial role in chlorosis, total plant and soil Fe are not always indicative of chlorosis in grapevines. Physiology of chlorosis in vineyards has been well-studied, but the soil microbial consequences of and contributions to chlorosis have received little attention. We used next-generation sequencing (NGS) to examine the bacterial and fungal communities associated with grapevines demonstrating varying degrees of visual chlorosis symptoms. Additionally, chemical analyses of soils and grape leaves were used to explore the influence of plant nutritional status and soil chemistry on microbial community composition. Finally, factors influencing bacterial community composition were correlated with predicted bacterial community function. Leaf tissue magnesium (leaf Mg) concentrations and chlorosis rank were correlated with bacterial community composition as determined via dbRDA (distance-based Redundancy Analysis) using Bray-Curtis dissimilarities. Non-metric multidimensional scaling (NMDS) revealed a significant correlation between fungal community composition and soil Fe and pH, along with leaf N, Mg, and Ca (mg.kg^-1). Chlorosis rank was moderately correlated with KEGG Orthology (KO) terms associated with nitrogen (N) and carbon (C) metabolism in soils, while leaf Mg was associated with a spectrum of KO terms including glycosphingolipid biosynthesis, glycan degradation, transporters, and porphyrin and chlorophyll metabolism. Additionally, abundance of many bacterial operational taxonomic units was significantly correlated with leaf Mg, including those from the following orders: Rhodobacterales, Acidobacteriales, Opitutales, Sphingomonadales, Burkholderiales, Saprospirales, and Flavobacteriales. Our findings suggest grapevine chlorosis is interrelated with soil microbial community structure and function, plant nutrition, and soil chemistry.

Chemical changes in organic matter after fungal colonization in a nitrogen fertilized and unfertilized Norway spruce forest

BACKGROUND AND AIMS

Decomposition and transformation of organic matter (OM) in forest soils are conducted by the concomitant action of saprotrophic and mycorrhizal fungi. Here, we examine chemical changes in OM after fungal colonization in nitrogen fertilized and unfertilized soils from a Norway spruce forest.

METHODS

Sand-filled bags amended with composted maize leaves were placed in the forest soil and harvested after 17 months. Infrared and near edge X-ray absorption fine structure spectroscopies were used to study the chemical changes in the OM. Fungal community composition of the bags was also evaluated.

RESULTS

The proportion of ectomycorrhizal fungi declined in the fertilized plots, but the overall fungal community composition was similar between N treatments. Decomposition of the OM was, independently of the N level or soil horizon, accompanied by an increase of C/N ratio of the mesh-bag content. Moreover, the proportions of carboxylic compounds in the incubated OM increased in the mineral horizon, while heterocyclic-N compounds decreased, especially in unfertilized plots with higher N demand from the trees.

CONCLUSIONS

Our results indicate that more oxidized organic C and less heterocyclic-N proportions in the OM remain after fungal colonization in the mineral layers, and suggest that ectomycorrhizal fungi transfer less heterocyclic-N from the mesh bags to the host trees under high N levels.

Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.