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Fungi play vital roles in the decomposition of deadwood due to their secretion of various enzymes that break down plant cell-wall complexes. The compositions of wood-inhabiting fungal (WIF) communities change over the course of the decomposition process as the remaining mass of wood decreases and both abiotic and biotic conditions of the wood significantly change. It is currently not resolved which substrate-related factors govern these changes in WIF communities and whether such changes influence the deadwood decomposition rate. Here we report a study on fungal richness and community structure in deadwood of Norway spruce and European beech in temperate forest ecosystems using 454 pyrosequencing. Our aims were to disentangle the factors that correspond to WIF community composition and to investigate the links between fungal richness, taxonomically-resolved fungal identity, and microbial-mediated ecosystem functions and processes by analyzing physico-chemical wood properties, lignin-modifying enzyme activities and wood decomposition rates. Unlike fungal richness, we found significant differences in community structure between deadwood of different tree species. The composition of WIF communities was related to the physico-chemical properties of the deadwood substrates. Decomposition rates and the activities of lignin-modifying enzymes were controlled by the succession of the fungal communities and competition scenarios rather than fungal OTU richness. Our results provide further insights into links between fungal community structure and microbial-mediated ecosystem functions and processes. [ABSTRACT FROM AUTHOR]

In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH. [ABSTRACT FROM AUTHOR]

Environmental selection and dispersal limitation are two of the primary processes structuring biotic communities in ecosystems, but little is known about these processes in shaping soil microbial communities during secondary forest succession., We examined the communities of ectomycorrhizal ( EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing., The EM fungal community consisted of 393 operational taxonomic units ( OTUs), belonging to 21 EM fungal lineages, in which three EM fungal lineages and 11 EM fungal OTUs showed significantly biased occurrence among the young, intermediate and old forests. The EM fungal community was structured by environmental selection and dispersal limitation in old forest, but only by environmental selection in young, intermediate, and whole forests. Furthermore, the EM fungal community was affected by different factors in the different forest successional stages, and the importance of these factors in structuring EM fungal community dramatically decreased along the secondary forest succession series., This study suggests that different assembly mechanisms operate on the EM fungal community at different stages in secondary subtropical forest succession. [ABSTRACT FROM AUTHOR]

S ulfurospirillum multivorans, a free-living ε-proteobacterium, is among the best studied organisms capable of organohalide respiration. It is able to use several halogenated ethenes as terminal electron acceptor. In this report, the complete genome sequence of S . multivorans including a comparison with genome sequences of two related non-dehalogenating species, S ulfurospirillum deleyianum and S ulfurospirillum barnesii, is described. The 3.2 Mbp genome of S . multivorans revealed a ∼ 50 kbp gene region encoding proteins required for organohalide respiration and corrinoid cofactor biosynthesis. This region includes genes for components not detected before in organohalide-respiring organisms. A transcript analysis of genes coding for some of these proteins indicates the involvement of a putative quinol dehydrogenase in organohalide respiration. The presence of genes encoding a variety of oxidoreductases reflects the organism's metabolic versatility. This was confirmed by growth studies with different electron acceptors including perchlorate and several sulfur-containing compounds. A comparison with other ε-proteobacteria indicates horizontal acquisition of many genes in the S . multivorans genome, which might be the basis of the bacterium's catabolic flexibility. [ABSTRACT FROM AUTHOR]

Exploring the relationships between the biodiversity of groups of interacting organisms yields insight into ecosystem stability and function (Hooper et al. ; Wardle ). We demonstrated positive relationships between host plant richness and ectomycorrhizal ( EM) fungal diversity both in a field study in subtropical China (Gutianshan) and in a meta-analysis of temperate and tropical studies (Gao et al. ). However, based on re-evaluation of our data sets, Tedersoo et al. () argue that the observed positive correlation between EM fungal richness and EM plant richness at Gutianshan and also in our metastudies was based mainly from (i) a sampling design with inconsistent species pool and (ii) poor data compilation for the meta-analysis. Accordingly, we checked our data sets and repeated the analysis performed by Tedersoo et al. (). In contrast to Tedersoo et al. (), our re-analysis still confirms a positive effect of plant richness on EM fungal diversity in Gutianshan, temperate and tropical ecosystems, respectively. [ABSTRACT FROM AUTHOR]

Oaks ( Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags ( ESTs) have been characterized in ectomycorrhizal ( EM) symbioses., We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone ( DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum., Using the Mimicking Intelligent Read Assembly ( MIRA) and Trinity assembler, the OakContig DF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated., In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees. [ABSTRACT FROM AUTHOR]

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Two new arbuscular mycorrhizal fungal species (Glomeromycota) of genus Glomus, G. africanum and G. iranicum, are described and illustrated. Both species formed spores in loose clusters and singly in soil and G. iranicum sometimes inside roots. G. africanum spores are pale yellow to brownish yellow, globose to subglobose, (60-)87(-125) µm diam, sometimes ovoid to irregular, 80-110 x 90-140 µm. The spore wall consists of a semipermanent, hyaline, outer layer and a laminate, smooth, pale yellow to brownish yellow, inner layer, which always is markedly thinner than the outer layer. G. iranicum spores are hyaline to pastel yellow, globose to subglobose, (13-)40(-56) µm diam, rarely egg-shaped, prolate to irregular, 39-54 x 48-65 µm. The spore wall consists of three smooth layers: one mucilaginous, short-lived, hyaline, outermost; one permanent, semirigid, hyaline, middle; and one laminate, hyaline to pastel yellow, innermost. Only the outermost spore wall layer of G. iranicum stains red in Melzer's reagent. In the field G. africanum was associated with roots of five plant species and an unrecognized shrub colonizing maritime sand dunes of two countries in Europe and two in Africa, and G. iranicum was associated with Triticum aestivum cultivated in southwestern Iran. In one-species cultures with Plantago lanceolata as the host plant G. africanum and G. iranicum formed arbuscular mycorrhizae. Phylogenetic analyses of partial SSU sequences of nrDNA placed the two new species in Glomus group A. Both species were distinctly separated from sequences of described Glomus species. [ABSTRACT FROM AUTHOR]

Features a study that aimed to illustrate morphological characteristics of Taxus baccata mycorrhizas and to investigate the molecular diversity of arbuscular mycorrhizal fungi (AMF) species in roots of Taxus baccata growitn in southern Germany. Use of polymerase chain reaction based molecular techniques; Amplification of the internal transcribed spacer region of the DNA from AMF within the roots; Phylogenetic position of the AMF sequences obtained.

The underlying processes of plant‐microbe associations particularly their interactions with their mycorrhizal fungal partners have been extensively studied. However, considerably less is known about the consequences of tree‐tree interactions on rooting zone soil microbiota when tree species of different mycorrhizal type (myco‐type) grow together as mono and mixed myco‐type mixtures along a tree diversity gradient. Using the MyDiv tree diversity experiment, where arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) trees and their mixtures were planted in monocultures, two‐species and four‐species mixture plots, we investigated the interplay of target tree myco‐type, myco‐type mixture, tree diversity and rooting zone compartment (target tree dominated and its interaction zones with neighbour trees) on the rooting zone soil mycobiota employing meta‐barcoding of the ITS2 rDNA fragment of the fungal internal transcribed spacer (ITS). Our results revealed significant individual and interaction effects of tree myco‐type, myco‐type mixture and tree diversity but not rooting zone compartment on the fungal taxonomic and functional alpha and beta diversity. This implies intermingling of roots of target and neighbouring tree species there by reducing the target tree species effect in its rooting zone. As tree diversity increases, we found convergence of the fungal community in general, where the fungal community dissimilarity varies depending on the co‐existing tree species myco‐type and tree species diversity. Furthermore, the fungal community composition in the two and four species mixtures were consistently influenced by soil pH, whereas in the mixed multi‐species stands basal respiration, N, PO4−, NO3− were found to be equally important unlike in AM and EcM multi‐species stands. Comparative analysis of the fungal taxa specialisation between mono and mixed myco‐type multi‐species stands revealed that the mixed myco‐type plots shared 23.5% (AM) and 19.7% (EcM) of the generalist fungal communities However, the percentage of specialised fungal community in mixed myco‐type plots (13.2%) was significantly higher as compared to EcM (9.5%), and significantly lower (9%) as compared to AM (11.7%) plots, resulting in myco‐type and myco‐type mixture specific fungal communities and functional guild patterns Our results provide novel insights on the significance of tree species and its co‐existing trees preferred mycorrhizal association in shaping the target tree rooting zone soil mycobiome along a tree diversity gradient. Furthermore, it highlights the significance of generalist and specialist fungal communities in mono and mixed myco‐type stands in modulating tree‐tree interaction, tree species co‐existence and regulating soil properties and ecosystem functions. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Following publication of the original article [1], we have been notified that three of the primer names identified as most promising candidates for fungal community surveys were incorrectly renamed following the primer nomenclature system proposed by Gargas & DePriest [2]. [ABSTRACT FROM AUTHOR]

Investigating the effects of individual tree species on fungal species in leaf litter allows a mechanistic understanding of how tree diversity affects the diversity and composition of fungal species at the community level. We collected freshly-fallen leaves of eight focal tree species at four tree species richness levels in a large-scale subtropical forest diversity experiment to estimate tree species richness effects on fungal species diversity and community composition at two spatial scales: at the local tree neighbourhood and at the tree community level. The identity of focal tree species affected both the diversity and composition of the fungal community in freshly-fallen leaves, particularly structuring the composition of both the pathogenic and non-pathogenic fungal community. Furthermore, we found that the effects of community tree species richness on fungal OTU composition were tree species-specific. Besides community tree species richness, the neighbour tree community had significant effects on the structure of the entire fungal community and of functional groups in freshly-fallen leaves. These findings highlight that the response of fungal species assemblages to tree species richness depends on fungal-associated tree species identity, and suggest that heterospecificity of local tree neighbours is an important driver of tree richness effects on litter fungal community. • Focal tree species identity may structure litter fungal community. • Community tree richness effects on litter fungal species are tree species-dependent. • Heterospecificity of local tree neighbours is a key driver of tree richness effects. [ABSTRACT FROM AUTHOR]

Background: Land use changes and related land management practices significantly alter soil physicochemical properties; however, their effects on the soil microbial community structure are still unclear. In this study, we used automated ribosomal intergenic spacer analysis to determine the fungal and bacterial community composition in soils from different land use areas in the Ethiopian highlands. Soil samples were collected from five areas with different land uses, natural forest, eucalyptus plantation, exclosure, grassland and cropland, which had all historically been natural forest. Results: Our results showed a significant shift in the soil bacterial and fungal community composition in response to land use change. We also identified soil physicochemical factors corresponding to the changes in bacterial and fungal communities. Although most soil attributes, including soil organic carbon, total soil nitrogen, labile P, soil pH and soil aggregate stability, were related to the change in bacterial community composition, the total soil nitrogen and soil organic carbon had the strongest relationships. The change in fungal community composition was correlated with soil nutrients, organic carbon, soil nitrogen and particularly the labile P concentration. Conclusions: The fungal community composition was likely affected by the alteration of vegetation cover in response to land use change, whereas the bacterial communities were mainly sensitive to changes in soil attributes. The study highlights the higher sensitivity of fungal communities than bacterial communities to land use changes. [ABSTRACT FROM AUTHOR]

Summary: Understanding the complex interactions between trees and fungi is crucial for forest ecosystem management, yet the influence of tree mycorrhizal types, species identity, and diversity on tree‐tree interactions and their root‐associated fungal communities remains poorly understood.Our study addresses this gap by investigating root‐associated fungal communities of different arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) tree species pairs (TSPs) in a subtropical tree diversity experiment, spanning monospecific, two‐species, and multi‐species mixtures, utilizing Illumina sequencing of the ITS2 region.The study reveals that tree mycorrhizal type significantly impacts the alpha diversity of root‐associated fungi in monospecific stands. Meanwhile, tree species identity's influence is modulated by overall tree diversity. Tree‐related variables and spatial distance emerged as major drivers of variations in fungal community composition. Notably, in multi‐species mixtures, compositional differences between root fungal communities of AM and EcM trees diminish, indicating a convergence of fungal communities irrespective of mycorrhizal type. Interestingly, dual mycorrhizal fungal communities were observed in these multi‐species mixtures.This research underscores the pivotal role of mycorrhizal partnerships and the interplay of biotic and abiotic factors in shaping root fungal communities, particularly in varied tree diversity settings, and its implications for effective forest management and biodiversity conservation. [ABSTRACT FROM AUTHOR]

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines. [ABSTRACT FROM AUTHOR]