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Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited. [ABSTRACT FROM AUTHOR]

Opencast limestone mines or limestone quarries are considered challenging ecosystems for soil fungi as they are highly degraded land with specific conditions, including high temperature, prolonged sunlight exposure, and a lack of organic matter, moisture, and nutrients in soil. In such ecosystems, certain fungi can survive and have a crucial function in maintaining soil ecosystem functions. Unfortunately, we know very little about taxonomic diversity, potential functions, and the ecology of such fungi, especially for a limestone quarry in a tropical region. Here, we characterized and compared the living soil fungal communities in an opencast limestone mine, including mining site and its associated rehabilitation site (9 months post-rehabilitation), with the soil fungal community in a reference forest, using the amplicon sequencing of enrichment culture. Our results showed that living fungal richness in the quarry areas was significantly lower than that in the reference forest, and their community compositions were also significantly different. Living fungi in the mining sites mostly comprised of Ascomycota (Eurotiomycetes and Sordariomycetes) with strongly declined abundance or absence of Basidiomycota and Mucoromycota. After nine months of rehabilitation, certain taxa were introduced, such as Hypoxylon spp. and Phellinus noxius, though this change did not significantly differentiate fungal community composition between the mining and rehabilitation plots. The majority of fungi in these plots are classified as saprotrophs, which potentially produce all fifteen soil enzymes used as soil health indicators. Network analysis, which was analyzed to show insight into complex structures of living fungal community in the limestone quarry, showed a clear modular structure that was significantly impacted by different soil properties. Furthermore, this study suggests potential taxa that could be useful for future rehabilitation. [ABSTRACT FROM AUTHOR]

Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and 15N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N2 fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and 15N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay. [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]

The home-field advantage (HFA) hypothesis has been used intensively to study leaf litter decomposition in various ecosystems. However, the HFA in woody substrates is still unexplored. Here, we reanalyzed and integrated existing datasets on various groups of microorganisms collected from natural deadwood of two temperate trees, Fagus sylvatica and Picea abies, from forests in which one or other of these species dominates but where both are present. Our aims were (i) to test the HFA hypothesis on wood decomposition rates of these two temperate tree species, and (ii) to investigate if HFA hypothesis can be explained by diversity and community composition of bacteria and in detail N-fixing bacteria (as determined by molecular 16S rRNA and nifH gene amplification) and fungi (as determined by molecular ITS rRNA amplification and sporocarp surveys). Our results showed that wood decomposition rates were accelerated at "home" versus "away" by 38.19% ± 20.04% (mean ± SE). We detected strong changes in fungal richness (increase 36–50%) and community composition (RANOSIM = 0.52–0.60, P < 0.05) according to HFA hypothesis. The changes of fungi were much stronger than for total bacteria and nitrogen fixing for both at richness and community composition levels. In conclusion, our results support the HFA hypothesis in deadwood: decomposition rate is accelerated at home due to specialization of fungal communities produced by the plant community above them. Furthermore, the higher richness of fungal sporocarps and nitrogen-fixing bacteria (nifH) may stimulate or at least stabilize wood decomposition rates at "home" versus "away." [ABSTRACT FROM AUTHOR]

Next‐generation sequencing (NGS) has significantly increased knowledge of microbial communities and their distribution. However, it is still not common to apply NGS technology to microbial conservation. We sought to use NGS technologies to evaluate conservation strategies for wood‐inhabiting fungi. Evaluating a deadwood experiment 3 years after it was established, we specifically examined which tree species combinations promoted the highest richness of wood‐inhabiting fungi. Deadwood enrichment was an effective strategy and logs of 6 tree species, either those with the highest wood‐inhabiting fungal α and γ diversity or those with the highest β diversity, maintained >1,000 operational taxonomic units (OTUs) spread over a wide range of taxonomic groups. In comparison, a conservation strategy based only on the results of sporocarp surveys yielded 591 OTUs. This result highlights the need to use NGS approaches to inform microbial conservation strategies. We also determined that 5 tree species with the highest saproxylic beetle γ diversity simultaneously conserved wood‐inhabiting fungi. Apart from deadwood volume, we suggest data on deadwood quality and species also be included as indicators, especially for wood‐inhabiting fungal diversity, and incorporated quickly in forest assessment and monitoring systems in Central Europe. Article impact statement: Enrichment of the species diversity of deadwood is an effective strategy for wood‐inhabiting fungal conservation in temperate forests. [ABSTRACT FROM AUTHOR]

Abstract Although fungi play important roles in biogeochemical cycling in aquatic ecosystems and have received a great deal of attention, much remains unknown about the living fractions of fungal communities in aquifers of the terrestrial subsurface in terms of diversity, community dynamics, functional roles, the impact of environmental factors and presence of fungal pathogens. Here we address this gap in knowledge by using RNA-based high throughput pair-end illumina sequencing analysis of fungal internal transcribed spacer (ITS) gene markers, to target the living fractions of groundwater fungal communities from fractured alternating carbonate-/siliciclastic-rock aquifers of the Hainich Critical Zone Exploratory. The probed levels of the hillslope multi-storey aquifer system differ primarily in their oxygen and nitrogen content due to their different connections to the surface. We discovered highly diverse living fungal communities (384 Operational Taxonomic Units, OTUs) with different taxonomic affiliations and ecological functions. The observed fungal communities primarily belonged to three phyla: Ascomycota, Basidiomycota and Chytridiomycota. Perceived dynamics in the composition of living fungal communities were significantly shaped by the concentration of ammonium in the moderately agriculturally impacted aquifer system. Apart from fungal saprotrophs, we also detected living plant and animal pathogens for the first time in this aquifer system. This work also demonstrates that the RNA-based high throughput pair-end illumina sequencing method can be used in future for water quality monitoring in terms of living fungal load and subsequent risk assessments. In general, this study contributes towards the growing knowledge of aquatic fungi in terrestrial subsurface biogeosphere. Highlights • First RNA-based study using Illumina platform studying fungi in the aquifer system. • A diverse pool of living aquatic fungal species detected in subsurface aquifers. • NH 4 + and TIC supply correlate with the living fungal community composition in the aquifers. • Saprotrophs along with animal and plant pathogens were most frequently detected living functional groups. [ABSTRACT FROM AUTHOR]

Summary: Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions and processes are still unclear. Here, we investigated the impacts of N deposition on wood‐inhabiting fungi (WIF) and their related ecological functions and processes in a highly N‐limited deadwood habitat. Based on high‐throughput sequencing, enzymatic activity assay and measurements of wood decomposition rates, we show that N addition has no significant effect on the overall WIF community composition or on related ecosystem functions and processes in this habitat. Nevertheless, we detected several switches in presence/absence (gain/loss) of wood‐inhabiting fungal OTUs due to the effect of N addition. The responses of WIF differed from previous studies carried out with fungi living in soil and leaf‐litter, which represent less N‐limited fungal habitats. Our results suggest that adaptation at different levels of organization and functional redundancy may explain this buffered response and the resistant microbial‐mediated ecosystem function and processes against N deposition in highly N‐limited habitats. [ABSTRACT FROM AUTHOR]

Microorganisms play a crucial role in the biological decomposition of plant litter in terrestrial ecosystems. Due to the permanently changing litter quality during decomposition, studies of both fungi and bacteria at a fine taxonomic resolution are required during the whole process. Here we investigated microbial community succession in decomposing leaf litter of temperate beech forest using pyrotag sequencing of the bacterial 16S and the fungal internal transcribed spacer ( ITS) rRNA genes. Our results reveal that both communities underwent rapid changes. Proteobacteria, Actinobacteria and Bacteroidetes dominated over the entire study period, but their taxonomic composition and abundances changed markedly among sampling dates. The fungal community also changed dynamically as decomposition progressed, with ascomycete fungi being increasingly replaced by basidiomycetes. We found a consistent and highly significant correlation between bacterial richness and fungal richness ( R = 0.76, P < 0.001) and community structure ( RMantel = 0.85, P < 0.001), providing evidence of coupled dynamics in the fungal and bacterial communities. A network analysis highlighted nonrandom co-occurrences among bacterial and fungal taxa as well as a shift in the cross-kingdom co-occurrence pattern of their communities from the early to the later stages of decomposition. During this process, macronutrients, micronutrients, C:N ratio and pH were significantly correlated with the fungal and bacterial communities, while bacterial richness positively correlated with three hydrolytic enzymes important for C, N and P acquisition. Overall, we provide evidence that the complex litter decay is the result of a dynamic cross-kingdom functional succession. [ABSTRACT FROM AUTHOR]

Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions. [ABSTRACT FROM AUTHOR]

Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA) is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub). Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify (in silico) sequences of some important crop species such as Sorghum bicolor and Zea mays. Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected. [ABSTRACT FROM AUTHOR]

The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function. [ABSTRACT FROM AUTHOR]

The impact of changes within a single land-use category or land-use intensity on microbial communities is poorly understood, especially with respect to fungi. Here we assessed how forest management regimes and a change in forest type affect the richness and community structure of wood-inhabiting fungi across Germany. We used molecular methods based on the length polymorphism of the internal transcribed spacers and the 5.8S rRNA gene to assess fungal operational taxonomic units (OTUs). A cloning/sequencing approach was used to identify taxonomic affinities of the fungal OTUs. Overall, 20–24% and 25–27% of native fungal OTUs from forest reserves and semi-natural forests became undetectable or were lost in managed and converted forests, respectively. Fungal richness was significantly reduced during a regeneration phase in age-class beech forests with a high level of wood extraction (P = 0.017), whereas fungal community structures were not significantly affected. Conversion of forests from native, deciduous to coniferous species caused significant changes in the fungal community structure (R = 0.64–0.66, P = 0.0001) and could reduce fungal richness (P < 0.05) which may depend on which coniferous species was introduced. Our results showed that Ascocoryne cylichnium, Armillaria sp., Exophiala moniliae, Hyphodontia subalutacea and Fomes fomentarius, all known for wood-decaying abilities were strongly reduced in their abundances when forests were converted from beech to coniferous. We conclude that changes within a single land-use category can be regarded as a major threat to fungal diversity in temperate forest ecosystems. [Copyright &y& Elsevier]

Leaf litter decomposition is the key ecological process that determines the sustainability of managed forest ecosystems, however very few studies hitherto have investigated this process with respect to silvicultural management practices. The aims of the present study were to investigate the effects of forest management practices on leaf litter decomposition rates, nutrient dynamics (C, N, Mg, K, Ca, P) and the activity of ligninolytic enzymes. We approached these questions using a 473 day long litterbag experiment. We found that age-class beech and spruce forests (high forest management intensity) had significantly higher decomposition rates and nutrient release (most nutrients) than unmanaged deciduous forest reserves (P<0.05). The site with near-to-nature forest management (low forest management intensity) exhibited no significant differences in litter decomposition rate, C release, lignin decomposition, and C/N, lignin/N and ligninolytic enzyme patterns compared to the unmanaged deciduous forest reserves, but most nutrient dynamics examined in this study were significantly faster under such near-to-nature forest management practices. Analyzing the activities of ligninolytic enzymes provided evidence that different forest system management practices affect litter decomposition by changing microbial enzyme activities, at least over the investigated time frame of 473 days (laccase, P<0.0001; manganese peroxidase (MnP), P = 0.0260). Our results also indicate that lignin decomposition is the rate limiting step in leaf litter decomposition and that MnP is one of the key oxidative enzymes of litter degradation. We demonstrate here that forest system management practices can significantly affect important ecological processes and services such as decomposition and nutrient cycling. [ABSTRACT FROM AUTHOR]

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. [ABSTRACT FROM AUTHOR]

Stingless bees play a crucial role in the environment and agriculture as they are effective pollinators. Furthermore, they can produce various products that can be exploited economically, such as propolis and honey. Despite their economic value, the knowledge of microbial community of stingless bees, and their roles on the bees' health, especially in Thailand, are in its infancy. This study aimed to investigate the composition and the functions of bacterial community associated with Tetragonula pagdeni stingless bees using culture-independent and culture-dependent approaches with emphasis on lactic acid bacteria. The culture-independent results showed that the dominant bacterial phyla were Firmicutes, Proteobacteria and Actinobacteria. The most abundant families were Lactobacillaceae and Halomonadaceae. Functional prediction indicated that the prevalent functions of bacterial communities were chemoheterotrophy and fermentation. In addition, the bacterial community might be able to biosynthesize amino acid and antimicrobial compounds. Further isolation and characterization resulted in isolates that belonged to the dominant taxa of the community and possessed potentially beneficial metabolic activity. This suggested that they are parts of the nutrient acquisition and host defense bacterial functional groups in Thai commercial stingless bees. [ABSTRACT FROM AUTHOR]

Background: Nonstructural carbohydrates (NSCs) reflect the carbon supply status and affect the construction and development of plants. Previous studies have focused on the dynamics of NSCs among plant organs, however, few studies have paid attention to the synergistic variations between fine root traits and NSCs under drought based on the perspective of branch order roots. This study aims to explore the responses of fine root traits and NSCs among root orders of Juglans mandshurica seedlings under different drought intensities and soil substrates. The 2-year-old J. mandshurica potted seedlings were planted in three different soil substrates (humus, loam and sandy-loam soil) and subjected to four drought intensities (CK, mild drought T1, moderate drought T2 and severe drought T3) for 60 days. Results: The root biomass of seedlings in sandy-loam soil under the same drought intensity was higher than that of seedlings in humus soil. With an increase in drought, the root biomass, average diameter, root tissue density and cortex thickness decreased significantly, and the specific root length, stele diameter and conduit density increased. The root NSC contents in humus soil were higher than those in sandy-loam soil. The fine root soluble sugar content in all soil substrates decreased with increasing drought intensity, while the root starch and total NSC contents varied among the different soil substrates. Compared with transportive roots, the morphological and anatomical traits jointly explained the higher variation in NSC contents of the absorptive roots. The anatomical traits explained the higher variation in the NSC content of first five order roots. Conclusion: Our results suggest that coordinated adaptation of the root traits and NSCs of Manchurian walnut seedlings exposed to water gradients in different soil substrates. [ABSTRACT FROM AUTHOR]

Expanding the use of environmentally friendly materials to protect the environment is one of the key factors in maintaining a sustainable ecological balance. Poly(butylene succinate-co-adipate) (PBSA) is considered among the most promising bio-based and biodegradable plastics for the future with a high number of applications in soil and agriculture. Therefore, the decomposition process of PBSA and its consequences for the carbon stored in soil require careful monitoring. For the first time, the stable isotope technique was applied in the current study to partitioning plastic- and soil-originated C in the CO2 released during 80 days of PBSA decomposition in a Haplic Chernozem soil as dependent on nitrogen availability. The decomposition of the plastic was accompanied by the C loss from soil organic matter (SOM) through priming, which in turn was dependent on added N. Nitrogen facilitated PBSA decomposition and reduced the priming effect during the first 6 weeks of the experiment. During the 80 days of plastic decomposition, 30% and 49% of the released CO2 were PBSA-derived, while the amount of SOM-derived CO2 exceeded the corresponding controls by 100.2 and 132.3% in PBSA-amended soil without and with N fertilization, respectively. Finally, only 4.1% and 5.4% of the PBSA added into the soil was mineralized to CO2, in the treatments without and with N amendment, respectively. [ABSTRACT FROM AUTHOR]

Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)–based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors. [ABSTRACT FROM AUTHOR]

Soils harbor a huge diversity of microorganisms that participate in various biogeochemical cycles and influence soil fertility. Our knowledge of soil microbiota, however, is limited by the complexity and heterogeneity of soil habitats and the huge microbial diversity. In this study, fertilized and unfertilized soils from a long-term fertilization experiment were gamma-sterilized before self- or cross-inoculation with non-sterilized soil aliquots containing their respective microbial communities. Bacterial community dynamics resulting from each reinoculated treatment was monitored over 90 days using B-ARISA. This study design allowed us to assess the respective influences of two driving factors, original community and soil nutrient availability, on microbial community assemblage dynamics. For all treatments, the bacterial communities that evolved in the sterilized soils differed from those in the original soils and displayed dynamic shifts over time. These shifts were particularly illustrated by the appearance of numerous OTUs that were undetectable in the original soils and suggest that community assembly is primarily determined by niche factors. However, stronger community shifts and higher variations among the replicates were observed after reinoculation of nutrient-rich soil, suggesting an increased impact of stochastic processes on community assembly. Our results demonstrate that reinoculation-based approaches are not only valid for detecting a variety of low abundant soil bacteria but also for distinguishing the soil characteristics and ecological rules that shape soil microbial population assemblage. [ABSTRACT FROM AUTHOR]

[Display omitted] • NGS was used to precisely describe the microbiome of three strawberry cultivars. • Plant organs and genotype shape the composition of the microbiomes. • Strawberry microbiome delivers several beneficial functions to the plant. • Functional microbiome diversity correlates with cultivars' phenotypical differences. • Microbiome manipulation may enhance agricultural performances. Specific microbial communities are associated to host plants, influencing their phenotype and fitness. Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked. This work provides the first comprehensive description of the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organs of three commercially important strawberry genotypes under cultural conditions. Strawberry-associated fungal and bacterial microbiomes were characterised by Next-Generation Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated. Results showed that the strawberry core microbiome included 24 bacteria and 15 fungal operational taxonomic units (OTUs). However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highest tolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonas fluorescens , and to establish a mutualistic symbiosis with the arbuscular mycorrhiza Rhizophagus irregularis. This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production. [ABSTRACT FROM AUTHOR]

The incomplete degradation of bio-based and biodegradable plastics (BBPs) in soils causes multiple threats to soil quality, human health, and food security. Plastic residuals can interact with soil microbial communities. We aimed to link the structure and enzyme-mediated functional traits of a microbial community composition that were present during poly (butylene succinate-co-butylene adipate (PBSA) decomposition in soil with (PSN) and without (PS) the addition of nitrogen fertilizer ((NH4)2SO4). We identified bacterial (Achromobacter, Luteimonas, Rhodanobacter, and Lysobacter) and fungal (Fusarium, Chaetomium, Clonostachys, Fusicolla, and Acremonium) taxa that were linked to the activities of ß-glucosidase, chitinase, phosphatase, and lipase in plastic-amended soils. Fungal biomass increased by 1.7 and 4 times in PS and PSN treatment, respectively, as compared to non-plastic amended soil. PBSA significantly changed the relationships between soil properties (C: N ratio, TN, and pH) and microbial community structure; however, the relationships between fungal biomass and soil enzyme activities remained constant. PBSA significantly altered the relationship between fungal biomass and acid phosphatase. We demonstrated that although the soil functions related to nutrient cycling were not negatively affected in PSN treatment, potential negative effects are reasoned by the enrichment of plant pathogens. We concluded that in comparison to fungi, the bacteria demonstrated a broader functional spectrum in the BBP degradation process. [ABSTRACT FROM AUTHOR]

Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood. This study used a field experimental facility settled in Central Germany to analyze the effects of ambient vs. future climate that is expected in 50–80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process. Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization. The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one. Using MiSeq Illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (Ca2+, and pH) and future (C/N, N, P, K+, Ca2+, pH, and moisture) climate conditions. Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate. Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates. Activities of microbial β-glucosidase and N-acetylglucosaminidase in wheat litter were increased over time. Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate. Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, we compared microbial communities in Lanna mural paintings in temples with different numbers of visitors using culture-dependent and culture independent approaches. The results showed that microorganisms could damage the colors that are used on murals. The process of degradation involved the production of organic acids and formation of the calcium crystal. Furthermore, we found that the site with higher number of visitors is associated with microbial contamination from humans while the site with lower number of visitors had higher saprotroph population. Further research into these microorganisms, their activities and functional roles may provide crucial information to aid the preservation of mural paintings. Lanna painting is a unique type of painting in many temples in the Northern Thai region. Similar to most mural paintings, they usually decay over time partly due to the activity of microbes. This study aimed to investigate the microorganisms from two Lanna masterpiece paintings in two temples that differ in the numbers of visitors using both culture-dependent and -independent approaches. The microorganisms isolated from the murals were also tested for the biodeterioration activities including discoloration, acid production and calcium precipitation. Most microorganisms extracted from the paintings were able to discolor the paints, but only fungi were able to discolor, produce acids and precipitate calcium. The microorganism communities, diversity and functional prediction were also investigated using the culture-independent method. The diversity of microorganisms and functional prediction were different between the two temples. Gammaproteobacteria was the predominant group of bacteria in both temples. However, the fungal communities were different between the two temples as Aspergillus was the most abundant genus in the site with higher number of visitors [Buak Krok Luang temple (BK)]. Conversely, mural paintings at Tha Kham temple (TK) were dominated by the Neodevriesia genera. We noticed that a high number of visitors (Buak Krok Luang) was correlated with microbial contamination from humans while the microbial community at Tha Kham temple had a higher proportion of saprotrophs. These results could be applied to formulate a strategy to mitigate the amount of tourists as well as manage microorganism to slow down the biodeterioration process. [ABSTRACT FROM AUTHOR]

Summary: Climate and agricultural practice interact to influence both crop production and soil microbes in agroecosystems. Here, we carried out a unique experiment in Central Germany to simultaneously investigate the effects of climates (ambient climate vs. future climate expected in 50–70 years), agricultural practices (conventional vs. organic farming), and their interaction on arbuscular mycorrhizal fungi (AMF) inside wheat (Triticum aestivum L.) roots. AMF communities were characterized using Illumina sequencing of 18S rRNA gene amplicons. We showed that climatic conditions and agricultural practices significantly altered total AMF community composition. Conventional farming significantly affected the AMF community and caused a decline in AMF richness. Factors shaping AMF community composition and richness at family level differed greatly among Glomeraceae, Gigasporaceae and Diversisporaceae. An interactive impact of climate and agricultural practices was detected in the community composition of Diversisporaceae. Organic farming mitigated the negative effect of future climate and promoted total AMF and Gigasporaceae richness. AMF richness was significantly linked with nutrient content of wheat grains under both agricultural practices. [ABSTRACT FROM AUTHOR]

Soil organisms are important drivers of the functioning of terrestrial ecosystems and co-determine how these ecosystems respond to human-induced changes in climate and land use. In the present study, we assessed the interacting effects of these two global change drivers on soil faunal communities. We carried out an experimental field study within the framework of the Global Change Experimental Facility (GCEF) manipulating (1) two climatic conditions (ambient vs. future) and (2) five land-use regimes (with two croplands: conventional farming and organic farming; and three grasslands: intensively-used meadow, extensively-used meadow and extensively-used pasture). The future climate treatment is characterized by a slight increase of soil temperature (~0.5 °C), whereas precipitation was strongly decreased during the summer (by ~20%) but moderately increased during spring and autumn (by ~10%). Soil fauna was sampled in two consecutive years in spring and autumn. Overall, future climate tented to have negative effects on soil fauna communities. For specific taxa, the detrimental effects of climate change were only evident for Isotomidae (Collembola) and Chilopoda. In general, soil faunal composition differed strongly between grasslands and croplands, with a higher number of macrofauna taxa and generally higher abundances of meso- and macrofauna in grasslands. However, land-use intensity within these land-use types had no further effect. Likewise, there were negligible interactive effects of climate and land use, and short-term effects of projected climate change on the community compositions of soil fauna were found to be more subtle than land-use effects. Land-use effects on soil fauna are therefore equally strong under ambient and future climatic conditions. [ABSTRACT FROM AUTHOR]

While the number of studies on the role of biodiversity on ecosystem functioning is steadily increasing, a key component of biogeochemical cycling in forests, dead wood decay, has been largely neglected. It remains widely unknown whether and how dead wood decay is affected by diversity loss in forests. We studied the hierarchical effects of tree species diversity on wood decay rates in a subtropical forest landscape in southeast China via its influence on fungal OTU richness and invertebrate diversity using piecewise structural equation models. The experiment was conducted in natural forest plots that span a wide gradient of tree species diversity embedded in a heterogeneous topography. To account for interactions between macro‐invertebrates and fungi, that potentially modify the influence of tree biodiversity and climate on dead wood decay, we compared a macro‐invertebrate exclusion treatment with a control treatment that allowed access to all types of decomposers. Diversity effects of trees on wood decay rates were mostly negative and mediated by the diversity of macro‐invertebrates. However, the effects of tree species diversity or fungal OTU richness and macro‐invertebrate diversity on wood decay rates were comparatively weak. Temperature affected decay rates positively and had the strongest influence in all treatments. While the exclusion of macro‐invertebrates did not lead to a reduction of wood decay rates, our results suggest that they may however have a mediating role in the process. In the presence of invertebrates the predictability of wood decay rates was higher and we observed a tendency of a stronger temperature control. Our results suggest that there is evidence for diversity effects on wood decomposition, but the temperature control is still more important. Thus, an increase in mean annual temperature will increase carbon and nutrient turnover through wood decomposition in subtropical forest irrespective of biotic composition. [ABSTRACT FROM AUTHOR]

Abstract Litter decomposition is a key process determining the cycling of nutrients in ecosystems. Soil fauna plays an essential role in this process, e.g., by fragmenting and burrowing surface litter material, and thereby enhancing microbial decomposition. However, soil fauna-mediated decomposition might be influenced by interacting factors of environmental changes. Here we used a large-scale global change field experiment to test potential interacting effects between land-use type (croplands and grasslands differing in management intensity) and projected climate change on litter decomposition rates over a period of two years. For that, climate and land-use treatments were orthogonally crossed: (1) two climate scenarios: ambient vs. future; and (2) five land-use regimes: conventional farming, organic farming, intensively used meadow, extensively used meadow, and extensively used pasture. Litterbags with two mesh sizes (5 mm and 0.02 mm) were used to differentiate contributions of microbes and fauna to the mass loss of standardized crop residues. Soil fauna accounted for more than 68% of surface litter mass loss. Future climate treatment decreased decomposition rates as a result of reduced precipitation and elevated temperature during summer months. Litter decomposition and the contribution of soil fauna to it were significantly higher in croplands than in grasslands, but did not differ due to management intensity within these land-use types. In grasslands, faunal contribution to decomposition decreased under future climate. There were no interacting effects between climate change and land use on decomposition rates. These findings indicate that predicted changes in precipitation patterns and temperature will consistently decelerate litter decomposition across land-used types via both microbial and faunal effects. Graphical abstract Image 1 Highlights • Future climate decreased litter decomposition, most in summer months. • This decrease in decomposition was due to soil fauna, but not microbes. • Soil fauna-mediated decomposition was higher in croplands than grasslands. • Climate change effects on decomposition were consistent across land-use types. [ABSTRACT FROM AUTHOR]

Abstract A major gap in understanding the relationship between tree diversity and litter decomposition concerns knowledge of the saprotrophic fungal communities mediating decomposition processes. Making use of experimental tree diversity plots in subtropical China, our objective was to disentangle the effects of tree species richness on diversity, abundance, and composition of saprotrophic fungal communities in freshly fallen leaf litter. We employed a meta-genomic approach and analysed enzymatic decomposition. Our results indicate the dominance of Ascomycota, with species from this phylum colonizing leaf litter more rapidly than Basidiomycota. Furthermore, Ascomycota was the most abundant when tree richness was intermediate. Both Ascomycota and Basidiomycota differed significantly in their species composition in response to varying tree species richness. However, saprotrophic fungal species diversity did not respond to tree species richness. Instead, litter C/N ratio, litter Ca and plot altitude were the strongest determinants of fungal species diversity. Carbon-degradation enzyme activities were also significantly associated with litter C/N ratio, Ca and Fe concentration and, in addition, with tree species richness. The responses of fungal species and enzyme activity to tree species richness were uncoupled from each other, although the two variables were significantly correlated. Overall, our findings highlight a significant effect of tree species richness on litter fungal species composition, but not diversity. Our findings also provide insight into the importance of enzyme-mediated C degradation for the response to tree species richness in early-stage leaf decay in subtropical forests. Highlights • Fungal diversity in litter did not respond to the increase of tree species richness. • Tree richness affect Ascomycota composition rather than Basidiomycota fungi. • Ascomycota fungi were highest at intermediate tree species richness level. • Carbon degradation-related enzymes were significantly affected by tree richness. [ABSTRACT FROM AUTHOR]

Forestry in Europe changed the tree species composition and reduced dead-wood amount and heterogeneity, and therefore negatively affected saproxylic diversity. Efficient conservation requires knowledge about the importance of the relevant diversity drivers across taxa. We examined the relative importance of space vs. host for saproxylic diversity at a spatial extend of 600 km in Germany. Further, we disentangled effects of among regions, forest stands, host clades, and tree species on saproxylic diversity. This allows inferences for spatial- and host tree-related conservation strategies. Beetle, fungal sporocarp, molecular-derived fungal, and bacterial communities were studied in a large nested dead-wood experiment comprising 11 tree species. We used multiplicative diversity partitioning to assess the diversity of rare, typical, and dominant species. The beta-diversity of beetles and fungal sporocarps was equally explained by space and host, but that of molecular fungi and bacteria mainly by the host. Across taxa, beta-diversity was higher among forest stands than among regions. However, for beetles and fungal sporocarps, differences among regions were also important. Host tree clade and host tree species were important for beetle and host clade for fungal sporocarp beta-diversity. Host tree species was more important than host clade for the beta-diversity of molecular fungi and bacteria. The divergent response of different taxa to space and host calls into question the use of a simple spatially-centered or host-centered strategy. Instead, a high dead-wood tree species diversity on a broad spatial coverage at the national scale in temperate European forests is necessary to maintain rare and abundant species. • Relative importance of space versus host across saproxylic taxa is unknown. • Beetle diversity is driven by space and host, microbial diversity mainly by the host. • Different fungal diversity measures yielded different results. • Conservation requires dead-wood enrichment with different clades and tree species. • Dead-wood enrichment must be established in different forest types across regions. [ABSTRACT FROM AUTHOR]

• The microbial co-occurrence networks along soil depths in Mt. Oakley were analyzed. • There were contrasting patterns between soil bacterial and fungal diversity along altitudinal gradient. • Altitude was more important than soil depth for shaping soil microbial communities. • Main drivers of microbial community structure are consistent for whole and sub-network communities. • Sub-network community analysis revealed important drivers that do not capture by whole community. Soil bacterial and fungal communities with different key ecological functions play important roles in boreal forest ecosystems. Although several studies have reported on the altitudinal distribution patterns of microbes, our understanding of the characteristics of the microbial community and the core composition of the microbiome in cold-temperate montane forests is still limited. In this study, Illumina MiSeq sequencing was used to investigate the changes in soil bacterial and fungal communities in surface and subsurface soils along an altitudinal gradient (from 830 m to 1300 m) on Oakley Mountain. The diversity of the bacterial and fungal communities showed a monotonic decrease and a monotonic increase with altitude, respectively. The influence of altitude on the bacterial and fungal community composition was stronger than that of soil depth. The variations in pH and dissolved organic nitrogen content at different altitudes were the main factors influencing the bacterial and fungal community structures, respectively. There was no obvious difference between the network structures of the surface and subsurface soil fungal communities, while the network of the subsurface soil bacterial community was more complex and intricate than that of the surface soil bacterial community. The network nodes mainly belonging to Proteobacteria and Actinobacteria were the key bacterial taxa in the two soil layers. Although the main drivers of microbial community structure are consistent for whole and sub-nerwork communities, the subnetwork community analysis revealed other important drivers (i.e. soil temperature and nitrate nitrogen) that do not capture by whole community analysis. Thus, the more comprehensive picture of the important factors shaping microbial community structure can be achieved by combining whole and subnetwork community analyses. Our results demonstrated that altitude had a stronger influence on soil bacterial and fungal communities than soil depth and that bacterial and fungal communities showed divergent patterns with altitude and soil depth. [ABSTRACT FROM AUTHOR]

Simple Summary: The study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community's information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications. This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step. [ABSTRACT FROM AUTHOR]