Spatial vs. temporal controls over soil fungal community similarity at continental and global scales

Consistent community assembly but contingent species pool effects drive β-diversity patterns of multiple microbial groups in desert biocrust systems

One of the key goals of ecology is to understand how communities are assembled. The species co-existence theory suggests that community β-diversity is influenced by species pool and community assembly processes, such as environmental filtering, dispersal events, ecological drift and biotic interactions. However, it remains unclear whether there are similar β-diversity patterns among different soil microbial groups and whether all these mechanisms play significant roles in mediating β-diversity patterns. By conducting a broad survey across Chinese deserts, we aimed to address these questions by investing biological soil crusts (biocrusts). Through amplicon-sequencing, we acquired β-diversity data for multiple microbial groups, that is, soil total bacteria, diazotrophs, phoD-harbouring taxa, and fungi. Our results have shown varying distance decay rates of β-diversity across microbial groups, with soil total bacteria showing a weaker distance-decay relationship than other groups. The impact of the species pool on community β-diversity varied across microbial groups, with soil total bacteria and diazotrophs being significantly influenced. While the contributions of specific assembly processes to community β-diversity patterns varied among different microbial groups, significant effects of local community assembly processes on β-diversity patterns were consistently observed across all groups. Homogenous selection and dispersal limitation emerged as crucial processes for all groups. Precipitation and soil C:P were the key factors mediating β-diversity for all groups. This study has substantially advanced our understanding of how the communities of multiple microbial groups are structured in desert biocrust systems.

Geographic Location Affects the Bacterial Community Composition and Diversity More than Species Identity for Tropical Tree Species

Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as well as how these communities respond to environmental changes. In this study, we aimed to elucidate the characteristics of bacterial community composition in association with two rare and endangered tropical tree species, Dacrydium pectinatum and Vatica mangachapoi, across various geographical locations on Hainan Island. Our findings can be summarized as follows: (1) Significant differences existed in the bacterial composition between D. pectinatum and V. mangachapoi, as observed in the diversity of bacterial populations within the root endosphere. Plant host-related variables, such as nitrogen content, emerged as key drivers influencing leaf bacterial community compositions, underscoring the substantial impact of plant identity on bacterial composition. (2) Environmental factors associated with geographical locations, including temperature and soil pH, predominantly drove changes in both leaf and root-associated bacterial community compositions. These findings underscored the influence of geographical locations on shaping plant-associated bacterial communities. (3) Further analysis revealed that geographical locations exerted a greater influence than tree species identity on bacterial community compositions and diversity. Overall, our study underscores that environmental variables tied to geographical location primarily dictate changes in plant bacterial community composition. These insights contribute to our understanding of microbial biogeography in tropical regions and carry significant implications for the conservation of rare and endangered tropical trees.

Microbial evolution-An under-appreciated driver of soil carbon cycling

Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with 'omics' and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10-20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.

Fungal community composition predicts forest carbon storage at a continental scale

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.

Niche differentiation in microbial communities with stable genomic traits over time in engineered systems

Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.

Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Arbuscular mycorrhizal fungal communities differ in neighboring vineyards of different ages

Arbuscular mycorrhizal fungi (AMF) are key organisms in viticultural ecosystems as they provide many ecosystem services to soils and plants. Data about AMF community dynamics over time are relatively scarce and at short time scales. Many factors such as the soil, climate, and agricultural practices could modify the dynamics and functions of microbial communities. However, the effects on microbial communities of plant phenology and changes in plant physiology over time largely have been overlooked. We analyzed the diversity of AMF in three geographically close vineyards with similar soil parameters for 2 years. The plots differed in grapevine age (11, 36, and 110 years), but had the same soil management practice (horse tillage). Diversity analyses revealed a difference in the composition of AMF communities between the soil and grapevine roots and among roots of grapevines of different ages. This underlines AMF adaptation to physiological changes in the host which can explain the development of different AMF communities. The dynamics of AMF communities can highlight their resilience to environmental changes and agricultural practices.

Universal Dynamics of Microbial Communities in Full-Scale Textile Wastewater Treatment Plants and System Prediction by Machine Learning

The performance of full-scale biological wastewater treatment plants (WWTPs) depends on the operational and environmental conditions of treatment systems. However, we do not know how much these conditions affect microbial community structures and dynamics across systems over time and predictability of the treatment performance. For over a year, the microbial communities of four full-scale WWTPs processing textile wastewater were monitored. During temporal succession, the environmental conditions and system treatment performance were the main drivers, which explained up to 51% of community variations within and between all plants based on the multiple regression models. We identified the universality of community dynamics in all systems using the dissimilarity-overlap curve method, with the significant negative slopes suggesting that the communities containing the same taxa from different plants over time exhibited a similar composition dynamic. The Hubbell neutral theory and the covariance neutrality test indicated that all systems had a dominant niche-based assembly mechanism, supporting that the communities had a similar composition dynamic. Phylogenetically diverse biomarkers for the system conditions and treatment performance were identified by machine learning. Most of the biomarkers (83%) were classified as generalist taxa, and the phylogenetically related biomarkers responded similarly to the system conditions. Many biomarkers for treatment performance perform functions that are crucial for wastewater treatment processes (e.g., carbon and nutrient removal). This study clarifies the relationships between community composition and environmental conditions in full-scale WWTPs over time.

Seasonal variation in the soil fungal community structure of Larix gmelinii forests in Northeast China

Soil fungi play an indispensable role in forest ecosystems by participating in energy flow, material circulation, and assisting plant growth and development. Larix gmelinii is the dominant tree species in the greater Khingan Mountains, which is the only cold temperate coniferous forest in China. Understanding the variations in underground fungi will help us master the situation of L. gmelinii above ground. We collected soil samples from three seasons and analyzed the differences in soil fungal community structure using high-throughput sequencing technology to study the seasonal changes in soil fungal community structure in L. gmelinii forests. We found that the Shannon and Chao1 diversity in autumn was significantly lower than in spring and summer. The community composition and functional guild varied significantly between seasons. Furthermore, we showed that ectomycorrhizal fungi dominated the functional guilds. The relative abundance of ectomycorrhizal fungi increased dramatically from summer to autumn and was significantly negatively correlated with temperature and precipitation. Temperature and precipitation positively affect the alpha diversity of fungi significantly. In addition, pH was negatively correlated with the Chao1 diversity. Temperature and precipitation significantly affected several dominant genera and functional guilds. Among the soil physicochemical properties, several dominant genera were affected by pH, and the remaining individual genera and functional guilds were significantly correlated with total nitrogen, available phosphorus, soil organic carbon, or cation exchange capacity. For the composition of total fungal community, temperature and precipitation, as well as soil physicochemical properties except AP, significantly drove the variation in community composition.

Inter-annual Persistence of Canopy Fungi Driven by Abundance Despite High Spatial Turnover

While it is now well established that fungal community composition varies spatially at a variety of scales, temporal turnover of fungi is less well understood. Here we studied inter-annual community compositional changes of fungi in a rainforest tree canopy environment. We tracked fungal community shifts over 3 years in three substrate types (live bryophytes, dead bryophytes, and host tree bark) and compared these changes to amounts of community turnover seen at small spatial scales in the same system. The effect of substrate type on fungal community composition was stronger than that of sampling year, which was very small but significant. Although levels of temporal turnover varied among substrates, with greater turnover in live bryophytes than other substrates, the amount of turnover from year to year was comparable to what is seen at spatial distances between 5 and 9 cm for the same substrate. Stability of communities was largely driven by a few fungi with high relative abundances. A majority of fungal occurrences were at low relative abundances (≤ 0.1%). These fungi tended to be short lived and persisted to following years ≤ 50% of the time, depending on substrate. Their presence and persistence are likely impacted by stochastic processes like dispersal limitation and disturbance. Most samples contained only one or a few fungi at high relative abundance (≥ 10%) that persisted half or more of the time. These more abundant and persistent fungi are expected to have sustained functional interactions within the canopy ecosystem.

Forest tree growth is linked to mycorrhizal fungal composition and function across Europe

Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.

Elevation Matters More than Season in Shaping the Heterogeneity of Soil and Root Associated Ectomycorrhizal Fungal Community

Ectomycorrhizal (EcM) fungi play important roles in forest ecosystems, and their richness and composition can change along with elevation and season changes. However, no study has estimated the relative importance of altitudinal and seasonal heterogeneity in predicting the distribution of EcM fungal communities by simultaneously considering different sample types (root versus soil). In this study, we collected root and soil samples along a > 1,500-m elevation gradient during wet and dry seasons from Baima Snow Mountain, located in “the Mountains of Southwest China,” one of the 34 biodiversity hot spots, and we analyzed them using next-generation sequencing. Regardless of the sample type, similar EcM fungal richness pattern with increasing elevation (decline in the forest zone, and an increase at the alpine meadow zone) and strong community turnovers among different elevational zones and between two seasons were detected, and changes of EcM fungal community similarity on 400-m altitude gradient were equivalent to the community turnover between dry and wet seasons. Elevation and edaphic factors were shown to have the largest effects on EcM fungal community. The heterogeneity of richness and community composition was stronger among different elevational zones than across different seasons, mainly because the elevation variations in the EcM fungal community were shaped by the combined effects of different environmental factors, while seasonal changes were mainly controlled by temperature and fast-changing soil nutrients.

IMPORTANCE Altitude and season represent two important environmental gradients that shape the structure of biome, including the heterogeneity of EcM fungi. Previous studies have separately considered the influences of altitude and season on EcM fungal communities, but the relative importance of altitude and season is still unknown. The present study revealed that elevation influences the heterogeneity of EcM fungal community more than season; this may be because the variability of environmental factors is higher across different elevations than that across seasons.

Seasonal dynamics of soil microbial diversity and functions along elevations across the treeline

Although microbial diversity patterns along elevations have been extensively studied, little is known about whether the patterns are influenced by seasonality. To test the seasonal and elevational effects on microbial communities and functions, we collected soil samples across a mountain gradient above and below the treeline in three seasons (spring, summer and autumn). Microbial diversity based on the sequencing of 16S rRNA, 18S rRNA and nifH genes was measured, and microbial functions represented by soil basal respiration and microbial biomass were analyzed. As expected, we found significant seasonal and elevational effects on microbial α- and β-diversity and functions, and the effects of elevations were greater than seasonal effects. Elevational patterns of microbial β-diversity and functions were not influenced by seasonality. However, the elevational α-diversity patterns showed by specific groups (bacteria, protist and metazoa) changed among seasons. Further, we identified key soil properties (i.e. moisture, total carbon, total nitrogen and nitrate) which had higher seasonal and elevational variations, mainly contributing to the spatiotemporal variations of microbial diversity and functions. The findings of higher soil nutrients, archaeal and metazoan richness, and microbial functions at the treeline elevation, imply a strong edge effect of treeline on microbial diversity and functions. Together, our study highlights that seasonality influences the elevational patterns of soil microbial α-diversity, rather than that of β-diversity and functions, thus provides new insights into the seasonal and elevational effects on microbial communities and functions.

Temporal turnover of the soil microbiome composition is guild-specific

Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.

Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity

Montane cloud forests are fragile biodiversity hotspots. To attain their conservation, disentangling diversity patterns at all levels of ecosystem organization is mandatory. Biotic communities are regularly structured by environmental factors even at small spatial scales. However, studies at this scale have received less attention with respect to larger macroscale explorations, hampering the robust view of ecosystem functioning. In this sense, fungal small-scale processes remain poorly understood in montane cloud forests, despite their relevance. Herein, we analyzed soil fungal diversity and ecological patterns at the small-scale (within a 10 m triangular transect) in a pristine montane cloud forest of Mexico, using ITS rRNA gene amplicon Illumina sequencing and biogeochemical profiling. We detected a taxonomically and functionally diverse fungal community, dominated by few taxa and a large majority of rare species (81%). Undefined saprotrophs represented the most abundant trophic guild. Moreover, soil biogeochemical data showed an environmentally heterogeneous setting with patchy clustering, where enzymatic activities suggest distinctive small-scale soil patterns. Our results revealed that in this system, deterministic processes largely drive the assemblage of fungal communities at the small-scale, through multifactorial environmental filtering.

Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau

Both habitats and seasons can determine the dynamics of microbial communities, but the relative importance of different habitats and seasonal changes in shaping the soil bacterial community structures on a small spatial scale in permafrost areas remains controversial. In this study, we explored the relative effect of four typical alpine meadow habitats (swamp wetland, swamp meadow, meadow and mature meadow) versus seasons on soil bacterial communities based on samples from the Qinghai-Tibetan Plateau in four months (March, May, July and September). The results showed that habitats, rather than seasons explained more variation of soil bacterial composition and structure. Environmental cofactors explained the greatest proportion of bacterial variation observed and can help elucidate the driving force of seasonal changes and habitats on bacterial communities. Soil temperature played the most important role in shaping bacterial beta diversities, followed by soil total nitrogen and pH. A group of microbial biomarkers, used as indicators of different months, were identified using random forest modeling, and for which relative abundance was shaped by different environmental factors. Furthermore, seasonality in bacterial co-occurrence patterns was observed. The data showed that co-occurrence relationships changed over months. The inter-taxa connections in May and July were more pronounced than that in March and September. Bryobacter, a genus of subgroup_22 affiliated to Acidobacteria, and Pseudonocardia belonging to Actinobacteria were observed as the keystone taxa in different months in the network. These results demonstrate that the bacterial community was clustered according to the seasonal mechanism, whereas the co-occurrence relationships changed over months, which indicated complex bacterial dynamics in a permafrost grassland on the eastern edge of Qinghai-Tibetan.

Soil microbial community variation with time and soil depth in Eurasian Steppe (Inner Mongolia, China)

Purpose

Soil microorganisms play an indispensable role in the material and energy cycle of grassland ecosystems. The abundance of these organisms vary according to environmental factors, such as time of year and soil depth. There have been few studies on the transformation of soil microbial communities in degraded typical steppe according to these temporal and spatial changes. In this study, we analyze the community structure and diversity of soil bacteria and fungi, and the impact of these changing temporal and spatial factors upon the community structure.

Methods

From May to September 2018, we collected 90 soil samples from different depths (10, 20, and 30 cm) from the typical degraded steppe area of Xilingol. We carried out studies on soil physical and chemical properties and soil microbial diversity using high-throughput sequencing technology.

Results

We found that depth significantly affected abundance and diversity of bacteria and fungi. Bacteria and fungi diversity at 10 cm was higher than that at 20 cm and 30 cm. The abundance of Acidobacteria, Proteobacteria, Actinomycetes, Ascomycetes, and Basidiomycetes varies significantly with depth. In addition, soil pH increased significantly with increasing depth, while soil organic matter (SOM), available nitrogen (AN), volume water content of soil (VWC), and soil temperature (ST) decreased significantly with increasing depth. Finally, the depth, total organic carbon (TOC), and AN had a significant impact on the bacterial and fungal communities’ abundance (p < 0.05).

Conclusions

Spatial heterogeneity (in soil depth) is more significant than the time of year (month) in predicting changes in microbial community composition and soil properties. SOM, VWC, and the abundance of Proteobacteria and Actinomycetes positively correlate with soil depth, while pH and the abundance of Acidobacteria, Ascomycetes, and Basidiomycetes negatively correlate with soil depth. We speculate that SOM and VWC account for the variations in the abundance of Acidobacteria and Proteobacteria, while pH causes variations in the abundance of Actinomycetes, Ascomycetes and Basidiomycota.

Progress and Prospects of Mycorrhizal Fungal Diversity in Orchids

Orchids form mycorrhizal symbioses with fungi in natural habitats that affect their seed germination, protocorm growth, and adult nutrition. An increasing number of studies indicates how orchids gain mineral nutrients and sometime even organic compounds from interactions with orchid mycorrhizal fungi (OMF). Thus, OMF exhibit a high diversity and play a key role in the life cycle of orchids. In recent years, the high-throughput molecular identification of fungi has broadly extended our understanding of OMF diversity, revealing it to be a dynamic outcome co-regulated by environmental filtering, dispersal restrictions, spatiotemporal scales, biogeographic history, as well as the distribution, selection, and phylogenetic spectrum width of host orchids. Most of the results show congruent emerging patterns. Although it is still difficult to extend them to all orchid species or geographical areas, to a certain extent they follow the "everything is everywhere, but the environment selects" rule. This review provides an extensive understanding of the diversity and ecological dynamics of orchid-fungal association. Moreover, it promotes the conservation of resources and the regeneration of rare or endangered orchids. We provide a comprehensive overview, systematically describing six fields of research on orchid-fungal diversity: the research methods of orchid-fungal interactions, the primer selection in high-throughput sequencing, the fungal diversity and specificity in orchids, the difference and adaptability of OMF in different habitats, the comparison of OMF in orchid roots and soil, and the spatiotemporal variation patterns of OMF. Further, we highlight certain shortcomings of current research methodologies and propose perspectives for future studies. This review emphasizes the need for more information on the four main ecological processes: dispersal, selection, ecological drift, and diversification, as well as their interactions, in the study of orchid-fungal interactions and OMF community structure.

Variation in hyphal production rather than turnover regulates standing fungal biomass in temperate hardwood forests

Soil fungi link above- and belowground carbon (C) fluxes through their interactions with plants and contribute to C and nutrient dynamics through the production, turnover, and activity of fungal hyphae. Despite their importance to ecosystem processes, estimates of hyphal production and turnover rates are relatively uncommon, especially in temperate hardwood forests. We sequentially harvested hyphal ingrowth bags to quantify the rates of Dikarya (Ascomycota and Basidiomycota) hyphal production and turnover in three hardwood forests in the Midwestern United States, where plots differed in their abundance of arbuscular (AM)- vs. ectomycorrhizal (ECM)-associated trees. Hyphal production rates increased linearly with the percentage of ECM trees and annual production rates were 66% higher in ECM- than AM-dominated plots. Hyphal turnover rates did not differ across the mycorrhizal gradient (plots varying in their abundance of AM vs. ECM trees), suggesting that the greater fungal biomass in ECM-dominated plots relates to greater fungal production rather than slower fungal turnover. Differences in hyphal production across the gradient aligned with distinctly different fungal communities and activities. As ECM trees increased in dominance, fungi inside ingrowth bags produced more extracellular enzymes involved in degrading nitrogen (N)-bearing relative to C-bearing compounds, suggesting greater fungal (and possibly plant) N demand in ECM-dominated soils. Collectively, our results demonstrate that shifts in temperate tree species composition that result in changes in the dominant type of mycorrhizal association may have strong impacts on Dikarya hyphal production, fungal community composition and extracellular enzyme activity, with important consequences for soil C and N cycling.

High resilience of the mycorrhizal community to prescribed seasonal burnings in eastern Mediterranean woodlands

Fire effects on ecosystems range from destruction of aboveground vegetation to direct and indirect effects on belowground microorganisms. Although variation in such effects is expected to be related to fire severity, another potentially important and poorly understood factor is the effect of fire seasonality on soil microorganisms. We carried out a large-scale field experiment examining the effects of spring (early-dry season) versus autumn (late-dry- season) burns on the community composition of soil fungi in a typical Mediterranean woodland. Although the intensity and severity of our prescribed burns were largely consistent between the two burning seasons, we detected differential fire season effects on the composition of the soil fungal community, driven by changes in the saprotrophic fungal guild. The community composition of ectomycorrhizal fungi, assayed both in pine seedling bioassays and from soil sequencing, appeared to be resilient to the variation inflicted by seasonal fires. Since changes in the soil saprotrophic fungal community can directly influence carbon emission and decomposition rates, we suggest that regardless of their intensity and severity, seasonal fires may cause changes in ecosystem functioning.

Fungal community structure and seasonal trajectories respond similarly to fire across pyrophilic ecosystems

Fire alters microbial community composition, and is expected to increase in frequency due to climate change. Testing whether microbes in different ecosystems will respond similarly to increased fire disturbance is difficult though, because fires are often unpredictable and hard to manage. Fire recurrent or pyrophilic ecosystems, however, may be useful models for testing the effects of frequent disturbance on microbes. We hypothesized that across pyrophilic ecosystems, fire would drive similar alterations to fungal communities, including altering seasonal community dynamics. We tested fire's effects on fungal communities in two pyrophilic ecosystems, a longleaf pine savanna and tallgrass prairie. Fire caused similar fungal community shifts, including (i) driving immediate changes that favored taxa able to survive fire and take advantage of post-fire environments and (ii) altering seasonal trajectories due to fire-associated changes to soil nutrient availability. This suggests that fire has predictable effects on fungal community structure and intra-annual community dynamics in pyrophilic ecosystems, and that these changes could significantly alter fungal function. Parallel fire responses in these key microbes may also suggest that recurrent fires drive convergent changes across ecosystems, including less fire-frequented systems that may start burning more often due to climate change.

Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System

We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.

IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale

Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation.

The relative importance of spatial and temporal variability in shaping the distribution of soil microbial communities at a large spatial scale remains poorly understood. Here, we explored the relative importance of space versus time when predicting the distribution of soil bacterial and fungal communities across North China Plain in two contrasting seasons (summer versus winter). Although we found that microbial alpha (number of phylotypes) and beta (changes in community composition) diversities differed significantly between summer and winter, space rather than season explained more of the spatiotemporal variation of soil microbial alpha and beta diversities. Environmental covariates explained some of microbial spatiotemporal variation observed, with fast-changing environmental covariates—climate variables, soil moisture, and available nutrient—likely being the main factors that drove the seasonal variation found in bacterial and fungal beta diversities. Using random forest modeling, we further identified a group of microbial exact sequence variants (ESVs) as indicators of summer and winter seasons and for which relative abundance was associated with fast-changing environmental variables (e.g., soil moisture and dissolved organic nitrogen). Together, our empirical field study’s results suggest soil microbial seasonal variation could arise from the changes of fast-changing environmental variables, thus providing integral support to the large emerging body of snapshot studies related to microbial biogeography.

IMPORTANCE Both space and time are key factors that regulate microbial community, but microbial temporal variation is often ignored at a large spatial scale. In this study, we compared spatial and seasonal effects on bacterial and fungal diversity variation across an 878-km transect and found direct evidence that space is far more important than season in regulating the soil microbial community. Partitioning the effect of season, space and environmental variables on microbial community, we further found that fast-changing environmental factors contributed to microbial temporal variation.

Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest

The spatial and temporal linkages between turnover of soil microbial communities and their associated functions remain largely unexplored in terrestrial ecosystems. Yet defining these relationships and how they vary across ecosystems and microbial lineages is key to incorporating microbial communities into ecological forecasts and ecosystem models. To define linkages between turnover of soil bacterial and fungal communities and their function we sampled fungal and bacterial composition, abundance, and enzyme activities across a 3-ha area of wet tropical primary forest over 2 yr. We show that fungal and bacterial communities both exhibited temporal turnover, but turnover of both groups was much lower than in temperate ecosystems. Turnover over time was driven by gain and loss of microbial taxa and not changes in abundance of individual species present in multiple samples. Only fungi varied over space with idiosyncratic variation that did not increase linearly with distance among sampling locations. Only phosphorus-acquiring enzyme activities were linked to shifts in septate, decomposer fungal abundance; no enzymes were affected by composition or diversity of fungi or bacteria. Although temporal and spatial variation in composition was appreciable, because turnover of microbial communities did not alter the functional repertoire of decomposing enzymes, functional redundancy among taxa may be high in this ecosystem. Slow temporal turnover of tropical soil microbial communities and large functional redundancy suggests that shifts in abundance of particular functional groups may capture ecosystem function more accurately than composition in these heterogeneous ecosystems.

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.

Early stage root-Associated fungi show a high temporal turnover, but Are independent of beech progeny

The relationship between trees and root-associated fungal communities is complex. By specific root deposits and other signal cues, different tree species are able to attract divergent sets of fungal species. Plant intraspecific differences can lead to variable fungal patterns in the root's proximity. Therefore, within the Beech Transplant Experiment, we analyzed the impact of three different European beech ecotypes on the fungal communities in roots and the surrounding rhizosphere soil at two time points. Beech nuts were collected in three German sites in 2011. After one year, seedlings of the different progenies were out-planted on one site and eventually re-sampled in 2014 and 2017. We applied high-throughput sequencing of the fungal ITS2 to determine the correlation between tree progeny, a possible home-field advantage, plant development and root-associated fungal guilds under field conditions. Our result showed no effect of beech progeny on either fungal OTU richness or fungal community structure. However, over time the fungal OTU richness in roots increased and the fungal communities changed significantly, also in rhizosphere. In both plant compartments, the fungal communities displayed a high temporal turnover, indicating a permanent development and functional adaption of the root mycobiome of young beeches.

Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities

Our findings highlight how soil fungal and bacterial communities respond to time, season, and plant species identity. We found that succession shapes the soil bacterial community, while plant species and the type of plant species that grows in the soil drive the assembly of soil fungal communities. Future research on the effects of plants on soil microbes should take into consideration the relative roles of both time and plant growth on creating soil legacies that impact future plants growing in the soil. Understanding the temporal (in)stability of microbial communities in soils will be crucial for predicting soil microbial composition and functioning, especially as plant species compositions will shift with global climatic changes and land-use alterations. As fungal and bacterial communities respond to different environmental cues, our study also highlights that the selection of study organisms to answer specific ecological questions is not trivial and that the timing of sampling can greatly affect the conclusions made from these studies.

Microorganisms are found everywhere and have critical roles in most ecosystems, but compared to plants and animals, little is known about their temporal dynamics. Here, we investigated the temporal stability of bacterial and fungal communities in the soil and how their temporal variation varies between grasses and forb species. We established 30 outdoor mesocosms consisting of six plant monocultures and followed microbial communities for an entire year in these soils. We demonstrate that bacterial communities vary greatly over time and that turnover plays an important role in shaping microbial communities. We further show that bacterial communities rapidly shift from one state to another and that this is related to changes in the relative contribution of certain taxa rather than to extinction. Fungal soil communities are more stable over time, and a large part of the variation can be explained by plant species and by whether they are grasses or forbs. Our findings show that the soil bacterial community is shaped by time, while plant group and plant species-specific effects drive soil fungal communities. This has important implications for plant-soil research and highlights that temporal dynamics of soil communities cannot be ignored in studies on plant-soil feedback and microbial community composition and function.