Mycorrhizal response to experimental pH and P manipulation in acidic hardwood forests

Halophyte Elymus dahuricus colonization regulates microbial community succession by mediating saline-alkaline and biogenic organic matter in bauxite residue

Alkalinity regulation and nutrient accumulation are critical factors in the construction of plant and microbial communities and soil formation in bauxite residue, and are extremely important for sustainable vegetation restoration in bauxite residue disposal areas. However, the establishment and succession of microbial communities driven by plant colonization-mediated improvements in the physicochemical properties of bauxite residues remain poorly understood. Thus, in this study, we determined the saline-alkali properties and dissolved organic matter (DOM) components under plant growth conditions and explored the microbial community diversity and structure using Illumina high-throughput sequencing. The planting of Elymus dahuricus (E. dahuricus) in the bauxite residue resulted in a significant decrease in total alkalinity (TA), exchangeable Na, and electrical conductivity (EC) as well as the release of more tryptophan-like protein compounds and low-molecular-weight humic substances associated with biological activities into the bauxite residue substrate. Taxonomical analysis revealed an initial-stage bacterial and fungal community dominated by alkaline-tolerant Actinobacteriota, Firmicutes, and Ascomycota, and an increase in the relative abundances of the phyla Bacteroidota, Cyanobacteria, Chloroflexi, and Gemmatimonadota. The biological activities of phylum Actinobacteriota, Bacteroidota, and Gemmatimonadota were significantly associated with protein-like and UVA-like humic substances. As eutrophic bacteria, Proteobacteria participate in the transformation of humic substances and can not only utilize small molecules of organic matter and convert them into humic substances but also promote the gradual conversion of humic acids into simple molecular compounds. Our results suggest that plant roots secrete organic matter and microbial metabolites as the main biogenic organic matter that participates in the establishment and succession of the microbial community in bauxite residues. Root length affects bacterial and fungal diversity by mediating the production of protein-like substances.

Soil Structure and Ectomycorrhizal Root Colonization of Pecan Orchards in Northern Mexico

Pecan trees form a symbiotic relationship with ectomycorrhizal fungi (ECM), which actively provide nutrition to the roots and protect them from phytopathogens. Although these trees originated in the southern United States and northern Mexico, information on their root colonization by ECM is insufficient in terms of a representative number of samples, both in these regions and worldwide. Therefore, the objectives of this study were to determine the percentage of ectomycorrhizal colonization (ECM) of pecan trees of different ages in conventional and organic agronomic orchards and to identify ectomycorrhizal sporocarps, both morphologically and molecularly. The rhizospheric soil properties and the ECM percentages were analyzed for 14 Western variety pecan tree orchards between 3 and 48 years of age and grouped according to the agronomic management method. DNA extraction, internal transcribed spacer amplification, and sequencing were conducted on the fungal macroforms. The ECM colonization percentage fluctuated between 31.44 and 59.89%. Soils with low phosphorus content showed higher ECM colonization. The ECM concentrations were relatively homogeneous in relation to the ages of the trees, and organic matter content did not affect the percentage of ECM colonization. The highest ECM percentages occurred with the sandy clay crumb texture soil, with an average of 55% ECM, followed by sandy clay loam soils with 49.5%. The Pisolithus arenarius and Pisolithus tinctorius fungi were molecularly identified from sporocarps associated with pecan trees. This is the first study that reports Pisolithus arenarius as being associated with this tree.

On the significance of long-term trends in tree-ring N isotopes - The interplay of soil conditions and regional NOx emissions

As anthropogenic nitrogen (N) emissions have been rising for decades, it is critical to develop natural archives that help understand how natural processes were modified in the past. Tree-ring δ¹⁵N values may represent such an indicator but its validity as faithful record of N cycling changes is still debated. Here we produce long-tree-ring δ¹⁵N series for five white spruce stands from two boreal regions submitted to moderate industrial N inputs. The obtained δ¹⁵N series show sharp differences among stands, even from the same region, despite the fact that they show similar increases in intrinsic water use efficiency (iWUE), a proxy for foliar strategies derived from δ¹³C values. The statistical modeling of these series and the basal area increment (BAI) of the trees allow to suggest that the mechanisms controlling the isotopic fractionation of N assimilated by tree rings are decoupled from the foliar strategies under the anthropogenic N emissions. The iWUE trends mainly reflect rise of pCO₂ and changes in air quality. The long-term δ¹⁵N trends echo different biogeochemical processes responding to N deposition due to distinct original soil pH at the various sites. We contend that tree-ring δ¹⁵N series can record changes in the forest N cycle, but their rigorous interpretation requires laborious work, particularly an understanding of the biogeochemistry in the soil immediately around the investigated trees. "Seek simplicity and distrust it", Alfred North Whitehead.

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.

Nitrogen isotopes in the soil-to-tree continuum - Tree rings express the soil biogeochemistry of boreal forests exposed to moderate airborne emissions

Anthropogenic N emissions represent a potential threat for forest ecosystems, and environmental indicators that provide insight into the changing forest N cycle are needed. Tree ring N isotopic ratios (δ¹⁵N) appear as a contentious choice for this role as the exact mechanisms behind tree-ring δ¹⁵N changes seldom benefit from a scrutiny of the soil-to-tree N continuum. This study integrates the results from the analysis of soil chemistry, soil microbiome genomics, and δ¹⁵N values of soil N compounds, roots, ectomycorrhizal (EcM) fungi and recent tree rings of thirteen white spruce trees sampled in five stands, from two regions exposed to moderate anthropogenic N emissions (3.9 to 8.1 kg/ha/y) with distinctive δ¹⁵N signals. Our results reveal that airborne anthropogenic N with distinct δ¹⁵N signals may directly modify the NO₃^- δ¹⁵N values in surface soils, but not the ones of NH₄⁺, the preferred N form of the studied trees. Hence, the tree-ring δ¹⁵N values reflect specific soil N conditions and assimilation modes by trees. Along with a wide tree-ring δ¹⁵N range, we report differences in: soil nutrient content and N transformation rates; δ¹⁵N values of NH₄⁺, total dissolved N (TDN) and EcM mantle enveloping the root tips; and bacterial and fungal community structures. We combine EcM mantle and root δ¹⁵N values with fungal identification to infer that hydrophobic EcM fungi transfer N from the dissolved organic N (DON) pool to roots under acidic conditions, and hydrophilic EcM fungi transfer various N forms to roots, which also assimilate N directly under less acidic conditions. Despite the complexities of soil biogeochemical properties and processes identified in the studied sites, in the end, the tree-ring δ¹⁵N averages inversely correlate with soil pH and anthropogenic N inputs, confirming white spruce tree-ring δ¹⁵N values as a suitable indicator for environmental research on forest N cycling.

Molecular Quantification of Arbuscular Mycorrhizal Fungal Root Colonization

Specific quantification of root-colonizing arbuscular mycorrhizal fungi (AMF) by quantitative real-time PCR is a high-throughput technique, most suitable for determining abundances of AMF species or isolates in previously characterized experimental systems. The principal steps are the choice and validation of an appropriate assay to specifically amplify a gene fragment of the target AMF, preparation of templates from root samples, and quantification of the fungal gene copy numbers in these templates. The use of a suitable assay is crucial for a correct data collection but also highly specific for each experimental system and is therefore covered by general recommendations. Subsequently, specific steps are described for the validation of the assay using a standard dilution series, the determination of appropriate dilutions of DNA extracts from roots, and the quantification of the gene copy numbers in samples including calculations.

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C. geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C. geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C. geophilum, we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.

Higher temperatures and lower annual rainfall do not restrict, directly or indirectly, the mycorrhizal colonization of barley (Hordeum vulgare L.) under rainfed conditions

Whereas the role of arbuscular mycorrhizal fungi (AMF) in plant growth improvement has been well described in agroecosystems, little is known about the effect of environmental factors on AMF root colonization status of barley, the fourth most important cereal crop all over the world. In order to understand the influence of environmental factors, such as climatic and soil physico-chemical properties, on the spontaneous mycorrhizal ability of barley (Hordeum vulgare L.), a field investigation was conducted in 31 different sites in sub-humid, upper and middle semi-arid areas of Northern Tunisia. Mycorrhizal root colonization of H. vulgare varied considerably among sites. Principal component analysis showed that barley mycorrhization is influenced by both climatic and edaphic factors. A partial least square structural equation modelling (PLS-SEM) revealed that 39% (R²) of the total variation in AMF mycorrhizal rate of barley roots was mainly explained by chemical soil properties and climatic characteristics. Whereas barley root mycorrhizal rates were inversely correlated with soil organic nitrogen (ON), available phosphorus amounts (P), altitude (Z), average annual rainfall (AAR), they were directly correlated with soil pH and temperature. Our results indicated that AMF root colonization of barley was strongly related to climatic characteristics than chemical soil properties. The current study highlights the importance of the PLS-SEM to understand the interactions between climate, soil properties and AMF symbiosis of barley in field conditions.

Legacy Effects Overshadow Tree Diversity Effects on Soil Fungal Communities in Oil Palm-Enrichment Plantations

Financially profitable large-scale cultivation of oil palm monocultures in previously diverse tropical rain forest areas constitutes a major ecological crisis today. Not only is a large proportion of the aboveground diversity lost, but the belowground soil microbiome, which is important for the sustainability of soil function, is massively altered. Intermixing oil palms with native tree species promotes vegetation biodiversity and stand structural complexity in plantations, but the impact on soil fungi remains unknown. Here, we analyzed the diversity and community composition of soil fungi three years after tree diversity enrichment in an oil palm plantation in Sumatra (Indonesia). We tested the effects of tree diversity, stand structural complexity indices, and soil abiotic conditions on the diversity and community composition of soil fungi. We hypothesized that the enrichment experiment alters the taxonomic and functional community composition, promoting soil fungal diversity. Fungal community composition was affected by soil abiotic conditions (pH, N, and P), but not by tree diversity and stand structural complexity indices. These results suggest that intensive land use and abiotic filters are a legacy to fungal communities, overshadowing the structuring effects of the vegetation, at least in the initial years after enrichment plantings.

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest

AIMS

The soil microbial community plays a critical role in increasing phosphorus (P) availability in low-P, weathered soils by "mining" recalcitrant organic P through the production of phosphatase enzymes. However, there is a lack of data on the fungal and bacterial taxa which are directly involved in P mining, which could also serve as potential microbial bioindicators of low P availability.

METHODS AND RESULTS

Leveraging a 5-year P enrichment experiment on low-P forest soils, high-throughput sequencing was used to profile the microbial community to determine which taxa associate closely with P availability. We hypothesized that there would be a specialized group of soil micro-organisms that could access recalcitrant P and whose presence could serve as a bioindicator of P mining. Community profiling revealed several candidate bioindicators of P mining (Russulales, Acidobacteria Subgroup 2, Acidobacteriales, Obscuribacterales and Solibacterales), whose relative abundance declined with elevated P and had a significant, positive association with phosphatase production. In addition, we identified candidate bioindicators of high P availability (Mytilinidales, Sebacinales, Chitinophagales, Cytophagales, Saccharimonadales, Opitulales and Gemmatales).

CONCLUSIONS

This research provides evidence that mitigating P limitation in this ecosystem may be a specialized trait and is mediated by a few microbial taxa.

SIGNIFICANCE AND IMPACT OF THE STUDY

Here, we characterize Orders of soil microbes associated with manipulated phosphorus availability in forest soils to determine bioindicator candidates for phosphorus. Likewise, we provide evidence that the microbial trait to utilize recalcitrant organic forms of P (e.g. P mining) is likely a specialized trait and not common to all members of the soil microbial community. This work further elucidates the role that a complex microbial community plays in the cycling of P in low-P soils, and provides evidence for future studies on microbial linkages to human-induced ecosystem changes.

Host plant phylogeny and geographic distance strongly structure Betulaceae-associated ectomycorrhizal fungal communities in Chinese secondary forest ecosystems

Environmental filtering and dispersal limitation are two of the primary drivers of community assembly in ecosystems, but their effects on ectomycorrhizal (EM) fungal communities associated with wide ranges of Betulaceae taxa at a large scale are poorly documented. In this study, we examined EM fungal communities associated with 23 species from four genera (Alnus, Betula, Carpinus and Corylus) of Betulaceae in Chinese secondary forest ecosystems, using Illumina MiSeq sequencing of the ITS2 region. Effects of host plant phylogeny, soil, climate and geographic distance on EM fungal community were explored. In total, we distinguished 1738 EM fungal operational taxonomic units (OTUs) at a 97% sequence similarity level. The EM fungal communities of Alnus had significantly lower OTU richness than those associated with the other three plant genera. The EM fungal OTU richness was significantly affected by geographic distance, host plant phylogeny, soil and climate. The EM fungal community composition was significantly influenced by host plant phylogeny (12.1% of variation explained in EM fungal community), geographic distance (7.7%), soil (4.6%) and climate (1.1%). This finding highlights that environmental filtering linked to host plant phylogeny and dispersal limitation strongly influence EM fungal communities associated with Betulaceae plants in Chinese secondary forest ecosystems.

Tree growth response to shifting soil nutrient economy depends on mycorrhizal associations

The mycorrhizal-associated nutrient economy hypothesis proposes a strong connection between plant and fungal traits and the dominant form of soil nutrients. If true, then shifting from an organic to an inorganic nutrient economy should benefit arbuscular mycorrhizal (AM) trees because they are more suited to acquiring inorganic forms of nutrients and have limited decomposing capabilities when compared with ectomycorrhizal (ECM) trees. An inorganic nutrient economy was experimentally promoted by applying inorganic phosphorus (P) fertiliser and/or elevating soil pH with lime in three Allegheny Plateau mixed-mesophytic forests. Trees were measured over seven growing seasons to determine how growth responded to the treatments based on mycorrhizal association. AM-associated trees showed increased growth in response to increased inorganic nutrients, but ECM tree growth was suppressed when compared with the control. We also observed that understory and mid-story trees responded to the treatments, but large overstory trees showed no significant growth response. Results support the hypothesis that AM trees respond positively to an inorganic nutrient economy. While raising pH in acidic soils can be detrimental to ECM tree growth, the exact mechanism for this response is unclear.

The Full-Size ABCG Transporter of Medicago truncatula Is Involved in Strigolactone Secretion, Affecting Arbuscular Mycorrhiza

Strigolactones (SLs) are plant-derived signaling molecules that stimulate the hyphal branching of arbuscular mycorrhizal fungi (AMF), and consequently promote symbiotic interaction between the fungus and the plant. Currently, our knowledge on the molecular mechanism of SL transport is restricted to the Solanaceae family. In the Solanaceae family, SL translocation toward the rhizosphere occurs through the exodermis via hypodermal passage cells and involves a member of the G subfamily, of the ATP-binding cassette (ABC) membrane transporters. Most Fabaceae species, including those that are agriculturally important, have a different root anatomy compared to most angiosperm plants (i.e., lacking an exodermis). Thus, we have investigated how SL transport occurs in the model legume Medicago truncatula. Here, we show that overexpression of a SL transporter from petunia (PaPDR1) enhances AMF colonization rates in M. truncatula. This result demonstrates the importance of ABCG proteins for the translocation of orobanchol-type molecules to facilitate arbuscular mycorrhiza, regardless of root anatomy and phylogenetic relationships. Moreover, our research has led to the identification of Medicago ABCG59, a close homologue of Petunia PDR1, that exhibits root specific expression and is up-regulated by phosphate starvation as well as in the presence of rac-GR24, a synthetic SL. Its promoter is active in cortical cells, root tips, and the meristematic zone of nodules. The mtabcg59 loss-of-function mutant displayed a reduced level of mycorrhization compared to the WT plants but had no impact on the number of nodules after Sinorhizobium meliloti inoculation. The reduced mycorrhization indicates that less SLs are secreted by the mutant plants, which is in line with the observation that mtabcg59 exudates exhibit a reduced stimulatory effect on the germination of the parasitic plant Phelipanche ramosa compared to the corresponding wild type.

Evaluation of host effects on ectomycorrhizal fungal community compositions in a forested landscape in northern Japan

Community compositions of ectomycorrhizal (ECM) fungi are similar within the same host taxa. However, careful interpretation is required to determine whether the combination of ECM fungi and plants is explained by the host preference for ECM fungi, or by the influence of neighbouring heterospecific hosts. In the present study, we aimed to evaluate the effects of host species on the ECM community compositions in a forested landscape (approx. 10 km) where monodominant forest stands of six ECM host species belonging to three families were patchily distributed. A total of 180 ECM operational taxonomic units (OTUs) were detected with DNA metabarcoding. Quantitative multivariate analyses revealed that the ECM community compositions were primarily structured by host species and families, regardless of the soil environments and spatial arrangements of the sampling plots. In addition, 38 ECM OTUs were only detected from particular host tree species. Furthermore, the neighbouring plots harboured similar fungal compositions, although the host species were different. The relative effect of the spatial factors on the ECM compositions was weaker than that of host species. Our results suggest that the host preference for ECM fungi is the primary determinant of ECM fungal compositions in the forested landscape.

Coyle K, A. Kluber L, J. Burke D. Fungal and Bacterial Communities Exhibit Consistent Responses to Reversal of Soil Acidification and Phosphorus Limitation over Time

Chronic acid deposition affects many temperate hardwood forests of the northeastern United States, reduces soil pH and phosphorus (P) availability, and can alter the structure and function of soil microbial communities. The strategies that microorganisms possess for survival in acidic, low P soil come at a carbon (C) cost. Thus, how microbial communities respond to soil acidification in forests may be influenced by plant phenological stage as C allocation belowground varies; however, this remains largely unexplored. In this study, we examined microbial communities in an ecosystem level manipulative experiment where pH and/or P availability were elevated in three separate forests in Northeastern Ohio. Tag-encoded pyrosequencing was used to examine bacterial and fungal community structure at five time points across one year corresponding to plant phenological stages. We found significant effects of pH treatment and time on fungal and bacterial communities in soil. However, we found no interaction between pH treatment and time of sampling for fungal communities and only a weak interaction between pH elevation and time for bacterial communities, suggesting that microbial community responses to soil pH are largely independent of plant phenological stage. In addition, fungal communities were structured largely by site, suggesting that fungi were responding to differences between the forests, such as plant community differences.

Exogenous Nitric Oxide and Phosphorus Stress Affect the Mycorrhization, Plant Growth, and Associated Microbes of Carya illinoinensis Seedlings Colonized by Tuber indicum

In the artificial cultivation of truffles, ectomycorrhizal colonization level, host plant quality, and the associated microbes in the rhizosphere soil are vitally important. To explore the effects of nitric oxide (NO) and phosphorus (P) stress on the early symbiosis of truffles and host plants, different concentrations of exogenous NO donor sodium nitroprusside (SNP) and P were applied to Carya illinoinensis seedlings inoculated with the Chinese black truffle (Tuber indicum). The growth of T. indicum-mycorrhized seedlings and their mycorrhizal colonization rate were investigated. Additionally, the denitrifying bacterial community harboring NO reductase (norB) genes and the fungal community in the rhizosphere of the host were analyzed by high-throughput sequencing. The results showed that the colonization rate of T. indicum was significantly influenced by SNP treatments and P stress, with the highest level being obtained when the SNP was 100 μmol/L under low P stress (5 μmol/L). Treatment with 100 μmol/L SNP alone also increased the colonization rate of T. indicum and had positive effects on the plant height, stem circumference, biomass, root-shoot ratio and root POD activity of the seedlings at different times after inoculation. Under low P stress, the 100 μmol/L SNP increased the richness of the norB-type denitrifying bacterial community. Interestingly, the diversity and richness of norB-type denitrifying bacteria were significantly positively correlated with the colonization rate of T. indicum. SNP treatments under low P stress altered the abundance of some dominant taxa such as Alphaproteobacteria, Gammaproteobacteria, Pseudomonas, Ensifer, and Sulfitobacter. Evaluation of the fungal community in the rhizosphere revealed that 100 μmol/L SNP treatment alone had no noticeable effect on their richness and diversity, but it did shape the abundance of some fungi. Buellia, Podospora, Phaeoisaria, Ascotaiwania, and Lophiostoma were more abundant following exogenous NO application, while the abundance of Acremonium, Monographella, and Penicillium were decreased. Network analysis indicated that T. indicum was positively and negatively correlated with some fungal genera when treated with 100 μmol/L SNP. Overall, these results revealed how exogenous NO and P stress influence the symbiosis of truffles and host plants, and indicate that application of SNP treatments has the potential for ectomycorrhizal synthesis and truffle cultivation.

Novel insights into how the mean and heterogeneity of abiotic conditions together shape forb species richness patterns in the Allegheny plateau ecoregion

ABSTRACT

While plant community theory tends to emphasize the importance of abiotic heterogeneity along niche axes, much empirical work seeks to characterize the influence of the absolute magnitude of key abiotic variables on diversity. Both magnitude (as reflected, e.g., by a mean) and heterogeneity (variance) in abiotic conditions likely contribute to biodiversity patterns in plant communities, but given the large number of putative abiotic drivers and the fact that each may vary at different spatiotemporal scales, the challenge of linking observed biotic patterns with the underlying environment remains acute. Using monitoring data from a natural resource agency, we compared how well statistical models of the mean, heterogeneity, and both the mean and heterogeneity combined of 17 abiotic factor variables explained patterns of forb species richness in Northeast Ohio, USA. We performed our analyses at two spatial scales, repeated in spring and summer across four forest types. Although all models explained a great deal of the variance in species richness, models including both the mean and heterogeneity of different abiotic factors together outperformed models including either the mean or the heterogeneity of abiotic factors alone. Variability in forb species richness was mostly due to changes in mean calcium levels regardless of forest type. After accounting for forest type, we were able to attribute variation in forb species richness to changes in the heterogeneity of different abiotic factors as well. Our results suggest that multiple mechanisms act simultaneously according to different aspects of the abiotic environment to structure forb communities, and this underscores the importance of considering both the magnitude of and heterogeneity in multiple abiotic factors when looking for links between the abiotic environment and plant community patterns. Finally, we identify novel patterns across spatial scales, forest types, and seasons that can guide future research in this vein.

OPEN RESEARCH BADGES

This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.kp3cb17.

Effects of earthworms and white-tailed deer on roots, arbuscular mycorrhizae, and forest seedling performance

Changes in understory plant composition and biodiversity declines in northeastern North American forests are widespread. Preserving species and ecosystem function requires appropriate identification and management of important stressors. Coexistence of stressors, among them earthworm invasions and white-tailed deer, makes correct identification of mechanisms that cause diversity declines challenging. We used an established factorial experiment to assess survival and growth of native seedlings (Actaea pachypoda, Aquilegia canadensis, Cornus racemosa, Quercus rubra, and Prenanthes alba) in response to presence/absence of deer and earthworms. We expected deer and earthworms to reduce seedling survival and biomass, and we evaluated potential pathways to explain this impact (soil N and P concentrations and pools, root architecture, and arbuscular mycorrhizal fungi [AMF] colonization). We developed structural equation models (SEM) to identify specific pathways through which earthworms and deer were impacting plant species with different life histories. Seedling survival was not affected by our treatments nor the plant and soil variables we tested. Actaea biomass was smaller in earthworm-invaded plots, and with larger total N pools. In contrast, both deer and earthworm treatments were associated with lower soil nutrient concentrations, and earthworm-invaded plots had smaller N and extractable P pools. Actaea, Cornus, Prenanthes, and Quercus seedlings had a lower proportion of fine roots in earthworm-invaded plots, while fine roots in Aquilegia made up a higher proportion of the root system. AMF colonization in Quercus was reduced in sites colonized by earthworms, but AMF in other species were unaffected. Our SEMs showed high correlation among soil variables, but because we do not know which variables are drivers of this change and which are passengers, we can only conclude that they are changing together as deer and earthworms exert their respective influence. Different plant species responded in idiosyncratic ways to earthworm and deer effects on soil fertility, root architecture and limited effects on AMF colonization. While earthworm and deer-mediated changes to fine roots, soil nutrients, and AMF may lead to changes in plant performance over time, these changes rarely translated to lower plant performance in our seedlings.

Mycorrhizal fungal community structure in tropical humid soils under fallow and cropping conditions

Little is known to what extent soil biota, in particular, the mycorrhizae are altered through different fallow durations/types in tropical soils. We found that soil-N, -C, -Al, -K and -Ca contents significantly differed due to the fallow durations/types. Subsequently, the effects of fallow types and soil depths on the diversity, species richness and community structure of arbuscular mycorrhizal (AM) fungi were examined. A higher AM species richness was identified in the cropping than in forest fallow fields, suggesting a positive cropping feedback on the AM community composition. Distribution of the AM species was positively related to soil properties, specifically soil-pH, and soil-Pi, -Ca and -Mg contents. The soil properties conjointly accounted for 78.5% of explained variation in the AM community composition, signifying that the main factors altering the community structure under different fallow and cropping systems were the soil properties. Among the soil chemical characteristics, the soil-pH disclosed a significant explained variation in the AM community composition in the topsoil layer under the short fallow. Structural modeling equation to understand multiple predictive pathways that connect soil properties, fallow practices and AM community structures indicated that soil-C, -N and -Ca contents were highlighted as important factors influencing the AM community compositions.

Host Phylogeny Is a Major Determinant of Fagaceae-Associated Ectomycorrhizal Fungal Community Assembly at a Regional Scale

Environmental filtering (niche process) and dispersal limitation (neutral process) are two of the primary forces driving community assembly in ecosystems, but how these processes affect the Fagaceae-associated ectomycorrhizal (EM) fungal community at regional scales is so far poorly documented. We examined the EM fungal communities of 61 plant species in six genera belonging to the Fagaceae distributed across Chinese forest ecosystems (geographic distance up to ∼3,757 km) using Illumina Miseq sequencing of ITS2 sequences. The relative effects of environmental filtering (e.g., host plant phylogeny, soil and climate) and dispersal limitation (e.g., spatial distance) on the EM fungal community were distinguished using multiple models. In total, 2,706 operational taxonomic units (OTUs) of EM fungi, corresponding to 54 fungal lineages, were recovered at a 97% sequence similarity level. The EM fungal OTU richness was significantly affected by soil pH and nutrients and by host phylogeny. The EM fungal community composition was significantly influenced by combinations of host phylogeny, spatial distance, soil and climate. Furthermore, host phylogeny had the greatest effect on EM fungal community. The study suggests that the assembly of the EM fungal community is governed by both environmental filtering and dispersal limitation, with host effect being the most important determinant at the regional scale.

Adaptive root foraging strategies along a boreal-temperate forest gradient

The tree root-mycorhizosphere plays a key role in resource uptake, but also in the adaptation of forests to changing environments. The adaptive foraging mechanisms of ectomycorrhizal (EcM) and fine roots of Picea abies, Pinus sylvestris and Betula pendula were evaluated along a gradient from temperate to subarctic boreal forest (38 sites between latitudes 48°N and 69°N) in Europe. Variables describing tree resource uptake structures and processes (absorptive fine root biomass and morphology, nitrogen (N) concentration in absorptive roots, extramatrical mycelium (EMM) biomass, community structure of root-associated EcM fungi, soil and rhizosphere bacteria) were used to analyse relationships between root system functional traits and climate, soil and stand characteristics. Absorptive fine root biomass per stand basal area increased significantly from temperate to boreal forests, coinciding with longer and thinner root tips with higher tissue density, smaller EMM biomass per root length and a shift in soil microbial community structure. The soil carbon (C) : N ratio was found to explain most of the variability in absorptive fine root and EMM biomass, root tissue density, N concentration and rhizosphere bacterial community structure. We suggest a concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in the root-mycorrhiza-bacteria continuum along climate and soil C : N gradients.

Seasonal variation in mycorrhizal fungi colonizing roots of Allium tricoccum (wild leek) in a mature mixed hardwood forest

The community of arbuscular mycorrhizal (AM) fungi colonizing roots of the forest herb Allium tricoccum Ait. (wild leek) was examined to assess whether colonization varied seasonally and spatially within the forest. Whole plants were collected to coincide with observed phenological stages, and the perennial tissue (i.e., the bulb) was used to analyze total C, N, and P over the growing season. AM fungal community composition, structure, and abundance were assessed in roots by terminal restriction fragment length polymorphism analysis and quantitative PCR. It was found that A. tricoccum rDNA co-amplified using the general AM primers NS31/AM1, and a new primer for qPCR was designed that discriminated against plant DNA to quantify AM colonization. Community structure of AM fungi did not vary seasonally, but did change spatially within the forest, and AM fungal communities were correlated with the presence of overstory tree species. Fungal colonization of roots, however, did change seasonally with a maximum observed in late winter and early spring following leaf emergence. Maximum AM fungal colonization was associated with declines in bulb N and P, suggesting that leaf emergence and growth were responsible for both declines in stored nutrients and increases in AM fungal colonization. Plant N and P contents increased between late summer and early spring while C contents remained unchanged. The observed increase in nutrient content during a time when A. tricoccum lacks leaves indicates that the roots or AM fungi are metabolically active and acquire nutrients during this time, despite an absence of photosynthesis and thus a direct supply of C from A. tricoccum.

Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus

Soil ecologists have debated the relative importance of dispersal limitation and ecological factors in determining the structure of soil microbial communities. Recent evidence suggests that 'everything is not everywhere', and that microbial communities are influenced by both dispersal limitation and ecological factors. However, we still do not understand the relative explanatory power of spatial and ecological factors, including plant species identity and even plant relatedness, for different fractions of the soil microbial community (i.e. bacterial and fungal communities). To ask whether factors such as plant species, soil chemistry, spatial location and plant relatedness influence rhizosphere community composition, we examined field-collected rhizosphere soil of seven congener pairs that occur at Bodega Bay Marine Reserve, CA, USA. We characterized differences in bacterial and fungal communities using terminal-restriction fragment length polymorphism. Plant species identity was the single best statistical predictor of both bacterial and fungal community composition in the root zone. Soil microbial community structure was also correlated with soil chemistry. The third best predictor of bacterial and fungal communities was spatial location, confirming that everything is not everywhere. Variation in microbial community composition was also related to combinations of spatial location, soil chemistry and plant relatedness, suggesting that these factors do not act independently. Plant relatedness explained less of the variation than plant species, soil chemistry, or spatial location. Despite some congeners occupying different habitats and being spatially distant, rhizosphere fungal communities of plant congeners were more similar than expected by chance. Bacterial communities from the same samples were only weakly similar between plant congeners. Thus, plant relatedness might influence soil fungal, more than soil bacterial, community composition.

Forest liming increases forest floor carbon and nitrogen stocks in a mixed hardwood forest

In acid-impacted forests, decreased soil pH and calcium (Ca) availability have the potential to influence biotic and abiotic controls on carbon (C) and nitrogen (N) cycling. We investigated the effects of liming on above- and belowground C and N pools and fluxes 19 years after lime addition to the Woods Lake Watershed, Adirondack Park, New York, USA. Soil pH and exchangeable Ca remained elevated in the forest floor and upper mineral soil of limed areas. Forest floor C and N stocks were significantly larger in limed plots (68 vs. 31 Mg C/ha, and 3.0 vs. 1.5 Mg N/ha), resulting from a larger mass of Oa material. Liming reduced soil basal respiration rates by 17% and 43% in the Oe and Oa horizons, respectively. Net N mineralization was significantly lower in the limed soils for both forest floor horizons. Additional measurements of forest floor depth outside of our study plots, but within the treatment and control subcatchments also showed a deeper forest floor in limed areas; however, the mean depth of limed forest floor was 5 cm shallower than that observed in our study plots. Using a differential equation model of forest floor C dynamics, we found that liming effects on C fluxes measured within our study plots could explain the small observed increase in the Oe C stock but were not large enough to explain the increase in the Oa. Our catchment-wide assessment of forest floor depth, however, indicates that our plot analysis may be an overestimate of ecosystem-scale C and N stocks. Our results suggest that the mechanisms identified in our study, primarily liming-induced reduction in decomposition rates, may account for much of the observed increase in forest floor C. These findings emphasize the importance of understanding of the effects of liming in hardwood forests, and the long-term impacts of acid deposition on forest C and N uptake and retention.