Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits

Root-associated fungal community reflects host spatial co-occurrence patterns in a subtropical forest

Plant roots harbor and interact with diverse fungal species. By changing these belowground fungal communities, focal plants can affect the performance of surrounding individuals and the outcome of coexistence. Although highly host related, the roles of these root-associated fungal communities per se in host plant spatial co-occurrence is largely unknown. Here, we evaluated the host dependency of root-associated communities for 39-plant species spatially mapped throughout a 50-ha subtropical forest plot with relevant environmental properties. In addition, we explored whether the differentiation in root fungal associations among plant species can reflect their observed co-occurrence patterns. We demonstrated a strong host-dependency by discriminating the differentiation of root-associated fungal communities regardless of background soil heterogeneity. Furthermore, Random Forest modeling indicated that these nonrandom root fungal associations significantly increased our ability to explain spatial co-occurrence patterns, and to a greater degree than the relative abundance, phylogenetic relatedness, and functional traits of the host plants. Our results further suggested that plants harbor more abundant shared, "generalist" pathogens are likely segregated, while hosting more abundant unique, "specialist" ectomycorrhizal fungi might be an important strategy for promoting spatial aggregation, particularly between early established trees and the heterospecific adults. Together, we provide a conceptual and testable approach to integrate this host-dependent root fungal "fingerprinting" into the plant diversity patterns. We highlight that this approach is complementary to the classic cultivation-based scheme and can deepen our understanding of the community-level effect from overall fungi and its contribution to the pairwise plant dynamics in local species-rich communities.

Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes

Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.

Faster recovery of soil biodiversity in native species mixture than in Eucalyptus monoculture after 60 years afforestation in tropical degraded coastal terraces

Afforestation is an effective method to restore degraded land. Afforestation methods vary in their effects on ecosystem multifunctionality, but their effects on soil biodiversity have been largely overlooked. Here, we mapped the biodiversity and functioning of multiple soil organism groups resulting from diverse afforestation methods in tropical coastal terraces. Sixty years after afforestation from bare land (BL), plant species richness and the abundance of plant litter (398 ± 85 g m^-2 ) and plant biomass (179 ± 3.7 t ha^-1 ) in native tree species mixtures (MF) were restored to the level of native forests (NF; 287 ± 21 g m^-2 and 243.0 ± 33 t ha^-1 , respectively), while Eucalyptus monoculture (EP) only successfully restored the litter mass (388 ± 43 g m^-2 ) to the level of NF. Soil fertility in EP and MF was increased but remained lower than in NF. For example, soil nitrogen and phosphorus concentrations in MF (1.2 ± 0.2 g kg^-1 and 408 ± 49 mg kg^-1 , respectively; p < 0.05) were lower than in NF (1.8 ± 0.2 g kg^-1 and 523 ± 24 mg kg^-1 , respectively; p < 0.05). Soil biodiversity, abundance (except for nematodes), and community composition in MF were similar or greater than those in NF. In contrast, restoration with EP only enhanced the diversity of microbes and mites to the level of NF, but not for other soil biota. Together, afforestation with native species mixtures can end up restoring vegetation and most aspects of the taxonomic and functional biodiversity in soil whereas monoculture using fast-growing non-native species cannot. Native species mixtures show a greater potential to reach completely similar levels of soil biodiversity in local natural forests if they are received some more decades of afforestation. Multifunctionality of soil biotic community should be considered to accelerate such processes in future restoration practices.

Warming intensifies soil pathogen negative feedback on a temperate tree

The soil pathogen-induced Janzen-Connell (JC) effect is considered as a primary mechanism regulating plant biodiversity worldwide. As predicted by the framework of the classic plant disease triangle, severity of plant diseases is often influenced by temperature, yet insufficient understanding of how increasing temperatures affect the JC effect contributes uncertainty in predictions about how global warming affects biodiversity. We conducted a 3-yr field warming experiment, combining open-top chambers with pesticide treatment, to test the effect of elevated temperatures on seedling mortality of a temperate tree species, Prunus padus, from a genus with known susceptibility to soil-borne pathogens. Elevated temperature significantly increased the mortality of P. padus seedlings in the immediate vicinity of parent trees, concurrent with increased relative abundance of pathogenic fungi identified to be virulent to Prunus species. Our study offers experimental evidence suggesting that global warming significantly intensifies the JC effect on a temperate tree species due to increased relative abundance of pathogenic fungi. This work advances our understanding about changes in the JC effect linked to ongoing global warming, which has important implications for predicting tree diversity in a warmer future.

Do soil depth and plant community composition interact to modify the resistance and resilience of grassland ecosystem functioning to drought?

While the effect of drought on plant communities and their associated ecosystem functions is well studied, little research has considered how responses are modified by soil depth and depth heterogeneity. We conducted a mesocosm study comprising shallow and deep soils, and variable and uniform soil depths, and two levels of plant community composition, and exposed them to a simulated drought to test for interactive effects of these treatments on the resilience of carbon dioxide fluxes, plant functional traits, and soil chemical properties. We tested the hypotheses that: (a) shallow and variable depth soils lead to increased resistance and resilience of ecosystem functions to drought due to more exploitative plant trait strategies; (b) plant communities associated with intensively managed high fertility soils, will have more exploitative root traits than extensively managed, lower fertility plant communities. These traits will be associated with higher resistance and resilience to drought and may interact with soil depth and depth heterogeneity to amplify the effects on ecosystem functions. Our results showed that while there were strong soil depth/heterogeneity effects on plant-driven carbon fluxes, it did not affect resistance or resilience to drought, and there were no treatment effects on plant-available carbon or nitrogen. We did observe a significant increase in exploitative root traits in shallow and variable soils relative to deep and uniform, which may have resulted in a compensation effect which led to the similar drought responses. Plant community compositions representative of intensive management were more drought resilient than more diverse "extensive" communities irrespective of soil depth or soil depth heterogeneity. In intensively managed plant communities, root traits were more representative of exploitative strategies. Taken together, our results suggest that reorganization of root traits in response to soil depth could buffer drought effects on ecosystem functions.

Diatoms in Volcanic Soils of Mutnovsky and Gorely Volcanoes (Kamchatka Peninsula, Russia)

Volcanic activity has a great impact on terrestrial ecosystems, including soil algae in general and diatoms in particular. To understand the influence of volcanoes on the biodiversity of diatoms, it is necessary to explore the flora of these microorganisms in regions with high volcanic activity, which includes the Kamchatka peninsula. During the study on diatoms in the soils of Mutnovsky and Gorely volcanoes of Kamchatka, 38 taxa were found. The Mutnovsky volcano diatom flora was more diverse and accounted for 35 taxa. Eunotia curtagrunowii, Humidophila contenta, and Pinnularia borealis were the dominant species. In the Gorely volcano, only 9 species were identified, with Caloneis bacillum and Pinnularia borealis prevailing in the samples. Overall, the genera Pinnularia and Eunotia were the most diverse in the studied area. The diatom flora of the studied volcanoes comprises mostly cosmopolitan small-sized taxa with a wide range of ecological plasticity. Our data confirm the high adaptive potential of diatom algae and add new knowledge about the ecology and biogeography of this group of microorganisms.

Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

Latitudinal variation in the diversity and composition of various organisms associated with an exotic plant: the role of climate and plant invasion

Climate and plant invasion can shape biotic communities at large spatial scales. Yet, how diverse groups of organisms associated with an invasive plant change simultaneously with latitude and the roles of climate and plant invasion remains unclear. We conducted a field survey of plants (native vs exotic), soil fungi (pathogenic, saprotrophic, arbuscular mycorrhiza fungi (AMF) and ectomycorrhizal (EcM) fungi) and arthropods (herbivores, predators and detritivores) associated with the invasive plant Alternanthera philoxeroides at 49 sites spanning 14 latitudinal degrees in China. Results showed that diversity and composition of these functional groups changed differently with latitude, partially due to their specific responses to climate, invasion of A. philoxeroides and other biotic environments. Moreover, A. philoxeroides invasion and/or composition of other plants, rather than climate, predicted the diversity and richness of major functional groups and partly explained variance in composition of putative fungal pathogens. Our results suggest that climate and plant invasion could affect the diversity and composition of diverse groups of organisms simultaneously and their relative importance might vary among functional groups. Thus, it is necessary to explore latitudinal patterns and underlying drivers of diverse groups of organisms simultaneously to improve our ability to predict and mitigate threats posed by plant invasion and climate change.

Root Functional Trait and Soil Microbial Coordination: Implications for Soil Respiration in Riparian Agroecosystems

Predicting respiration from roots and soil microbes is important in agricultural landscapes where net flux of carbon from the soil to the atmosphere is of large concern. Yet, in riparian agroecosystems that buffer aquatic environments from agricultural fields, little is known on the differential contribution of CO₂ sources nor the systematic patterns in root and microbial communities that relate to these emissions. We deployed a field-based root exclusion experiment to measure heterotrophic and autotrophic-rhizospheric respiration across riparian buffer types in an agricultural landscape in southern Ontario, Canada. We paired bi-weekly measurements of in-field CO₂ flux with analysis of soil properties and fine root functional traits. We quantified soil microbial community structure using qPCR to estimate bacterial and fungal abundance and characterized microbial diversity using high-throughput sequencing. Mean daytime total soil respiration rates in the growing season were 186.1 ± 26.7, 188.7 ± 23.0, 278.6 ± 30.0, and 503.4 ± 31.3 mg CO₂-C m^-2 h^-1 in remnant coniferous and mixed forest, and rehabilitated forest and grass buffers, respectively. Contributions of autotrophic-rhizospheric respiration to total soil CO₂ fluxes ranged widely between 14 and 63% across the buffers. Covariation in root traits aligned roots of higher specific root length and nitrogen content with higher specific root respiration rates, while microbial abundance in rhizosphere soil coorindated with roots that were thicker in diameter and higher in carbon to nitrogen ratio. Variation in autotrophic-rhizospheric respiration on a soil area basis was explained by soil temperature, fine root length density, and covariation in root traits. Heterotrophic respiration was strongly explained by soil moisture, temperature, and soil carbon, while multiple factor analysis revealed a positive correlation with soil microbial diversity. This is a first in-field study to quantify root and soil respiration in relation to trade-offs in root trait expression and to determine interactions between root traits and soil microbial community structure to predict soil respiration.

Diversity of rhizobia and non-rhizobia endophytes isolated from root nodules of Trifolium sp. growing in lead and zinc mine site Guelma, Algeria

High concentrations of heavy metals in mine soil disturb the interactions between legumes and microorganisms leading to select strains adapted to these specific conditions. In this work, we analyzed the diversity of fifty strains isolated from Trifolium sp. nodules growing on Pb-Zn mine soil, in the Northeastern of Algeria and highlighted their potential symbiotic traits. The phylogeny of the 16S rRNA gene sequences revealed a high bacterial diversity with a predominance of non-rhizobial endophytes. The identified isolates belong to the thirteen following genera Cupriavidus, Pseudomonas, Bacillus, Acinetobacter, Enterobacter, Roseomonas, Paracoccus, Frondihabitans, Microbacterium, Kocuria, Providencia, Micrococcus and Staphylococcus. Regarding rhizobial strains, only isolates affiliated to Rhizobium genus were obtained. The symbiotic gene nodC and the nitrogen fixation gene nifH present showed that Rhizobium isolates belonged to the symbiovar trifolii. In addition to bacterial, one yeast strain was isolated and identified as Rhodotorula mucilaginosa by sequencing the internal transcribed spacer (ITS) region.

Driving factors influencing the rhizobacteriome community structure of plants adapted to multiple climatic stressors in edaphic savannas

The natural variation of multiple abiotic stresses in hyper-seasonal edaphic savanna provides a unique opportunity to study the rhizobacteriome community structure of plants adapted to climate change-like conditions in the humid tropics. In this study, we evaluated changes in soil, plant and rhizobacteriome community structure parameters across seasons (wet and dry) in two edaphic savannas (SV-1 and SV-5) using four dominant plant species. We then examined relationships between rhizobacteriome community structure and soil properties, plant biomass, and conventional and novel root traits. We further hypothesized that plants adapted to the Aripo Savanna had a core rhizobacteriome, which was specific to plant species and related to root foraging traits. Our results showed that cation exchange capacity (CEC) and the concentration of micronutrients (Fe, Cu and B) were the only soil factors that differed across savanna and season, respectively. Plant biomass traits were generally higher in the dry season, with a higher allocation to root growth in SV-5. Root traits were more plastic in SV-5, and network length-distribution was the only root trait which showed a consistent pattern of lower values in the dry season for three of the dominant plant species. Rhizobacterial community compositions were dominated by Proteobacteria and Acidobacteria, as well as WPS-2, which is dominant in extreme environments. We identified a shared core rhizobacteriome across plant species and savannas. Cation exchange capacity was a major driver of rhizobacterial community assemblies across savannas. Savanna-specific drivers of rhizobacterial community assemblies included CEC and Fe for SV-1, and CEC, TDS, NH₄⁺, NO₃^-, Mn, K, and network length-distribution for SV-5. Plant factors on the microbiome were minimal, and host selectivity was mediated by the seasonal changes. We conclude that edaphoclimatic factors (soil and season) are the key determinants influencing rhizobacteriome community structure in multiple stressed-environments, which are ecologically similar to the Aripo Savanna.

Increased plant species richness associates with greater soil bacterial diversity in urban green spaces

The vegetation and soil microbiome within urban green spaces is increasingly managed to help conserve biodiversity and improve human health concurrently. However, the effects of green space management on urban soil ecosystems is poorly understood, despite their importance. Across 40 urban green spaces in metropolitan Adelaide, South Australia, we show that soil bacterial communities are strongly affected by urban green space type (incl. sport fields, community gardens, parklands and revegetated areas), and that plant species richness is positively associated with soil bacterial diversity. Importantly, these microbiome trends were not affected by geographic proximity of sample sites. Our results provide early evidence that urban green space management can have predictable effects on the soil microbiome, at least from a diversity perspective, which could prove important to inform policy development if urban green spaces are to be managed to optimise population health benefits.

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants

Soil legacies play an important role for the creation of priority effects. However, we still poorly understand to what extent the metabolome found in the soil solution of a plant community is conditioned by its species composition and whether soil chemical legacies affect subsequent species during assembly. To test these hypotheses, we collected soil solutions from forb or grass communities and evaluated how the metabolome of these soil solutions affected the growth, biomass allocation and functional traits of a forb (Dianthus deltoides) and a grass species (Festuca rubra). Results showed that the metabolomes found in the soil solutions of forb and grass communities differed in composition and chemical diversity. While soil chemical legacies did not have any effect on F. rubra, root foraging by D. deltoides decreased when plants received the soil solution from a grass or a forb community. Structural equation modelling showed that reduced soil exploration by D. deltoides arose via either a root growth-dependent pathway (forb metabolome) or a root trait-dependent pathway (grass metabolome). Reduced root foraging was not connected to a decrease in total N uptake. Our findings reveal that soil chemical legacies can create belowground priority effects by affecting root foraging in later arriving plants.

Differential response of abundant and rare bacterial subcommunities to abiotic and biotic gradients across temperate deserts

The biogeography of soil bacterial communities has been well documented, yet the associated difference in spatial distribution and drivers between abundant and rare bacteria still remains unclear. Here, we compared the species richness, composition, and their drivers of rare and abundant bacteria along a 2500-km regional transect in Chinese deserts. Our results demonstrated that abundant and rare bacterial diversities were determined by plant community together with climatic, soil and spatial factors, but the shifts in bacterial richness and composition caused by abiotic and biotic variations varied between abundant and rare subcommunities. Rare bacterial richness significantly decreased with increasing temperature, drought and nutrient limitation, while abundant bacterial richness showed an increasing trend. Plant richness was negatively associated with abundant bacterial richness, but positively related to rare bacterial richness. Abiotic and biotic differences caused greater variations in rare species composition than that in abundant species composition. Furthermore, our results also confirmed that the spatial patterns of abundant and rare bacterial distribution differed remarkably. Our findings collectively suggest that similar abiotic and biotic drivers but distinct influences lead to distinct spatial distribution patterns of abundant and rare bacteria in harsh deserts. Therefore, taking more ecological traits such as stress tolerance and abundance into account will strengthen our understanding of soil bacterial assembly mechanisms.

Spatial factors and plant attributes influence soil fungal community distribution patterns in the lower reaches of the Heihe River Basin, Northwest China

Inland river basins include critical habitats and provide various ecosystem services in extremely arid lands. However, we know little about the distribution patterns of soil fungal communities in these river basins. We investigated the distribution patterns of soil fungal communities from the riparian oasis zone (ROZ) to the circumjacent desert zone (CDZ) at the lower reaches of the Heihe River. The results indicated that soil fungal communities were mainly dominated by the phyla Ascomycota and Basidiomycota across all samples. The dominant soil fungi taxa were significantly different between ROZ and CDZ habitats at both the phylum and genus levels. Fungal alpha diversity was mainly affected by spatial factors and plant functional traits, and Pearson correlation analysis revealed that fungal alpha diversity was more closely related to plant functional traits than soil properties. Furthermore, fungal community structure was best explained by spatial factors and plant attributes (including plant diversity and plant functional traits). Together, our findings provide new insights into the significance of spatial factors and plant attributes for predicting distributions of fungal communities in arid inland river basins, which will help us better understand the functions and services of these ecosystems.

Soil Bacterial Communities and Diversity in Alpine Grasslands on the Tibetan Plateau Based on 16S rRNA Gene Sequencing

The Tibetan Plateau, widely known as the world’s “Third Pole,” has gained extensive attention due to its susceptibility to climate change. Alpine grasslands are the dominant ecosystem on the Tibetan Plateau, albeit little is known about the microbial community and diversity among different alpine grassland types. Here, soil bacterial composition and diversity in the upper soils of five alpine grassland ecosystems, alpine meadow (AM), alpine steppe (AS), alpine meadow steppe (AMS), alpine desert (AD), and alpine desert steppe (ADS), were investigated based on the 16S rRNA gene sequencing technology. Actinobacteria (46.12%) and Proteobacteria (29.67%) were the two dominant soil bacteria at the phylum level in alpine grasslands. There were significant differences in the relative abundance at the genus level among the five different grassland types, especially for the Rubrobacter, Solirubrobacter, Pseudonocardia, Gaiella, Haliangium, and Geodermatophilus. Six alpha diversity indices were calculated based on the operational taxonomic units (OTUs), including Good’s coverage index, phylogenetic diversity (PD) whole tree index, Chao1 index, observed species index, Shannon index, and Simpson index. The Good’s coverage index value was around 0.97 for all the grassland types in the study area, meaning the soil bacteria samplings sequenced sufficiently. No statistically significant difference was shown in other diversity indices’ value, indicating the similar richness and evenness of soil bacteria in these alpine grasslands. The beta diversity, represented by Bray–Curtis dissimilarity and the non-metric multidimensional scaling (NMDS), showed that OTUs were clustered within alpine grasslands, indicating a clear separation of soil bacterial communities. In addition, soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), pH, and soil water content (SWC) were closely related to the variations in soil bacterial compositions. These results indicated that soil bacterial taxonomic compositions were similar, while soil bacterial community structures were different among the five alpine grassland types. The environmental conditions, including SOM, TN, TP, pH, and SWC, might influence the soil bacterial communities on the Tibetan Plateau.

Root traits explain rhizosphere fungal community composition among temperate grassland plant species

While it is known that interactions between plants and soil fungi drive many essential ecosystem functions, considerable uncertainty exists over the drivers of fungal community composition in the rhizosphere. Here, we examined the roles of plant species identity, phylogeny and functional traits in shaping rhizosphere fungal communities and tested the robustness of these relationships to environmental change. We conducted a glasshouse experiment consisting of 21 temperate grassland species grown under three different environmental treatments and characterised the fungal communities within the rhizosphere of these plants. We found that plant species identity, plant phylogenetic relatedness and plant traits all affected rhizosphere fungal community composition. Trait relationships with fungal communities were primarily driven by interactions with arbuscular mycorrhizal fungi, and root traits were stronger predictors of fungal communities than leaf traits. These patterns were independent of the environmental treatments the plants were grown under. Our results showcase the key role of plant root traits, especially root diameter, root nitrogen and specific root length, in driving rhizosphere fungal community composition, demonstrating the potential for root traits to be used within predictive frameworks of plant-fungal relationships. Furthermore, we highlight how key limitations in our understanding of fungal function may obscure previously unmeasured plant-fungal interactions.

Plant-microbiome interactions for sustainable agriculture: a review

Plant-microbiome interactions are significant determinant for plant growth, fitness and productivity. Depending upon the specific habitat, plants' microbial communities are classified as the rhizo-, phyllo-, and endospheric regions. Understanding the plant microbiome interactions could provide an opportunity to develop strategies for sustainable agricultural practices. There is a necessity to decipher the complex structural and functional diversity within plant microbiomes to reveal its immense potential in agriculture. The plant microbiota harbors enormous microbial communities that defy analytical methodologies to study dynamics underlying plant microbiome interactions. Findings based on conventional approaches have ignored many beneficial microbial strains, which creates a serious gap in understanding the microbial communications along with the genetic adaptations, which favors their association with host plant. The new era of next generation sequencing techniques and modern cost-effective high-throughput molecular approaches can decipher microbial community composition and function. In this review, we have presented the overview of the various compartments of plants, approaches to allow the access to microbiome and factors that influence microbial community composition and function. Next, we summarize how plant microbiome interactions modulate host beneficial properties particularly nutrient acquisition and defense, along with future agricultural applications.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at. 10.1007/s12298-021-00927-1.

Mucilage Polysaccharide Composition and Exudation in Maize From Contrasting Climatic Regions

Mucilage, a gelatinous substance comprising mostly polysaccharides, is exuded by maize nodal and underground root tips. Although mucilage provides several benefits for rhizosphere functions, studies on the variation in mucilage amounts and its polysaccharide composition between genotypes are still lacking. In this study, eight maize (Zea mays L.) genotypes from different globally distributed agroecological zones were grown under identical abiotic conditions in a randomized field experiment. Mucilage exudation amount, neutral sugars and uronic acids were quantified. Galactose (∼39-42%), fucose (∼22-30%), mannose (∼11-14%), and arabinose (∼8-11%) were the major neutral sugars in nodal root mucilage. Xylose (∼1-4%), and glucose (∼1-4%) occurred only in minor proportions. Glucuronic acid (∼3-5%) was the only uronic acid detected. The polysaccharide composition differed significantly between maize genotypes. Mucilage exudation was 135 and 125% higher in the Indian (900 M Gold) and Kenyan (DH 02) genotypes than in the central European genotypes, respectively. Mucilage exudation was positively associated with the vapor pressure deficit of the genotypes' agroecological zone. The results indicate that selection for environments with high vapor pressure deficit may favor higher mucilage exudation, possibly because mucilage can delay the onset of hydraulic failure during periods of high vapor pressure deficit. Genotypes from semi-arid climates might offer sources of genetic material for beneficial mucilage traits.

The role of root community attributes in predicting soil fungal and bacterial community patterns

Roots are assumed to play a major role in structuring soil microbial communities, but most studies exploring the relationships between microbes and plants at the community level have only used aboveground plant distribution as a proxy. However, a decoupling between belowground and aboveground plant components may occur due to differential spreading of plant canopies and root systems. Thus, soil microbe-plant links are not completely understood. Using a combination of DNA metabarcoding and spatially explicit sampling at the plant neighbourhood scale, we assessed the influence of the plant root community on soil bacterial and fungal diversity (species richness, composition and β-diversity) in a dry Mediterranean scrubland. We found that root composition and biomass, but not richness, predict unique fractions of variation in microbial richness and composition. Moreover, bacterial β-diversity was related to root β-diversity, while fungal β-diversity was related to aboveground plant β-diversity, suggesting that plants differently influence both microbial groups. Our study highlights the role of plant distribution both belowground and aboveground, soil properties and other spatially structured factors in explaining the heterogeneity in soil microbial diversity. These results also show that incorporating data on both plant community compartments will further our understanding of the relationships between soil microbial and plant communities.

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.

Evidence for Elton's diversity-invasibility hypothesis from belowground

Sixty year ago, Charles Elton posed that species-rich communities should be more resistant to biological invasion. Still, little is known about which processes could drive the diversity-invasibility relationship. Here we examined whether soil-microbe-mediated apparent competition on alien invaders is more negative when the soil originates from multiple native species. We trained soils with five individually grown native species and used amplicon sequencing to analyze the resulting bacterial and fungal soil communities. We mixed the soils to create trained soils from one, two or four native species. We then grew four alien species separately on these differently trained soils. In the soil-conditioning phase, the five native species built species-specific bacterial and fungal communities in their rhizospheres. In the test phase, it did not matter for biomass of alien plants whether the soil had been trained by one or two native species. However, the alien species achieved 11.7% (95% CI: 3.7-20.1%) less aboveground biomass when grown on soils trained by four native species than on soils trained by two native species. Our results revealed soil-microbes-mediated apparent competition as a mechanism underlying the negative relationship between diversity and invasibility.

Towards Unraveling Macroecological Patterns in Rhizosphere Microbiomes

It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further involves a hierarchy of constraints with varying strengths across spatial and temporal scales. However, our knowledge of rhizosphere microbiomes is largely based on single-location and time-point studies. Consequently, it remains difficult to predict patterns at large landscape scales, and we lack a clear understanding of how the rhizosphere microbiome forms and is maintained by drivers beyond the influence of the plant. By synthesizing recent literature and collating data on rhizosphere microbiomes, we point out the opportunities and challenges offered by advances in molecular biology, bioinformatics, and data availability. Specifically, we highlight the use of exact sequence variants, coupled with existing and newly generated data to decipher the rules of rhizosphere community assembly across large spatial and taxonomic scales.

Environmental adaptation of the root microbiome in two rice ecotypes

The root microbiome plays a key role that can influence host plant growth and abiotic stress. While there has been extensive characterization of community structure, spatial compartmentalization, and the impact of drought stresses on the root microbiome in rice and other plants, there is relatively little known about the differences in root microbiome among rice ecotypes in natural upland and lowland fields. Herein, we used two rice ecotypes, upland and irrigated ecotype rice (two Indica and two Japonica genotypes), as a model to explore the responses of the root microbiome under different environmental conditions. We aimed to identify environment-induced adaptation in the root bacterial and fungal composition of rice ecotypes by high-throughput sequencing. Rice from lowland field or upland had significantly altered overall bacterial and fungal community compositions of the two ecotypes, with diversity of both ecotypes greatly decreased from lowland field to upland. The overall response of the root microbiome to upland conditions was taxonomically driven by the enrichment of family Enterobacteriaceae and genera Serratia, and phylum Ascomycota. Interestingly, rice ecotypes specifically enriched root microbes when they were transferred from their original environment, such as the enrichment of class Thermoleophilia and phylum Actinobacteria when the irrigated ecotype rice was moved from lowland to upland field. These results revealed that different environmental conditions and rice ecotypes resulted in a restructuring of root microbiome communities, and suggested the possibility that components responsible for the beneficial attributes in the altered root microbiome might contribute to the adaptation of different ecotypes in natural fields.

Plant species identity drives soil microbial community structures that persist under a following crop

Compared to monocultures, multi-species swards have demonstrated numerous positive diversity effects on aboveground plant performance, such as yield, N concentration, and even legacy effects on a following crop. Whether such diversity effects are seen in the soil microbiome is currently unclear. In a field experiment, we analyzed the effect that three plant species (a grass, forb, and legume), and mixtures of these, had on soil fungal and bacterial community structures, as well as their associated legacy effects under a following crop, the grass Lolium multiflorum. We utilized six sward types, three monocultures (Lolium perenne, Cichorium intybus and Trifolium pratense), two bi-species mixtures, and a mixture of the three species. Soil samples were taken from these swards in March (at the end of a three year conditioning phase) and in June, August, and September after L. multiflorum was established, that is, the legacy samplings. When present, the differing monocultures had a significant effect on various aspects of the fungal community: structure, OTU richness, the relative abundance of the phylum Glomeromycota, and indicator OTUs. The effect on bacterial community structure was not as strong. In the multi-species swards, a blending of individual plant species monoculture effects (identity effect) was seen in (a) fungal and bacterial community structure and (b) fungal OTU richness and the relative abundance of the Glomeromycota. This would indicate that plant species identity, rather than diversity effects (i.e., the interactions among the plant species), was the stronger determinant. During the legacy samplings, structural patterns in the fungal and bacterial communities associated with the previous swards were retained, but the effect faded with time. These results highlight that plant species identity can be a strong driver of soil microbial community structures. They also suggest that their legacy effect on the soil microbiome may play a crucial role in following crop performance.

One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland

Species coexistence in grasslands is regulated by several environmental factors and interactions with the soil microbial community. Here, the development of the Basidiomycetes fungus Agaricus arvensis, forming fairy rings, in a species-rich Mediterranean grassland, is described. Effects of the mycelial front on plants, fungi and bacteria were assessed by vegetation survey and next generation sequencing approaches. Our results showed a fungal-dependent shift in the community structure operated by a wave-like spread of fairy rings that decreased plant, fungal and bacterial diversity, indicating a detrimental effect of fairy rings on most species. The fairy rings induced successional processes in plants that enhanced the replacement of a community dominated by perennial plants with short-living and fast-growing plant species. In parallel, fungal and bacterial communities showed evident differences in species composition with several taxa associated within distinct sampling zone across the fairy rings. Notably, bacteria belonging to the Burkholderia genus and fungi of the genus Trichoderma increased in response to the advancing mycelium of A. arvensis. The profound changes in community composition and the overall increase in taxa diversity at ecosystemic scale suggest that fairy ring-forming fungi may act as ecosystem engineer species in Mediterranean grasslands.

It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome

The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.

Living Litter: Dynamic Trait Spectra Predict Fauna Composition

Understanding what drives soil fauna species composition through space and time is crucial because we should preserve soil fauna biodiversity and its key role in ecosystem functioning in this era of fast environmental change. As plant leaf litter provides both food and habitat for soil fauna, a focus on litter traits that relate to these two functions will help in understanding soil invertebrate community structure and dynamics comprehensively. To advance this agenda, we propose a conceptual framework to explicitly link the invertebrate community composition to the temporal dynamics of the litter trait space defined by two axes: a food-quality axis related to plant resource economics and chemistry and a habitat-quality axis related to litter particle size and shape.

Microbial diversity-ecosystem function relationships across environmental gradients

In light of increasing anthropogenic pressures on ecosystems around the globe, the question how biodiversity change of organisms in the critical zone between Earth’s canopies and bedrock relates to ecosystem functions is an urgent issue, as human life relies on these functions. Particularly, soils play vital roles in nutrient cycling, promotion of plant growth, water purification, litter decomposition, and carbon storage, thereby securing food and water resources and stabilizing the climate. Soil functions are carried to a large part by complex communities of microorganisms, such as bacteria, archaea, fungi and protists. The assessment of microbial diversity and the microbiome's functional potential continues to pose significant challenges. Next generation sequencing offers some of the most promising tools to help shedding light on microbial diversity-function relationships. Studies relating microbial diversity and ecosystem functions are rare, particularly those on how this relationship is influenced by environmental gradients. The proposed project focuses on decomposition as one of the most important microbial soil ecosystem functions. The researchers from the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig combine an unparalleled range of expertise from next generation sequencing- based analysis of microbial communities (“meta-omics”) to soil ecology and biodiversity-ecosystem function research. This consortium will make use of soil samples from large international networks to assess microbial diversity both at the taxonomic and functional level and across the domains of life. By linking microbial diversity to functional measurements of decomposition and environmental gradients, the proposed project aims to achieve a comprehensive scale-independent understanding of environmental drivers and anthropogenic effects on the structural and functional diversity of microbial communities and subsequent consequences for ecosystem functioning.

Microbial taxonomic and functional attributes consistently predict soil CO2 emissions across contrasting croplands

Despite distinct roles of soil microbes in regulating carbon (C) respiration in diverse environments, it remains unclear whether microbial taxonomic and functional attributes can consistently predict soil C emissions across contrasting ecosystems. Here, we conducted a large-scale sampling event across two contrasting croplands (rice and wheat-corn crop rotation) to identify specific soil microbial phylotypes and functional genes associated with soil respiration rates. The results of structural equation modeling indicated that bacterial community composition had a strong link with C respiration rates in the two contrasting cropland types; however, this link was weaker for fungal communities. More importantly, we found that the relative abundances of bacterial Solirubrobacterales_480-2, Myxococcales_mle1-27 and fungal Westerdykella had consistently negative correlation with respiration rates across paddy and upland soils. We also identified taxa that are significantly correlated to C respiration in the paddy (e.g. Methylocaldum) and upland soils (e.g. Kribbella), respectively. Further, we found multiple associations between functional genes involved in microbial C metabolism and soil respiration rates. Our findings provide novel insights into understanding microbial predictors of soil CO₂ emissions in diverse croplands, which have important implications for improving C emission predictions in terrestrial ecosystems.

Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems

Plants are known to modulate their own rhizosphere mycobiome. However, field studies that use resident plants to relate the microbiome assemblage to environmental factors such as land-use suffer from the problem that confounding factors such as plant age and performance may override the targeted effects. In contrast, the use of even-aged phytometer plants pre-cultivated under uniform conditions helps to reduce such random variation. We investigated the rhizosphere mycobiomes of phytometer and resident plants of two common grassland species, Dactylis glomerata L. s. str. and Plantago lanceolata L. along a land-use intensity gradient using ITS rRNA Illumina amplicon sequencing. Remarkably, we did not detect effects of the plant types (resident vs. phytometer plant, even though some fungal taxa exhibited plant species specificity), indicating that phytometer plants hosted a comparable rhizosphere mycobiome as resident plants. Our data indicate that the plant species harbor distinct fungal communities, with fungal richness in the rhizosphere of P. lanceolata being substantially higher than that of D. glomerata. Land-use intensity had a clear impact on the mycobiome of both plant species, with specific fungal genera showing differential tolerance to high intensities. Overall, the phytometer approach has a high potential to reveal environmental impacts on rhizosphere communities.

Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen

Interactions between plants and soil microbes are important for plant growth and resistance. Through plant–soil‐feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant–soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant‐induced changes in soil microbiomes on the growth of the commercially important cut‐flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next‐generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species‐specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.

Microbial Communities in Bioswale Soils and Their Relationships to Soil Properties, Plant Species, and Plant Physiology

Bioswales and other forms of green infrastructure can be effective means to reduce environmental stresses in urban ecosystems; however, few studies have evaluated the ecology of these systems, or the role that plant selection and microbial assembly play in their function. For the current study, we examined the relationship between plant transpiration rates for five commonly planted herbaceous species in three bioswales in New York City, as well as bioswale soil microbial composition and soil chemistry. Soils were sampled near individual plants, with distinction made between upper (bioswale inlet) and lower slopes (bioswale outlet). We found high variation in transpiration rates across species, and that Nepeta × faassenii was the highest conductor (13.65 mmol H2O m-2s-1), while Panicum virgatum was the lowest conductor (2.67 mmol H2O m-2s-1) (p < 0.001). There was significant variation in percent N of leaves and soil, which did not relate to the higher water conductance in bioswales. Significantly higher C, N, and water content on the high end of bioswale slopes suggest storm water run-off is mostly absorbed on the inlet side. Bacterial and fungal communities were significantly clustered by bioswale and by plant species within each bioswale implying there are micro-environmental controls on the soil microbial composition, and that plant composition matters for microbial assemblages within bioswales. Plants with higher transpiration rates were associated with greater fungal and bacterial diversity at the level of the bioswale and at scale of the individual plant, suggesting a possible link between plant physiological traits and soil microbial communities. These data suggest that the specific plant palette selected for planting bioswales can have deterministic effects on the surrounding microbial communities which may further influence functions such as transpiration and nutrient cycling. These results may have implications for bioswale management to improve urban water quality and reduce stress on sewage systems after storm events by revising plant species palette selection based on the functional consequences of plant-microbial associations in engineered green infrastructure.

Mixed-Cropping Between Field Pea Varieties Alters Root Bacterial and Fungal Communities

Modern agricultural practices have vastly increased crop production but negatively affected soil health. As such, there is a call to develop sustainable, ecologically-viable approaches to food production. Mixed-cropping of plant varieties can increase yields, although impacts on plant-associated microbial communities are unclear, despite their critical role in plant health and broader ecosystem function. We investigated how mixed-cropping between two field pea (Pisum sativum L.) varieties (Winfreda and Ambassador) influenced root-associated microbial communities and yield. The two varieties supported significantly different fungal and bacterial communities when grown as mono-crops. Mixed-cropping caused changes in microbial communities but with differences between varieties. Root bacterial communities of Winfreda remained stable in response to mixed-cropping, whereas those of Ambassador became more similar to Winfreda. Conversely, root fungal communities of Ambassador remained stable under mixed-cropping, and those of Winfreda shifted towards the composition of Ambassador. Microbial co-occurrence networks of both varieties were stronger and larger under mixed-cropping, which may improve stability and resilience in agricultural soils. Both varieties produced slightly higher yields under mixed-cropping, although overall Ambassador plants produced higher yields than Winfreda plants. Our results suggest that variety diversification may increase yield and promote microbial interactions.

Exploring the accuracy of amplicon-based internal transcribed spacer markers for a fungal community

With the continual improvement in high-throughput sequencing technology and constant updates to fungal reference databases, the use of amplicon-based DNA markers as a tool to reveal fungal diversity and composition in various ecosystems has become feasible. However, both primer selection and the experimental procedure require meticulous verification. Here, we computationally and experimentally evaluated the accuracy and specificity of three widely used or newly designed internal transcribed spacer (ITS) primer sets (ITS1F/ITS2, gITS7/ITS4 and 5.8S-Fun/ITS4-Fun). In silico evaluation revealed that primer coverage varied at different taxonomic levels due to differences in degeneracy and the location of primer sets. Using even and staggered mock community standards, we identified different proportions of chimeric and mismatch reads generated by different primer sets, as well as great variation in species abundances, suggesting that primer selection would affect the results of amplicon-based metabarcoding studies. Choosing proofreading and high-fidelity polymerase (KAPA HiFi) could significantly reduce the percentage of chimeric and mismatch sequences, further reducing inflation of operational taxonomic units. Moreover, for two types of environmental fungal communities, plant endophytic and soil fungi, it was demonstrated that the three primer sets could not reach a consensus on fungal community composition or diversity, and that primer selection, not experimental treatment, determines observed soil fungal community diversity and composition. Future DNA marker surveys should pay greater attention to potential primer effects and improve the experimental scheme to increase credibility and accuracy.

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.

Soil microbes drive phylogenetic diversity-productivity relationships in a subtropical forest

The relationship between plant diversity and productivity and the mechanisms underpinning that relationship remain poorly resolved in species-rich forests. We combined extensive field observations and experimental manipulations in a subtropical forest to test how species richness (SR) and phylogenetic diversity (PD) interact with putative root-associated pathogens and how these interactions mediate diversity-productivity relationships. We show that (i) both SR and PD were positively correlated with biomass for both adult trees and seedlings across multiple spatial scales, but productivity was best predicted by PD; (ii) significant positive relationships between PD and productivity were observed in nonsterile soil only; and (iii) root fungal diversity was positively correlated with plant PD and SR, while the relative abundance of putative pathogens was negatively related to plant PD. Our findings highlight the key role of soil pathogenic fungi in tree diversity-productivity relationships and suggest that increasing PD may counteract negative effects of plant-soil feedback.

Non-symbiotic soil microbes are more strongly influenced by altered tree biodiversity than arbuscular mycorrhizal fungi during initial forest establishment

While the relationship between plant and microbial diversity has been well studied in grasslands, less is known about similar relationships in forests, especially for obligately symbiotic arbuscular mycorrhizal (AM) fungi. To assess the effect of varying tree diversity on microbial alpha- and beta-diversity, we sampled soil from plots in a high-density tree diversity experiment in Minnesota, USA, 3 years after establishment. About 3 of 12 tree species are AM hosts; the other 9 primarily associate with ectomycorrhizal fungi. We used phospho- and neutral lipid fatty acid analysis to characterize the biomass and functional identity of the whole soil bacterial and fungal community and high throughput sequencing to identify the species-level richness and composition of the AM fungal community. We found that plots of differing tree composition had different bacterial and fungal communities; plots with conifers, and especially Juniperus virginiana, had lower densities of several bacterial groups. In contrast, plots with a higher density or diversity of AM hosts showed no sign of greater AM fungal abundance or diversity. Our results indicate that early responses to plant diversity vary considerably across microbial groups, with AM fungal communities potentially requiring longer timescales to respond to changes in host tree diversity.

Drought soil legacy overrides maternal effects on plant growth

Maternal effects (i.e. trans-generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects of these factors on plant growth dynamics remain poorly understood.We used soil and seeds from an existing plant diversity and drought manipulation field experiment in temperate grassland to test maternal, soil drought and diversity legacy effects, and their interactions, on offspring plant performance of two grassland species (Alopecurus pratensis and Holcus lanatus) under contrasting glasshouse conditions.Our results showed that drought soil legacy effects eclipsed maternal effects on plant biomass. Drought soil legacy effects were attributed to changes in both abiotic (i.e. nutrient availability) and biotic soil properties (i.e. microbial carbon and enzyme activity), as well as plant root and shoot atom 15N excess. Further, plant tissue nutrient concentrations and soil microbial C:N responses to drought legacies varied between the two plant species and soils from high and low plant diversity treatments. However, these diversity effects did not affect plant root or shoot biomass.These findings demonstrate that while maternal effects resulting from drought occur in grasslands, their impacts on plant performance are likely minor relative to drought legacy effects on soil abiotic and biotic properties. This suggests that soil drought legacy effects could become increasingly important drivers of plant community dynamics and ecosystem functioning as extreme weather events become more frequent and intense with climate change. A plain language summary is available for this article.

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples

BACKGROUND

Biological invasions are major drivers of environmental change that can significantly alter ecosystem function and diversity. In plants, soil microbes play an important role in plant establishment and growth; however, relatively little is known about the role they might play in biological invasions. A first step to assess whether root microbes may be playing a role in the invasion process is to find out if invasive plants host different microbes than neighbouring native plant species.

METHODS

In this study we investigated differences in root associated microbes of native sugar maple (Acer saccharum Marsh.) and exotic Norway maple (A. platanoides L.) collected from a forested reserve in eastern Canada. We used microscopy to examine root fungi and high-throughput sequencing to characterize the bacterial, fungal and arbuscular mycorrhizal communities of both maple species over one growing season.

RESULTS

We found differences in root associated bacterial and fungal communities between host species. Norway maple had a higher bacterial and fungal OTU (operational taxonomic units) richness compared to sugar maple, and the indicator species analysis revealed that nine fungal OTUs and three bacterial OTUs had a significant preference for sugar maple. The dominant bacterial phyla found on the roots of both maple species were Actinobacteria and Proteobacteria. The most common fungal orders associated with the Norway maple roots (in descending order) were Helotiales, Agaricales, Pleosporales, Hypocreales, Trechisporales while the Agaricales, Pleosporales, Helotiales, Capnodiales and Hypocreales were the dominant orders present in the sugar maple roots. Dark septate fungi colonization levels were higher in the sugar maple, but no differences in arbuscular mycorrhizal fungal communities and colonization rates were detected between maple species.

DISCUSSION

Our findings show that two congeneric plant species grown in close proximity can harbor distinct root microbial communities. These findings provide further support for the importance of plant species in structuring root associated microbe communities. The high colonization levels observed in Norway maple demonstrates its compatibility with arbuscular mycorrhizal fungi in the introduced range. Plant-associated microbial communities can affect host fitness and function in many ways; therefore, the observed differences suggest a possibility that biotic interactions can influence the dynamics between native and invasive species.

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association (R2 = 0.366; P < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.

Relationships between plant traits, soil properties and carbon fluxes differ between monocultures and mixed communities in temperate grassland

The use of plant traits to predict ecosystem functions has been gaining growing attention. Above-ground plant traits, such as leaf nitrogen (N) content and specific leaf area (SLA), have been shown to strongly relate to ecosystem productivity, respiration and nutrient cycling. Furthermore, increasing plant functional trait diversity has been suggested as a possible mechanism to increase ecosystem carbon (C) storage. However, it is uncertain whether below-ground plant traits can be predicted by above-ground traits, and if both above- and below-ground traits can be used to predict soil properties and ecosystem-level functions.Here, we used two adjacent field experiments in temperate grassland to investigate if above- and below-ground plant traits are related, and whether relationships between plant traits, soil properties and ecosystem C fluxes (i.e. ecosystem respiration and net ecosystem exchange) measured in potted monocultures could be detected in mixed field communities.We found that certain shoot traits (e.g. shoot N and C, and leaf dry matter content) were related to root traits (e.g. root N, root C:N and root dry matter content) in monocultures, but such relationships were either weak or not detected in mixed communities. Some relationships between plant traits (i.e. shoot N, root N and/or shoot C:N) and soil properties (i.e. inorganic N availability and microbial community structure) were similar in monocultures and mixed communities, but they were more strongly linked to shoot traits in monocultures and root traits in mixed communities. Structural equation modelling showed that above- and below-ground traits and soil properties improved predictions of ecosystem C fluxes in monocultures, but not in mixed communities on the basis of community-weighted mean traits. Synthesis. Our results from a single grassland habitat detected relationships in monocultures between above- and below-ground plant traits, and between plant traits, soil properties and ecosystem C fluxes. However, these relationships were generally weaker or different in mixed communities. Our results demonstrate that while plant traits can be used to predict certain soil properties and ecosystem functions in monocultures, they are less effective for predicting how changes in plant species composition influence ecosystem functions in mixed communities.

Soil Abiotic Properties and Plant Functional Traits Mediate Associations Between Soil Microbial and Plant Communities During a Secondary Forest Succession on the Loess Plateau

In the context of secondary forest succession, aboveground-belowground interactions are known to affect the dynamics and functional structure of plant communities. However, the links between soil microbial communities, soil abiotic properties, plant functional traits in the case of semi-arid and arid ecosystems, are unclear. In this study, we investigated the changes in soil microbial species diversity and community composition, and the corresponding effects of soil abiotic properties and plant functional traits, during a ≥150-year secondary forest succession on the Loess Plateau, which represents a typical semi-arid ecosystem in China. Plant community fragments were assigned to six successional stages: 1-4, 4-8, 8-15, 15-50, 50-100, and 100-150 years after abandonment. Bacterial and fungal communities were analyzed by high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene and the internal transcribed spacer (ITS2) region of the rRNA operon, respectively. A multivariate variation-partitioning approach was used to estimate the contributions of soil properties and plant traits to the observed microbial community composition. We found considerable differences in bacterial and fungal community compositions between the early (S1-S3) and later (S4-S6) successional stages. In total, 18 and 12 unique families were, respectively, obtained for bacteria and fungi, as indicators of microbial community succession across the six stages. Bacterial alpha diversity was positively correlated with plant species alpha diversity, while fungal diversity was negatively correlated with plant species diversity. Certain fungal and bacterial taxa appeared to be associated with the occurrence of dominant plant species at different successional stages. Soil properties (pH, total N, total C, NH4-N, NO3-N, and PO4-P concentrations) and plant traits explained 63.80% and 56.68% of total variance in bacterial and fungal community compositions, respectively. These results indicate that soil microbial communities are coupled with plant communities via the mediation of microbial species diversity and community composition over a long-term secondary forest succession in the semi-arid ecosystem. The bacterial and fungal communities show distinct patterns in response to plant community succession, according to both soil abiotic properties and plant functional traits.

Root traits and belowground herbivores relate to plant-soil feedback variation among congeners

Plant–soil feedbacks contribute to vegetation dynamics by species-specific interactions between plants and soil biota. Variation in plant–soil feedbacks can be predicted by root traits, successional position, and plant nativeness. However, it is unknown whether closely related plant species develop more similar plant–soil feedbacks than more distantly related species. Where previous comparisons included plant species from distant phylogenetic positions, we studied plant–soil feedbacks of congeneric species. Using eight intra-continentally range-expanding and native Geranium species, we tested relations between phylogenetic distances, chemical and structural root traits, root microbiomes, and plant–soil feedbacks. We show that root chemistry and specific root length better predict bacterial and fungal community composition than phylogenetic distance. Negative plant–soil feedback strength correlates with root-feeding nematode numbers, whereas microbiome dissimilarity, nativeness, or phylogeny does not predict plant–soil feedbacks. We conclude that root microbiome variation among congeners is best explained by root traits, and that root-feeding nematode abundances predict plant–soil feedbacks.

Most studies of plant–soil feedbacks and associated traits look at remotely-related species. Here the authors look at congeners, and show that nematode-driven plant–soil feedbacks depend on root chemical and morphological traits, independent of phylogenetic distance.