Species phylogeny, ecology, and root traits as predictors of root exudate composition

Phylogenetic relatedness predicts plant-plant nitrogen transfer better than the duration of water scarcity periods

Intermittent water availability is a significant stress factor for plants, particularly in arid and semi-arid ecosystems. Plant nutrient demands often do not align with precipitation pulses that trigger nutrient mobilization and availability, but biotic interactions like plant facilitation (e.g. through nitrogen transfer among distant relatives) and mycorrhizal symbiosis may mitigate this asynchrony, enabling nutrient access despite temporal disparities. We conducted a field experiment with 324 plant individuals to test two hypotheses: (1) greater mycorrhizal fungi abundance increases the amount of 15N transferred between plants, particularly under conditions of fluctuating water availability, and (2) the amount of 15N transferred is affected by the phylogenetic relatedness between donor and receiver plants. We show that 15N transfer is prevalent in the studied semi-arid communities, occurring between all species pairs in 68% of the trials. Interestingly, we observed an increase in 15N transfer between distantly related species, and this phylogenetic pattern remained consistent across fungicide and water regime treatments, which did not affect 15N transfer. Elucidating the drivers of N transfer between plants under different environmental conditions can improve our predictions on how plant communities will respond to future climate challenges, especially prolonged droughts in Mediterranean ecosystems.

Tree carbon allocation to root exudates: implications for carbon budgets, soil sequestration and drought response

Root carbon (C) exudation plays a central role in nutrient acquisition, microbially mediated organic matter decomposition and many other critical ecosystem processes. While it is well known that roots respond strongly to belowground resources, we have a limited quantitative understanding about C allocation to exudates and its fate in soil under changing water availability. This review synthesizes the importance of exudate C fluxes, summarizes studies quantifying mass-specific exudation rate (SER), total exudation rate (TER) and root exudate fraction (REF; the proportion of TER in a plant's C allocation), examines drought effects and highlights key research priorities to advance the understanding of C allocation to exudates in forest ecosystems. On average, SER is often <1 mg C gdry root-1 day-1, TER is 3.8 Pg C year-1 and REF varies between 1 and 17% of net primary production. Spatiotemporal variations in exudation, including seasonal and daily patterns and subsoil exudation, remain critical knowledge gaps. We show that many studies report a 1.2- to 11-fold increase in SER and REF in response to drought. However, TER often remains unchanged, suggesting that absolute exudate C inputs to the soil may stay constant under drought conditions. Disentangling the individual impacts of soil and air drought as well as drought legacy impacts on ecosystem C dynamics are overlooked aspects. By estimating the differences in rhizosphere formation and exudation across various forest biomes, we find that exudate-affected soil volumes are highest in tropical forests and lowest in boreal forests. While current research emphasizes significant C allocation from the canopy to soil via exudates, understanding exudation dynamics and biome-specific responses to drought by using standardized protocols is essential. Expanding these insights is critical for comprehending the role of root exudates in soil organic matter formation, ecosystem resilience and adaptation to climate change.

Impacts of plant root traits and microbial functional attributes on soil respiration components in the desert-oasis ecotone

Dividing soil respiration (Rs) into autotrophic respiration (Ra) and heterotrophic respiration (Rh) represents a pivotal step in deciphering how Rs responds to environmental perturbations. Nevertheless, in arid ecosystems beset by environmental stress, the partitioning of Rs and the underlying mechanisms through which microbial and root traits govern the distinct components remain poorly understood. This study was strategically designed to investigate Rs and its components (Ra and Rh), soil properties, and root traits within the desert-oasis ecotone (encompassing the river bank, transitional zone, and desert margin) of northwest China. Employing metagenomics, we quantitatively characterized microbial taxonomic attributes (i.e., taxonomic composition) and functional attributes (specifically, functional genes implicated in microbial carbon metabolism). Field measurements during the growing season of 2019 unveiled a pronounced decline in soil respiration rates along the environmental gradient from the river bank to the desert margin. The mean soil respiration rate was recorded as 1.82 ± 0.41 μmol m-2 s-1 at the river bank, 0.49 ± 0.15 μmol m-2 s-1 in the transitional zone, and a meager 0.45 ± 0.12 μmol m-2 s-1 in the desert margin. Concomitantly, the Ra and Rh components exhibited a similar trend throughout the study period, with Rh emerging as the dominant driver of Rs. Utilizing random forest modeling, we unearthed significant associations between microbial taxonomic and functional features and Rs components. Notably, both Ra and Rh displayed robust positive correlations with the abundance of phosphatidylinositol glycan A, a key player in microbial carbon metabolism. Partial least squares path modeling further elucidated that soil properties and microbial functions exerted direct and positive influences on both Ra and Rh, whereas taxonomic features failed to register a significant impact. When considering the combined effects of biotic and abiotic factors, microbial functional attributes emerged as the linchpin in dictating Rs composition. Collectively, these findings suggest that a trait-based approach holds great promise in more effectively revealing the response mechanisms of Rs composition to environmental changes, thereby offering novel vistas for future investigations into carbon cycling in terrestrial soils.

Root Exudates in Soilless Culture Conditions

Root metabolite secretion plays a critical role in increasing nutrient acquisition, allelopathy, and shaping the root-associated microbiome. While much research has explored the ecological functions of root exudates, their relevance to horticultural practices, particularly soilless cultivation, remains underexplored. Steering root exudation could help growers enhance the effectiveness of plant growth-promoting bacteria. This review summarizes current knowledge on root exudation in soilless systems, examining its process and discussing environmental influences in the context of soilless cultivation. Plants in soilless systems exhibit higher total carbon exudation rates compared to those in natural soils, with exudation profiles varying across systems and species. Root exudation decreases with plant age, with most environmental adaptations occurring during early growth stages. Several environmental factors unique to soilless systems affect root exudation. For instance, nutrient availability has a major impact on root exudation. Light intensity reduces exudation rates, and light quality influences exudation profiles in a species- and environment-dependent manner. Elevated CO2 and temperature increase exudation. Factors related to the hydroponic nutrient solution and growing media composition remain insufficiently understood, necessitating further research.

Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula

Plant root exudates are involved in nutrient acquisition, microbial partnerships, and inter-organism signaling. Yet, little is known about the genetic and environmental drivers of root exudate variation at large geographical scales, which may help understand the evolutionary trajectories of plants in heterogeneous environments. We quantified natural variation in the chemical composition of Arabidopsis thaliana root exudates in 105 Iberian accessions. We identified up to 373 putative compounds using ultra-high-performance liquid chromatography coupled with mass spectrometry. We estimated the broad-sense heritability of compounds and conducted a genome-wide association (GWA) study. We associated variation in root exudates to variation in geographic, environmental, life history, and genetic attributes of Iberian accessions. Only 25 of 373 compounds exhibited broad-sense heritability values significantly different from zero. GWA analysis identified polymorphisms associated with 12 root exudate compounds and 26 known genes involved in metabolism, defense, signaling, and nutrient transport. The genetic structure influenced root exudate composition involving terpenoids. We detected five terpenoids related to plant defense significantly varying in mean abundances in two genetic clusters. Our study provides first insights into the extent of root exudate natural variation at a regional scale depicting a diversified evolutionary trajectory among A. thaliana genetic clusters chiefly mediated by terpenoid composition.

Effects of salinity on iron-organic carbon binding in the rhizosphere of Kandelia obovata: Insights from root exudate analysis

Iron (Fe) oxides in wetland soils are crucial for stabilizing soil organic carbon (SOC) by forming stable Fe-OC complexes, thus protecting SOC from microbial breakdown and aiding its preservation. This study delves into the response of Fe (hydr-)oxides to salt stress, a relatively unexplored area, by examining Kandelia obovata, a key mangrove species. Through controlled climate chamber experiments, we investigated how salt stress affects the interactions between Fe (hydr-)oxides and SOC in root exudates (REs) and rhizosphere soils. Our results demonstrate that salinity at 30 ppt significantly increases the release of sugars, amino acids, inorganic nutrients (NH4+, NO3-), and phosphorus in K. obovata's REs, while reducing crystalline and amorphous Fe (hydr-)oxides and increasing complexed Fe (hydr-)oxide levels, thereby reducing their crystallinity in rhizosphere soils. Importantly, at elevated salinity (30 ppt), the Fe-OC bond in the rhizosphere shows greater stability, indicating enhanced resilience to salt stress compared to bulk soil. Salt stress also raises the carbon to nitrogen (C/N) ratio in REs. Testing artificial REs (AREs) with different C/N ratios showed that Fe (hydr-)oxide content decreases at C/N ratios of 10 and 30 compared to the control, whereas Fe-OC content increases with higher C/N ratios. Introduction of AREs with a C/N ratio of 20 significantly affected rhizosphere crystalline Fe (hydr-)oxide and Fe-OC content, highlighting AREs' impact on the binding of Fe (hydr-) oxides and OC. The presence of soil microorganisms was critical for the binding of Fe (hydr-) oxides and OC, as sterilized soil exhibited significantly lower levels of Fe (hydr-) oxides and Fe-OC compared to unsterilized soil. This research reveals that under salt stress, mangrove plants play a crucial role in stabilizing rhizosphere SOC by influencing Fe (hydr-) oxide crystallinity and promoting the formation of stable Fe-OC complexes, highlighting the complex interactions between plant REs, salt stress, and soil minerals.

Beyond the rootzone: Unveiling soil property and biota gradients around plants

Although the effects of plants on soil properties are well known, the effects of distance from plant roots to root-free soil on soil properties and associated soil organisms are much less studied. Previous research on the effects of distance from a plant explored specific soil organisms and properties, however, comparative studies across a wide range of plant-associated organisms and multiple model systems are lacking. We conducted a controlled greenhouse experiment using soil from two contrasting habitats. Within each soil type, we cultivated two plant species, individually and in combination, studying soil organisms and properties in the root centre, the root periphery, and the root-free zones. We showed that the distance from the cultivated plant (representing decreasing amount of plant roots) had a significant impact on the abiotic properties of the soil (pH and available P and N) and also on the composition of the fungal, bacterial, and nematode communities. The specific patterns, however, did not always match our expectations. For example, there was no significant relationship between the abundance of fungal pathogens and the distance from the cultivated plant compared to a strong decrease in the abundance of arbuscular mycorrhizal fungi. Changes in soil chemistry along the distance from the cultivated plant were probably one of the important drivers that affected bacterial communities. The abundance of nematodes also decreased with distance from the cultivated plant, and the rate of their responses reflected the distribution of their food sources. The patterns of soil changes along the gradient from plant to root-free soil were largely similar in two contrasting soil types and four plant species or their mixtures. This suggests that our results can be generalised to other systems and contribute to a better understanding of the mechanisms of soil legacy formation.

Plant species and associated root nutritional traits influence soil dominant bacteria in coastal wetlands across China

Climate and edaphic properties drive the biogeographic distribution of dominant soil microbial phylotypes in terrestrial ecosystems. However, the impact of plant species and their root nutritional traits on microbial distribution in coastal wetlands remains unclear. Here, we investigated the nutritional traits of 100 halophyte root samples and the bacterial communities in the corresponding soil samples from coastal wetlands across eastern China. This study spans 22° of latitude, covering over 2500 km from north to south. We found that 1% of soil bacterial phylotypes accounted for nearly 30% of the soil bacterial community abundance, suggesting that a few bacterial phylotypes dominated the coastal wetlands. These dominated phylotypes could be grouped into three ecological clusters as per their preference over climatic (temperature and precipitation), edaphic (soil carbon and nitrogen), and plant factors (halophyte vegetation, root carbon, and nitrogen). We further provide novel evidence that plant root nutritional traits, especially root C and N, can strongly influence the distribution of these ecological clusters. Taken together, our study provides solid evidence of revealing the dominance of specific bacterial phylotypes and the complex interactions with their environment, highlighting the importance of plant root nutritional traits on biogeographic distribution of soil microbiome in coastal wetland ecosystems.

Evolutionary history and root trait coordination predict nutrient strategy in tropical legume trees

Plants express diverse nutrient use and acquisition traits, but it is unclear how trait combinations at the species level are constrained by phylogeny, trait coordination, or trade-offs in resource investment. One trait - nitrogen (N) fixation - is assumed to correlate with other traits and used to define plant functional groups, despite potential confounding effects of phylogeny. We quantified growth, carbon metabolism, fixation rate, root phosphatase activity (RPA), mycorrhizal colonization, and leaf and root morphology/chemistry across 22 species of fixing and nonfixing tropical Fabaceae trees under common conditions. Belowground trait variation was high even among closely related species, and most traits displayed a phylogenetic signal, including N-fixation rate and nodule biomass. Across species, we observed strong positive correlations between physiological traits such as RPA and root respiration. RPA increased ~ fourfold per unit increase in fixation, supporting the debated hypothesis that N-fixers 'trade' N for phosphatases to enhance phosphorus acquisition. Specific root length and root N differed between functional groups, though for other traits, apparent differences became nonsignificant after accounting for phylogenetic nonindependence. We conclude that evolutionary history, trait coordination, and fixation ability contribute to nutrient trait expression at the species level, and recommend explicitly considering phylogeny in analyses of functional groupings.

Bio-manure substitution declines soil N2O and NO emissions and improves nitrogen use efficiency and vegetable quality index

Substituting mineral fertilizer with manure or a combination of organic amendments plus beneficial soil microorganisms (bio-manure) in agriculture is a standard practice to mitigate N2O and NO emissions while enhancing crop performance and nitrogen use efficiency (NUE). Here, we conducted a greenhouse trial for three consecutive vegetable growth seasons for Spinach, Coriander herb, and Baby bok choy to reveal the response of N2O and NO emissions, NUE, and vegetable quality index (VQI) to fertilization strategies. Strategies included solely chemical nitrogen fertilizer (CN), 20 (M1N4) and 50% (M1N1) substitution with manure, 20 (BM1N4) and 50% (BM1N1) substitution with bio-manure, and no fertilization as a control and were organized in a completely randomized design (n = 3). Manure decreased N2O emissions by 24-45% and bio-manure by 44-53% compared to CN. Manure reduced NO emissions by 28-41% and bio-manure by 55-63%. Bio-manure increased NUE by 0.04-31% and yields by 0.05-61% while improving VQI, attributed to yield growth and reduced vegetable NO3- contents. Improvement of root growth was the main factor that explained the rise of NUE; NUE declined with the increase of N2O emissions, showing the loss of vegetable performance under conditions when denitrification processes prevailed. Under the BM1N1, the highest VQI and the lowest yield-scaled N-oxide emissions were observed, suggesting that substitution with bio-manure can improve vegetable quality and mitigate N-oxide emissions. These findings indicate that substituting 50% of mineral fertilizer with bio-manure can effectively improve NUE and VQI and mitigate N-oxides in intensive vegetable production.

Arsenic-Hyperaccumulator Pteris vittata Effectively Uses Sparingly-Soluble Phosphate Rock: Rhizosphere Solubilization, Nutrient Improvement, and Arsenic Accumulation

Sparingly-soluble phosphate rock (PR), a raw material for P-fertilizer production, can be effectively utilized by the As-hyperaccumulator Pteris vittata but not most plants. In this study, we investigated the associated mechanisms by measuring dissolved organic carbon (DOC) and acid phosphatase in the rhizosphere, and nutrient uptake and gene expression related to the As metabolism in P. vittata. The plants were grown in a soil containing 200 mg kg-1 As and/or 1.5% PR for 30 days. Compared to the As treatment, the P. vittata biomass was increased by 33% to 4.6 g plant-1 in the As+PR treatment, corresponding to 27% decrease in its frond oxidative stress as measured by malondialdehyde. Due to PR-enhanced DOC production in the rhizosphere, the Ca, P, and As contents in P. vittata fronds were increased by 17% to 9.7 g kg-1, 29% to 5.0 g kg-1, and 57% to 1045 mg kg-1 in the As+PR treatment, thereby supporting its better growth. Besides, PR-induced rhizosphere pH increase from 5.0 to 6.9 promoted greater P uptake by P. vittata probably via upregulating low-affinity P transporters PvPTB1;1/1;2 by 3.7-4.1 folds. Consequently, 29% lower available-P induced the 3.3-fold upregulation of high-affinity P transporter PvPht1;3 in the As+PR treatment, which was probably responsible for the 58% decrease in available-As content in the rhizosphere. Consistent with the enhanced As translocation and sequestration, arsenite antiporters PvACR3/3;3 were upregulated by 1.8-4.4 folds in the As+PR than As treatment. In short, sparingly-soluble PR enhanced the Ca, P, and As availability in P. vittata rhizosphere and improved their uptake via upregulating genes related to As metabolism, suggesting its potential application for improving phytoremediation in As-contaminated soils.

Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO2 in northern peatlands

Warming and elevated CO2 (eCO2) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland

BACKGROUND

Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is.

RESULTS

To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site.

CONCLUSIONS

Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.