The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair-controlled exudation

Impacts of biodegradable microplastics on rhizosphere bacterial communities of Arabidopsis thaliana: Insights into root hair-dependent colonization

Biodegradable microplastics (MPs) affect plant health by altering rhizosphere microbial communities. Root hairs create a unique niche for diverse microbes, but the effects of biodegradable MPs on root hair-dependent bacterial colonization are unclear, particularly the direct relationship between microbes in the rhizosphere and bulk soil. Here, the effects of polybutylene adipate terephthalate (PBAT) MPs on root hair-dependent bacterial colonization and diversity in the rhizosphere were revealed using an absolute quantitative method and in-situ zymography with two genotypes of Arabidopsis thaliana (long root hair, wild-type, WT and short root hair, rop2-1 mutant, ROP). The results showed that rhizosphere enzyme activity hotspots, bacterial diversity, and colonization increased from ROP to WT plants. PBAT MPs reduced root hair-dependent bacterial colonization and β-glucosidase hotspots by 17.1 % and 9.8 %, respectively. Despite increasing bacterial absolute abundance in both rhizosphere and bulk soil, PBAT MPs diminished bacterial community modularity and shifted bacterial life strategies from K- to r-strategy via elevated rRNA (rrn) copy numbers and copiotroph/oligotroph ratio. This study indicated that PBAT MPs decreased root hair-dependent bacterial colonization and diversity in the rhizosphere by altering the microbial life history strategies and increasing copiotrophic abundance. This study explained the effects of PBAT MPs on rhizosphere bacterial colonization and diversity from the perspective of root hairs.

Molecular and physiological characterizations of roots under drought stress in rice: A comprehensive review

Drought stress poses a major challenge to rice (Oryza sativa L.) production, significantly threatening global food security, especially in the context of climate change. Root architecture plays a key role in drought resistance, as rice plants require substantial water throughout their growth. The genetic diversity of rice root systems exhibits various growth patterns and adaptive traits that enable plants to endure water-deficient conditions. Harnessing this diversity to improve drought resilience demands a thorough understanding of critical root traits and adaptive mechanisms. This review explores rice roots' anatomical, physiological, and biochemical responses to drought, emphasizing important traits such as root architecture, xylem vessel modifications, root cortical aerenchyma (RCA), and water transport mechanisms. The role of biochemical regulators, including phytohormones, sugars, lipids, and reactive oxygen species (ROS), in root adaptation to drought is also explored. Additionally, the genetic and molecular pathways influencing root development under drought stress are discussed, with a focus on key genes and transcription factors (TFs) such as NAC, bZIP, AP2/ERF, and others that contribute to enhanced drought tolerance. Understanding these complex interactions is crucial for breeding drought-tolerant rice varieties, ultimately improving crop productivity under challenging environmental conditions.

Both light and soil moisture affect the rhizosphere microecology in two oak species

Understanding the mechanisms by which seedlings respond to light and water regulation, as well as studying the response of rhizosphere microecology to drought stress, are crucial for forest ecosystem management and ecological restoration. To elucidate the response of the rhizosphere microecology of Quercus dentata and Quercus variabilis seedlings to water and light conditions, and to clarify how plants modulate the structure and function of rhizosphere microbial communities under drought stress, we conducted 12 water-light gradient control experiments. These experiments aimed to offer scientific theoretical support for the dynamic changes in rhizosphere soil enzyme activities and microbial community compositions of these two oak species under varying light and moisture conditions, and subsequently assist in the future breeding and cultivation efforts. The results are summarized as follows: (1) The activities of cellulase, urease, and chitinase in the rhizosphere soil of Q. dentata and Q. variabilis were significantly influenced by water and light treatments (p < 0.05). Urease was particularly sensitive to light, while sucrase exhibited sensitivity to light in Q. dentata and no significant difference in Q. variabilis. (2) Compared to Q. dentata, the rhizosphere bacteria of Q. variabilis demonstrated greater adaptability to drought conditions. Significant differences were observed in the composition of microorganisms and types of fungi in the rhizosphere soil of the two Quercus seedlings. The fungal community is significantly influenced by light and moisture, and appropriate shading treatment can increase the species diversity of fungi; (3) Under different water and light treatments, the rhizosphere soil microbial composition and dominant species differed significantly between the two Quercus seedlings. For instance, Streptomyces, Mesorhizobium, and Paecilomyces exhibited significant variations under different treatment conditions. Specifically, under L3W0 (25% light, 75-85% moisture) conditions, Hyphomonadaceae and SWB02 dominated in the Q. dentata rhizosphere, whereas Burkholderiales and Nitrosomonadaceae were prevalent in the Q. variabilis rhizosphere. Overall, the rhizosphere microecology of Q. dentata and Q. variabilis exhibited markedly distinct responses to varying light and water regimen conditions. Under identical conditions, however, the enzyme activity and microbial community composition in the rhizosphere soil of these two oak seedlings were found to be similar.

Trade-off between soil enzyme activities and hotspots area depends on long-term fertilization: In situ field zymography

Mineral fertilizers and livestock manure have been found to impact soil enzyme activities and distributions, but their trade-off and subsequent effects on soil functioning related to nutrient cycling are rarely evaluated. Here, we investigated the long-term effects of manure and mineral fertilization on the spatial distribution of enzyme activities related to carbon, nitrogen, and phosphorus cycling under field-grown maize. We found that the legacy of mineral fertilizers increased the rhizosphere extension for β-glucosidase and N-acetylglucosaminidase by 16-170 %, and the hotspots area by 37-151 %, compared to manure. The legacy of manure, especially combined with mineral fertilizers, increased enzyme activities and formed non-rhizosphere hotspots. Furthermore, we found a trade-off between hotspots area and enzyme activities under the legacy effect of long-term fertilization. This suggested that plants and microorganisms regulate nutrient investments by altering spatial distribution of enzyme activities. The positive correlation between hotspots area and nutrient contents highlights the importance of non-rhizosphere hotspots induced by manure in maintaining soil fertility. Compared to mineral fertilization, the legacy effect of manure expanded the soil functions for nutrient cycling in both rhizosphere and non-rhizosphere by >1.7 times. In conclusion, the legacy of manure expands non-rhizosphere hotspots and enhances soil functioning, while mineral fertilization expands rhizosphere extension and intensifies hotspots area for nutrient exploitation.

Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae

Drought is one of the most serious abiotic stresses, and emerging evidence suggest plant microbiome affects plant drought tolerance. However, there is a lack of genetic evidence regarding whether and how plants orchestrate the dynamic assembly of the microbiome upon drought. By utilizing mutants with enhanced or decreased root hair densities, we find that root hair regulators also affect drought induced root microbiome changes. Rhizobiaceae is a key biomarker taxa affected by root hair related mutants. We isolated and sequenced 1479 root associated microbes, and confirmed that several Rhizobium strains presented stress-alleviating activities. Metagenome, root transcriptome and root metabolome studies further reveal the multi-omic changes upon drought stress. We knocked out an ornithine cyclodeaminase (ocd) gene in Rhizobium sp. 4F10, which significantly dampens its stress alleviating ability. Our genetic and integrated multi-omics studies confirm the involvement of host genetic effects in reshaping a stress-alleviating root microbiome during drought, and provide mechanistic insights into Rhizobiaceae mediated abiotic stress protection.

Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize

Increasing biological nitrogen (N) fixation (BNF) in maize production could reduce the environmental impacts of N fertilizer use, but reactive N in the rhizosphere of maize limits the BNF process. Using non-transgenic methods, we developed gene-edited strains of Klebsiella variicola (Kv137-2253) and Kosakonia sacchari (Ks6-5687) bacteria optimized for root-associated BNF and ammonium excretion in N-rich conditions. The aim of this research was to elucidate the mechanism of action of these strains. We present evidence from in vitro, in planta and field experiments that confirms that our genetic remodeling strategy derepresses BNF activity in N-rich systems and increases ammonium excretion by orders of magnitude above the respective wildtype strains. BNF is demonstrated in controlled environments by the transfer of labeled 15N2 gas from the rhizosphere to the chlorophyll of inoculated maize plants. This was corroborated in several 15N isotope tracer field experiments where inoculation with the formulated, commercial-grade product derived from the gene-edited strains (PIVOT BIO PROVEN® 40) provided on average 21 kg N ha-1 to the plant by the VT-R1 growth stages. Data from small-plot and on-farm trials suggest that this technology can improve crop N status pre-flowering and has potential to mitigate the risk of yield loss associated with a reduction in synthetic N fertilizer inputs.

RhizoMAP: a comprehensive, nondestructive, and sensitive platform for metabolic imaging of the rhizosphere

BACKGROUND

Elucidating the intricate structural organization and spatial gradients of biomolecular composition within the rhizosphere is critical to understanding important biogeochemical processes, which include the mechanisms of root-microbe interactions for maintaining sustainable plant ecosystem services. While various analytical methods have been developed to assess the spatial heterogeneity within the rhizosphere, a comprehensive view of the fine distribution of metabolites within the root-soil interface has remained a significant challenge. This is primarily due to the difficulty of maintaining the original spatial organization during sample preparation without compromising its molecular content.

RESULTS

In this study, we present a novel approach, RhizoMAP, in which the rhizosphere molecules are imprinted on selected polymer membranes and then spatially profiled using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI). We enhanced the performance of RhizoMAP by combining the use of two thin (< 20 μm) membranes (polyester and polycarbonate) with distinct MALDI sample preparations. This optimization allowed us to gain insight into the distribution of over 500 different molecules within the rhizosphere of poplar (Populus trichocarpa) grown in rhizoboxes filled with mycorrhizae soil. These two membranes, coupled with three different sample preparation conditions, enabled us to capture the distribution of a wide variety of molecules that included phytohormones, amino acids, sugars, sugar glycosides, polycarboxylic acids components of the Krebs cycle, fatty acids, short aldehydes and ketones, terpenes, volatile organic compounds, fertilizers from the soil, and others. Their spatial distribution varies greatly, with some following root traces, others showing diffusion from roots, some associated with soil particles, and many having distinct hot spots along the plant root or surrounding soil. Moreover, we showed how RhizoMAP can be used to localize the origin of the molecules and molecular transformation during root growth. Finally, we demonstrated the power of RhizoMAP to capture molecular distributions of key metabolites throughout a 20 cm deep rhizosphere.

CONCLUSIONS

RhizoMAP is a method that provides nondestructive, untargeted, broad, and sensitive metabolite imaging of root-associated molecules, exudates, and soil organic matter throughout the rhizosphere, as demonstrated in a lab-controlled native soil environment.

Harnessing root-soil-microbiota interactions for drought-resilient cereals

Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.

Rhizosheath drought responsiveness is variety-specific and a key component of belowground plant adaptation

Biophysicochemical rhizosheath properties play a vital role in plant drought adaptation. However, their integration into the framework of plant drought response is hampered by incomplete mechanistic understanding of their drought responsiveness and unknown linkage to intraspecific plant-soil drought reactions. Thirty-eight Zea mays varieties were grown under well-watered and drought conditions to assess the drought responsiveness of rhizosheath properties, such as soil aggregation, rhizosheath mass, net-rhizodeposition, and soil organic carbon distribution. Additionally, explanatory traits, including functional plant trait adaptations and changes in soil enzyme activities, were measured. Drought restricted soil structure formation in the rhizosheath and shifted plant-carbon from litter-derived organic matter in macroaggregates to microbially processed compounds in microaggregates. Variety-specific functional trait modifications determined variations in rhizosheath drought responsiveness. Drought responses of the plant-soil system ranged among varieties from maintaining plant-microbial interactions in the rhizosheath through accumulation of rhizodeposits, to preserving rhizosheath soil structure while increasing soil exploration through enhanced root elongation. Drought-induced alterations at the root-soil interface may hold crucial implications for ecosystem resilience in a changing climate. Our findings highlight that rhizosheath soil properties are an intrinsic component of plant drought response, emphasizing the need for a holistic concept of plant-soil systems in future research on plant drought adaptation.

Location: root architecture structures rhizosphere microbial associations

Root architectural phenotypes are promising targets for crop breeding, but root architectural effects on microbial associations in agricultural fields are not well understood. Architecture determines the location of microbial associations within root systems, which, when integrated with soil vertical gradients, determines the functions and the metabolic capability of rhizosphere microbial communities. We argue that variation in root architecture in crops has important implications for root exudation, microbial recruitment and function, and the decomposition and fate of root tissues and exudates. Recent research has shown that the root microbiome changes along root axes and among root classes, that root tips have a unique microbiome, and that root exudates change within the root system depending on soil physicochemical conditions. Although fresh exudates are produced in larger amounts in root tips, the rhizosphere of mature root segments also plays a role in influencing soil vertical gradients. We argue that more research is needed to understand specific root phenotypes that structure microbial associations and discuss candidate root phenotypes that may determine the location of microbial hotspots within root systems with relevance to agricultural systems.

The impact of fast-growing eucalypt plantations on C emissions in tropical soil: effect of belowground and aboveground C inputs

Planted forest soils can have great potential for CO2-C sequestration, mainly due to belowground C inputs, which impact deep soil C (DSC) accumulation. However, there are still gaps in understanding the CO2 emission dynamics in eucalypt plantations. Therefore, we used isotopic techniques to investigate the dynamics of the soil surface CO2-C flux and CO2-C concentration with depth for a eucalypt plantation influenced by different C inputs (above- and belowground). The gas evaluations were carried in depth the root to valuation of root priming effect (RPE) was calculated. In addition, measurements of the plant (C-fine root and C-litterfall) and soil (total organic carbon - TOC, total nitrogen - TN, soil moisture - SM, and soil temperature - ST) were performed. After planting the eucalypt trees, there was an increase in the soil surface CO2-C flux with plant growth. Root growth contributed greatly to the soil surface CO2-C flux, promoting greater surface RPE over time. In comparison to the other factors, SM had a greater influence on litterfall decomposition and root respiration. It was not possible to detect losses in TOC and TN in the different soil layers for the 31-month-old eucalypt. However, the 40-month-old eucalypt showed a positive RPE with depth, indicating possible replacement of DSC ("old C") by rhizodeposition-C ("new C") in the soil. Thus, in eucalyptus plantations, aboveground plant growth influences CO2 emissions on the soil surface, while root growth and activity influence C in deeper soil layers. This information indicates the need for future changes in forest management, with a view to reducing CO2 emissions.

Contribution of Biogas Slurry-Derived Colloids to Plant P Uptake and Phosphatase Activities: Spatiotemporal Response

The bioavailability for varied-size phosphorus (P)-binding colloids (Pcoll) especially from external P sources in soil terrestrial ecosystems remains unclear. This study evaluated the differential contribution of various-sized biogas slurry (BS)-derived colloids to plant available P uptake in the rhizosphere and the corresponding patterns of phosphatase response. Keeping the same content of total P input (15 mg kg-1), we applied different size-fractioned BS-derived colloids including nanosized colloids (NCs, 1-20 nm), fine-sized colloids (FCs, 20-220 nm), and medium-sized colloids (MCs, 220-450 nm) respectively to conduct a 45-day rice (Oryza sativa L.) rhizotron experiment. During the whole cultivation period, the dynamics of chemical characteristics and P fractions in each experimental rhizosphere soil solution were analyzed. The spatial and temporal dynamics examination of P-transforming enzymes (acid phosphatases) in the rice rhizosphere was visualized by a soil zymography technique after 5, 25, and 45 days of rice transplantation. The results indicated that the acid phosphatase activities and its hot spot areas were significantly 1) correlated with the relative bioavailability of colloidal P (RBAcoll), 2) increased with the colloid-free (truly dissolved P) and BS-derived NC addition, and 3) affected by the plant growth stage. With the nanosized BS colloid addition, the RBAcoll and plant biomass were respectively found to be the highest (64% and 1.22 g plant-1), in which the acid phosphatase-catalyzed hydrolysis of organic Pcoll played an important role. All of the above suggested that nanosized BS-derived colloids are an effective alternative to conventional phosphorus fertilizer for promoting plant P uptake and P bioavailability.

Impact of drought on soil microbial biomass and extracellular enzyme activity

Introduction

With the continuous changes in climate patterns due to global warming, drought has become an important limiting factor in the development of terrestrial ecosystems. However, a comprehensive understanding of the impact of drought on soil microbial activity at a global scale is lacking.

Methods

In this study, we aimed to examine the effects of drought on soil microbial biomass (carbon [MBC], nitrogen [MBN], and phosphorus [MBP]) and enzyme activity (β-1, 4-glucosidase [BG]; β-D-cellobiosidase [CBH]; β-1, 4-N-acetylglucosaminidase [NAG]; L-leucine aminopeptidase [LAP]; and acid phosphatase [AP]). Additionally, we conducted a meta-analysis to determine the degree to which these effects are regulated by vegetation type, drought intensity, drought duration, and mean annual temperature (MAT).

Result and discussion

Our results showed that drought significantly decreased the MBC, MBN, and MBP and the activity levels of BG and AP by 22.7%, 21.2%, 21.6%, 26.8%, and 16.1%, respectively. In terms of vegetation type, drought mainly affected the MBC and MBN in croplands and grasslands. Furthermore, the response ratio of BG, CBH, NAG, and LAP were negatively correlated with drought intensity, whereas MBN and MBP and the activity levels of BG and CBH were negatively correlated with drought duration. Additionally, the response ratio of BG and NAG were negatively correlated with MAT. In conclusion, drought significantly reduced soil microbial biomass and enzyme activity on a global scale. Our results highlight the strong impact of drought on soil microbial biomass and carbon- and phosphorus-acquiring enzyme activity.