Soil Microorganisms Research Articles

Enhanced carbon use efficiency and warming resistance of soil microorganisms under organic amendment

The frequency and intensity of extreme weather events, including rapid temperature fluctuations, are increasing because of climate change. Long-term fertilization practices have been observed to alter microbial physiology and community structure, thereby affecting soil carbon sequestration. However, the effects of warming on the carbon sequestration potential of soil microbes adapted to long-term fertilization remain poorly understood. In this study, we utilized 18O isotope labeling to assess microbial carbon use efficiency (CUE) and employed stable isotope probing (SIP) with 18O-H2O to identify growing taxa in response to temperature changes (5–35 °C). Organic amendment with manure or straw residue significantly increased microbial CUE by 86–181 % compared to unfertilized soils. The microorganisms inhabiting organic amended soils displayed greater resistance of microbial CUE to high temperatures (25–35 °C) compared to those inhabiting soils fertilized only with minerals. Microbial growth patterns determined by the classification of taxa into incorporators or non-incorporators based on 18O incorporation into DNA exhibited limited phylogenetic conservation in response to temperature changes. Microbial clusters were identified by grouping taxa with similar growth patterns across different temperatures. Organic amendments enriched microbial clusters associated with increased CUE, whereas clusters in unfertilized or mineral-only fertilized soils were linked to decreased CUE. Specifically, shifts in the composition of growing bacteria were correlated with enhanced microbial CUE, whereas modifications in the composition of growing fungi were associated with diminished CUE. Notably, the responses of microbial CUE to temperature fluctuations were primarily driven by changes in the bacterial composition. Overall, our findings demonstrate that organic amendments enhance soil microbial CUE and promote the enrichment of specific microbial clusters that are better equipped to cope with temperature changes. This study establishes a theoretical foundation for manipulating soil microbes to enhance carbon sequestration under global climate scenarios.

Scaling up taxon-specific microbial traits to predict community-level microbial activity in agricultural systems

Soil microorganisms perform many important ecosystem functions including nitrogen (N) cycling which dictates plant productivity in agricultural ecosystems. Despite the importance of these communities, connecting microbial composition with ecosystem function has been a long standing challenge. Taxon-specific substrate assimilation traits, measured with quantitative stable isotope probing (qSIP), may provide a means to scale from microbial community composition to community-level process rates. To test the potential for scaling up taxon-specific N assimilation to predict community-level rates of carbon mineralization, N mineralization, and N immobilization we measured soil properties, microbial activity, and N assimilation using 15N qSIP in soils from six distinct farms. N assimilation, measured as DNA 15N enrichment, varied among taxa and within taxa across farms. Taxon specific N assimilation was aggregated to calculate a community-weighted mean, which when combined with measures of microbial biomass was used to estimate new microbial biomass N production. This estimate of new microbial biomass production reflects the growth of active microbes over the incubation period and related to microbial activity. The new microbial biomass N produced was predictive of soil C and N mineralization rates, explaining 37-47% of the observed variation across the six farming systems. This approach highlights the ability of trait-based methods to relate microbial community structure data to microbially-mediated functional process rates. Such advances may enhance our ability to understand and manage microbially mediated processes, such as N cycling, in both natural and agricultural ecosystems.

Temperature sensitivity quandary of soil microbial community structure in Tibetan alpine grasslands: A meta-analysis and field experiment

Soil microorganisms act as the primary decomposers in global terrestrial ecosystems. Whether climate warming will lead to the convergence of the temperature sensitivity of soil microbial community structure and the convergence of the responses of soil microbial community structure to warming remains controversial. This study explored how warming amplitude affected the temperature sensitivity of soil bacteria and fungi community structures, and how it influenced the responses of soil bacteria and fungi community structures to warming on the Qinghai-Tibet Plateau based on meta-analysis and a single-site warming experiment. The temperature sensitivity of soil microbial community structure did not consistently decline with increasing warming magnitude; instead, it even rose, which might be associated with the nonlinear relationships of the warming magnitude with the temperature sensitivity of ecological processes of soil microbial community assembly or the topological parameters of species co-occurrence network. Meta-analysis indicated that responses of soil microbial community to warming were independent of warming amplitude. However, the single-site warming experiment demonstrated that responses of soil microbial community to warming varied with warming amplitude. These inconsistent results might be attributed to distinct spatial scales, grassland types, climatic conditions and warming magnitudes between the single-site experiment and the meta-analysis. Therefore, the temperature sensitivity of soil microbial community and its response to climate warming cannot be simply characterized as monotonically decreasing or increasing in relation to increasing warming magnitude.

Recent trends and open questions regarding the effects of microplastics on soil, plants and soil microorganisms

In recent years, microplastics have been extensively detected in sea, freshwater, soils and organisms. The microplastics pollution is of increasing concerns for soil health. Microplastics are considered as an emerging threat to the agroecosystems, where soils may represent a reservoir for plastics pollution. Microplastics in soils could alter soil properties, plant growth, soil invertebrate, abundance and activity of soil microorganisms. Further investigations are needed to evaluate the overall effect of microplastics on soil ecosystems services.

LASSOCIATION MAIS-NIEBE ET LA RESTITUTION ORGANIQUE SONT-ELLESLE MOTEUR DUNE GESTION DURABLE DES SOLS A LOUEST DU BURKINA FASO ?

Are maize-cowpea associations and organic restitution the driving force behind sustainable soil management in western Burkina Faso? Soil fertility management is one of the key factors in the sustainability of cropping systems in western Burkina Faso. With this in mind, a study was carried out on the management of crop residues, fertilization and the inclusion of legumes in the cropping system. The aim was to determine the effects of mulching, insertion of cowpeas into the cropping system and organo-mineral fertilization on soil fertility. The experimental design was a strip split plot with 4 replications and three treatments corresponding to 3 crop residue management methods, 3 cropping systems with or without maize and cowpea, and 2 types of fertilization. Trials were conducted from the 2018 to 2020 cropping seasons. Soil moisture, the number of fungal and bacterial colonies and soil chemical characteristics were determined in 2020. The results show a significant increase in soil moisture on maize-wheat association plots of 9.28 and 8.58% for the 0-20 cm depth and 6.85 and 5.31% for the 20-40 cm depth respectively compared with pure maize and cowpea cultivation. For crop residue management and fertilization, soil moisture levels were identical for all treatments. Concerning soil micro-organisms, the results show that five (05) types of fungi were identified on the different treatments: Aspergillus flavus, Aspergillus niger, Fusarium moniliforme, Geotrichumcandidum and Trichoderma sp. The results obtained show no significant difference between treatments at the 5% threshold, either for fungi, bacteria or soil chemical characteristics. Consequently, the maize-cowpea association can be considered a sustainable soil fertility management practice in the western region of Burkina Faso. However, the choice between recycling crop residues by mulching and applying organo-mineral fertilizer must be determined by the farms themselves, according to their socio-economic reality.

Synergistic Mechanisms of Plant Phosphorus (P) Resorption and Microbial P‐Limitation Affecting Soil P During Grassland Vegetation Succession

AbstractPhosphorus (P), a crucial element for all life forms on Earth, is often insufficiently available in terrestrial ecosystems. The interaction and feedback between plants and soil microorganisms are crucial links integrating above‐ and below‐ground ecosystems. However, changes in soil P fractions in response to plant‐microbe interactions during vegetation succession remain poorly understood. This study investigated the trends and relationships between plant resorption, microbial properties, and soil P fractions in the transformation interface soil layer (TIS) and underlying topsoil layer (UTS) during grassland vegetation succession. The results point to a combination of soil properties, alongside microbial and plant factors driving soil P changes. However, the TIS and UTS layers differ, with phosphorus dynamics in the TIS layer primarily influenced by microorganisms. Microorganisms are co‐limited by C and P in both the TIS and UTS layers. Under microbial P‐limitation, microorganisms produce alkaline phosphatases (AP), while C deficiency stimulates the production of C‐acquiring enzymes, subtly regulating soil P dynamics through organic matter decomposition. Plant P resorption efficiency and microbial P‐limitation exhibit synergistic variations, reaching their lowest levels during the mixed Bothriochloa ischaemum and Stipa bungeana Trin (Bo.I + St.B) stage. This study emphasizes that P cycling is influenced by plant‐microbe‐soil interactions and feedback. Plants and soil microorganisms jointly regulate soil nutrient effectiveness and partitioning in the ecosystem.

Climate smart agriculture in sub-Saharan Africa: Role of arbuscular mycorrhiza fungi

Climate change affects many areas of human lives, including agriculture. Interestingly, agriculture contributes to climate change, necessitating climate smart approaches to ensure a win-win situation; wherein agricultural production is sustainable and meets current and future needs. Climate smart agriculture is a collection of agricultural practices that increase productivity, adaptation, and mitigation of climate change contribution to agriculture. While many global regions depend on agriculture directly and indirectly, the sub-Saharan Africa region is directly dependent on agriculture. Existing “climate smart” activities in this region must be better defined and strengthened to achieve its objectives – increasing agricultural productivity, adapting agricultural systems, and mitigating emissions from agricultural activities. Among these climate smart activities are the significance of soil microorganisms, particularly arbuscular mycorrhizal fungi in sustainable agricultural systems, where they provide limited plant nutrients, control pests and diseases, aid drought adaptation, improve soil structure, reduce nutrient loss during leaching, leading to sustainable soil management.

Differential effects of urbanization-induced heavy metal pollution on soil microbial communities under evergreen and deciduous trees

Urbanization has significantly increased heavy metal contamination in urban soils, adversely affecting soil microorganisms, which are vital indicators of soil quality. However, the effects of urbanization-induced metal pollution on soil microbial communities remains largely underestimated. This study examines soil microbial communities and properties beneath the canopy of three deciduous and three evergreen trees in urban parks, situated at varying distances from the city center. The results demonstrated that urbanization consistently alters soil physicochemical properties, including pH, soil moisture, and specific heavy metal contents (e.g., Zn, Mn, Cr). The α-diversity of soil bacterial community was significantly influenced by pH and specific heavy metals (e.g., Cr, Cd), whereas the α-diversity of fungal community was affected by pH, independent of heavy metal concentrations. The response of heavy metal content to urbanization exhibited a consistent pattern across both deciduous and evergreen trees, although the effect differed between these tree types. Furthermore, urbanization impacts the diversity, structure, composition and network of soil microbial communities. Notably, the Shannon index of soil fungal communities under deciduous species shows an initial increase, followed by a decline as urbanization intensifies. In contrast, the Simpson index of soil bacteria under evergreen tree species decreases with increased urbanization. Moreover, urbanization alters soil bacterial networks, with higher network density observed in less urbanized areas. It may also affect microbial functions, such as xenobiotic and lipid metabolism. This study provided a theoretical basis for urban park soil management, which is crucial for enhancing urban soil ecosystem services and mitigating the adverse effects of urbanization.

Altitudinal Variation in Soil Acid Phosphomonoesterase Activity in Subalpine Coniferous Forests in China

Studying the altitudinal variation and driving factors of soil acid phosphomonoesterase (ACP) activity in subalpine regions is crucial for understanding nutrient cycling processes within mountainous ecosystems. This study focused on fir (Abies fabri (Mast.) Craib) forests located at three altitudes (2781 m, 3044 m, and 3210 m) on the eastern slope of Mt. Gongga in southwest China. We measured soil ACP activity alongside soil climate, nutrients, and microorganisms at various depths and elevations to investigate how these factors influence ACP activity. The results indicated that in the organic matter horizons (Oe and Oa horizons), ACP activity gradually decreased with elevation. However, the surface mineral horizon (A horizon) did not show a decline in ACP activity with increasing elevation, which could be attributed to significantly lower ACP activity recorded at the 2781 m sample site compared to the 3044 m site. Variance partitioning analysis revealed that among soil climate, nutrients, and microorganisms, soil nutrients had the most substantial impact on ACP activity across all horizons, with a particularly high contribution of 89.4% observed in the A horizon. Random forest model analysis further demonstrated that soil total carbon (TC) played a crucial role in determining ACP activity in the Oe and Oa horizons, with importance values of 8.5% and 7.3%, respectively. Additionally, soil total nitrogen (TN) was identified as the primary factor influencing ACP activity in the A horizon, with an importance value of 12.6%. Furthermore, soil ACP activity was positively regulated by the soil TC:TP and TN:TP ratios, indicating a stoichiometric control of ACP activity in the Abies fabri (Mast.) Craib forests on Mt. Gongga.

Community structure of soil microorganisms and endophytes of honeysuckle at different ecological niche specificities

BackgroundThe plant microbiome is one of the key determinants of healthy plant growth. However, the complexity of microbial diversity in plant microenvironments in different regions, especially the relationship between subsurface and aboveground microorganisms, is not fully understood. The present study investigated the diversity of soil microorganisms in different regions and the diversity of microorganisms within different ecological niches, and compared soil microorganisms and endophytic microorganisms.Methods16 S and ITS sequencing was used to sequence the soil and endophytes microbiome of honeysuckle. Alpha diversity analysis and principal component analysis (PCoA) were used to study the soil and endophyte microbial communities, and the function of endophyte bacteria and fungi was predicted based on the PICRUST2 process and FUNGuild.ResultsIn total, there were 382 common bacterial genera and 139 common fungal genera in the soil of different producing areas of honeysuckle. There were 398 common bacterial genera and 157 common fungal genera in rhizosphere soil. More beneficial bacteria were enriched in rhizosphere soil. Endophytic bacteria were classified into 34 phyla and 770 genera. Endophytic fungi were classified into 11 phyla and 581 genera, among which there were significant differences in the dominant genera of roots, stems, leaves, and flowers, as well as in community diversity and richness. Endophytic fungal functions were mainly dominated by genes related to saprophytes, functional genes that could fight microorganisms were also found in KEGG secondary functional genes.ConclusionMore beneficial bacteria were enriched in rhizosphere soil of honeysuckle, and the microbial network of the rhizosphere is more complex than that of the soil. Among the tissues of honeysuckle, the flowers have the richest diversity of endophytes. The endogenous dominant core bacteria in each part of honeysuckle plant have a high degree of overlap with the dominant bacteria in soil. Functional prediction suggested that some dominant core bacteria have antibacterial effects, providing a reference for further exploring the strains with antibacterial function of honeysuckle. Understanding the interaction between honeysuckle and microorganisms lays a foundation for the study of growth promotion, quality improvement, and disease and pests control of honeysuckle from the perspective of microorganisms.

Characteristics of Pinus hwangshanensis Rhizospheric Fungal Community along Huangshan Mountain's Elevation Gradients, China.

Elevation gradients strongly influence the diversity pattern of soil microorganisms. To date, many studies have elucidated the response of soil microbes to changes in elevation gradients. However, the effects of these gradients on the assembly mechanisms and network complexity of rhizospheric microbial communities remain underexplored. To bridge this knowledge gap, this study assessed the response of rhizospheric fungal communities of Pinus hwangshanensis along different elevation gradients in the Huangshan Mountain scenic area with regard to diversity, community composition, and assembly mechanisms using high-throughput amplicon sequencing. The results revealed significant differences in rhizospheric fungal community composition across three elevation gradients. The soil organic matter and pH were the most relevant factors influencing the changes in rhizospheric fungal community composition. The rhizospheric fungal diversity was significantly lower at both low and high elevations compared to the medium elevation. The rhizospheric fungal community assembly showed a more deterministic process at low and high elevations than at the medium elevation, indicating that stronger environmental filtering contributed to reduced fungal diversity at the extremes of the elevation gradient. In addition, rhizospheric pathogens, particularly Dermateaceae, acted as keystone taxa, diminishing the stability of co-occurrence networks at the medium elevation. This study contributes to a more comprehensive understanding of rhizospheric fungal community patterns and their ecological functions along elevation gradients in mountainous regions.

Differential spatial responses and assembly mechanisms of soil microbial communities across region-scale Taiga ecosystems

Different soil microbial communities play distinct key roles in regulating forest ecosystem processes and functions. However, the differences in spatial variability and assembly mechanisms of various taiga forest soil microbial taxa remain poorly understood. Here, we assessed the spatial patterns of bacterial and fungal communities, their assembly processes, and the influencing factors in taiga forest ecosystems in Xinjiang, China. A significant distance decay pattern was observed in the similarity of bacterial and fungal communities, with bacterial communities exhibiting a more pronounced pattern than fungal communities. Stochastic and deterministic processes governed together to drive soil bacterial community assembly, whereas stochastic processes dominated fungal community assembly. The coexistence networks revealed that the interactions of bacterial and fungal networks in the four regions are primarily based on interspecies symbiosis, with fungal coexistence networks demonstrating greater stability than bacterial networks. Additionally, the study identified a positive relationship between the modularity of bacterial networks and dispersal limitation. Analysis of environmental factors revealed that soil pH primarily affects the characteristics and assembly mechanisms of bacterial communities, while vegetation conditions primarily affect fungal diversity and composition, with other unconsidered environmental variables influencing the fungal community assembly process. This study emphasized the distinct ways in which bacteria and fungi respond to environmental factors and interspecies interactions. Our results suggested that distinct restoration measures should be implemented for bacteria and fungi in future conservation efforts for forest soil microorganisms.

Soil microbial community construction under revegetation in newly created land

Revegetation represents the primary method for restoring the ecological balance of the Loess Plateau. The assessment of revegetation efficacy on degraded lands can be facilitated through the utilization of soil microorganisms as indicators. We chose Medicago sativa L. (MX), Trifolium repens L. (BSY), Festuca arundinacea Schreb. (GYM), Elymus dahuricus Turcz. (PJC) and natural grass (CK) as the research objects, the soil microbial community composition, function and co-occurrence patterns of the five treatments were analyzed. The results showed that the microbial community composition was similar among the different vegetation types, but there were differences in abundance. Bacteria were significantly correlated with OM, BD and sand. Fungi were significantly correlated with sand and BD. Notably, BD showed highly significant correlation with microbial communities (P < 0.001). Microbial function prediction was dominated by metabolism at the bacterial level, and fungal function was predicted with eight trophic types dominated by parthenogenetic trophic types, and the microbial function prediction analyses showed that in bacteria, BSY had a high abundance of gene functions, and in fungi, PJC had a high abundance of gene functions. Network analysis revealed that the microbial community had small-world characteristics, a modular structure and a non-random co-occurrence pattern. Bacterial interactions included both competition and cooperation, further suggesting that growing raw grass increased the stability of the bacterial community. Overall, our results elucidated the changes in microbial communities and their correlations after raw grass cultivation, which could provide a more comprehensive perspective on microbial community assembly, and provide a theoretical basis for future ecological restoration on the Loess Plateau.

Influence of Varied Phosphorus Fertilizer Ratios on the Rhizosphere Soil Microbial Community in Idesia polycarpa Seedlings

Phosphorus (P) is crucial for tree growth and development, and it significantly influences the rhizosphere microbial community. However, the effects of phosphorus addition on the microbial communities in the rhizosphere soil of Idesia polycarpa remain understudied. In this study, two-year-old “Yuji” Idesia polycarpa seedlings were used to investigate the effects of phosphorus fertilization at four different levels of 0 g (control, CK), 0.92 g (low phosphorus, LP), 1.83 g (medium phosphorus, MP), and 2.75 g (high phosphorus, HP) per plant. The fertilizers were applied every 40 days over 120 days. MiSeq high-throughput sequencing of the 16S rRNA and ITS1 genes was employed to analyze the microbial community composition and diversity of bacteria and fungi in the rhizosphere soil under different phosphorus levels. The results showed that compared with CK treatment, the application of phosphorus fertilizer changed the physicochemical properties of the soil. The LP treatment significantly increased the soil pH, while the HP treatment group exhibited the highest soil-available phosphorus (AP) content. LP treatment significantly increased the number of microbial OTUs in the early and rapid growth stages and the richness and diversity of microbial communities. In addition, the bacterial community structure was significantly correlated with soil pH and AP, while the fungal community had no significant effect. The primary metabolic pathway function of bacteria in the rhizosphere soil of Idesia polycarpa seedlings is mainly metabolism, while fungi are mainly biosynthesis. Compared with CK treatment, 20 differential metabolic pathways were screened out in the bacterial community. Only two differential metabolic pathways were screened out in the fungal community by LP treatment at 120 days. In summary, applying low-level phosphate fertilizer is conducive to promoting the diversity of rhizosphere soil microorganisms. Therefore, potted planting of Idesia polycarpa seedlings is more suitable for applying low phosphorus levels.

Study of Plant Growth Promoting Abilities of Rhizobium Strains Isolated from Mungbean Root Nodules

Background: Plant Growth Promoting Rhizobacteria (PGPR) are a type of bacteria that use biofertilizers and other plant growth-promoting agents to increase plant output and growth. In the last several decades, there has been a global surge in the usage of beneficial soil microorganisms like PGPR for safe and sustainable agriculture due to the detrimental effects of artificial fertilizers on the environment and their rising prices. Plant-beneficial rhizobacteria have the potential to reduce the world's reliance on dangerous agricultural chemicals that upset agro-ecosystems. Today a large part of yield is lost due to the various stress mechanisms of plants. It could be classified into biotic and abiotic stress. These are generally a group of microorganisms that is found either in the rhizosphere or in the root nodules of plants. PGPR has beneficial impact, they colonize in the plant roots and improve crop yields and agricultural productivity and also produce some useful growth promoting growth hormones viz., IAA, Auxins, Cytokinin and Gibberellins. Methods: The bacterial isolates were screened for plant growth promoting traits such as phosphate solubilization, IAA production and siderophore production was tested qualitatively by using pikovskayas media, TSB (Tryptone Soy Broth) agar and Chrome Azurol Sulphate (CAS) blue agar respectively. Results: In present study out of the eight rhizobial isolates, five exhibited the phosphate solubilization zones, three shows negative result. However out of eight isolates five isolates produced IAA and three showed negative result. Among all isolates seven isolates were able to produce siderophore, while one showed negative result.

Modulating reactive oxygen species and ion homeostasis for combined salt and cadmium stress tolerance in Brassica campestris: The role of beneficial microbes

The land areas and crop species adversely impacted by salinity and heavy metals are growing rapidly. Current research indicates that plant growth-promoting microorganisms offer an environmentally friendly option for improving physiological and biochemical processes in plants growing under stress conditions. The aim of the present study was to investigate the potential mitigation of simultaneous salinity and cadmium (Cd) stress in rapeseed (Brassica campestris cv. BARI Sarisha-17) by the application of Azospirillum sp. (Az), phosphate solubilizing bacteria (PSB), potassium mobilizing bacteria (KMB), and vesicular arbuscular mycorrhiza (VAM). Seeds were treated with PSB or KMB prior to sowing, whereas Az, PSB, KMB, or VAM were added as supplements during soil preparation. At 21 days after sowing, the plants were treated with a combination of salt (100 mM NaCl) and Cd (0.25 mM CdCl2), with several applications at 7-day intervals. The combination of salt and Cd stress decreased plant growth and biomass, relative water content, and photosynthetic pigment levels, while also increased electrolyte leakage, lipid peroxidation, and the generation of excess reactive oxygen species (ROS). Salt and Cd stress also impaired plant ion balances of sodium, potassium and nitrate, antioxidant defenses, and glyoxalase system activity. Application of Az, PSB, or KMB restored these parameters to unstressed levels by facilitating the scavenging of ROS, maintaining water status, restoring ion balances, enhancing plant antioxidant defenses, and increasing glyoxalase enzyme activity, while reducing methylglyoxal toxicity and improving photosynthetic activity. The application of KMB was the most effective; however, all microbe supplementations showed the ability to alleviate the damage caused by stress in rapeseed. These findings highlight the ability of soil microorganisms with plant growth-promoting properties to improve the physiological and biochemical functions of rapeseed under Cd and salt stress.

Control of inorganic and organic phosphorus molecules on microbial activity, and the stoichiometry of nutrient cycling in soils in an arid, agricultural ecosystem

Background The dynamics of carbon (C), nitrogen (N), and phosphorus (P) in soils determine their fertility and crop growth in agroecosystems. These dynamics depend on microbial metabolism, which in turn depends on nutrient availability. Farmers typically apply either mineral or organic fertilizers to increase the availability of nutrients in soils. Phosphorus, which usually limits plant growth, is one of the most applied nutrients. Our knowledge is limited regarding how different forms of P impact the ability of microbes in soils to produce the enzymes required to release nutrients, such as C, N and P from different substrates. Methods In this study, we used the arable layer of a calcareous soil obtained from an alfalfa cropland in Cuatro Cienegas, México, to perform an incubation experiment, where five different phosphate molecules were added as treatments substrates: three organic molecules (RNA, adenine monophosphate (AMP) and phytate) and two inorganic molecules (calcium phosphate and ammonium phosphate). Controls did not receive added phosphorus. We measured nutrient dynamics and soil microbial activity after 19 days of incubation. Results Different P molecules affected potential microbial C mineralization (CO2-C) and enzyme activities, specifically in the organic treatments. P remained immobilized in the microbial biomass (Pmic) regardless of the source of P, suggesting that soil microorganisms were limited by phosphorus. Higher mineralization rates in soil amended with organic P compounds depleted dissolved organic carbon and increased nitrification. The C:N:P stoichiometry of the microbial biomass implied a change in the microbial community which affected the carbon use efficiency (CUE), threshold elemental ratio (TER), and homeostasis. Conclusion Different organic and inorganic sources of P affect soil microbial community structure and metabolism. This modifies the dynamics of soil C, N and P. These results highlight the importance of considering the composition of organic matter and phosphate compounds used in agriculture since their impact on the microbial activity of the soil can also affect plant productivity.

Regenerative soil management practices no‐till and sheep grazing induce significant but contrasting short‐term changes in the vineyard soil microbiome

Societal Impact StatementWinegrape production is an essential cultural heritage and economic engine of many regions of the world. Regenerative management, which is gaining traction with industry and consumers alike, relies on soil biodiversity for agroecosystem function, reducing external inputs and increasing ecosystem resilience to climate change. We evaluated the effects of no‐till and sheep integration on vineyard soil biodiversity and soil ecosystem function. No‐till had stronger effects on microbial diversity, while sheep grazing stimulated microbial functioning. By providing a better understanding of the practices, we provide fundamental information for growers that want to embrace regenerative principles, ultimately contributing to the sustainability and resilience of the winegrape industry.Summary Regenerative management aims to optimize soil microbial function and diversity for enhanced agroecosystem functionality. Understanding the effects of management practices on soil microorganisms is crucial in the context of growing societal interest in this type of management. This study evaluated the short‐term effects of two soil conservation practices: sheep grazing and no‐till, on abundance, diversity, activity, and network complexity of prokaryotes and fungi in a vineyard soil. Four treatments were applied for 3 years: (1) grazed and tilled, (2) grazed and non‐tilled, (3) non‐grazed and tilled, and (4) non‐grazed and non‐tilled. We hypothesized that stacking of conservation practices (grazing and no‐till) would increase microbial diversity, function, and network complexity. Grazing had strong effects on microbial function, increasing the α‐glucosidase, β‐glucosidase, cellulase, phosphatase, and β‐xylosidase enzymatic activity by 82%, 48%, 61%, 39%, and 55%, respectively, compared to non‐grazed soils, while not causing significant changes in soil microbial diversity. Tillage had strong effects on soil prokaryotic and fungal diversity. For prokaryotes, significant interactions in alpha diversity were found between tillage and grazing, and between tillage and sampling location (tractor row and under vine). Fungal Shannon diversity index was higher in the subsoil (15–30 cm) while a significant interaction between depth, location, tillage, and grazing was found for the Chao‐1 index. Microbial network properties were only significantly affected by sampling depth. This study shows that the lack of disturbance in non‐tilled and non‐grazed soils resulted in a more diverse soil community, while grazing stimulated microbial function, thus showing a decoupling between diversity and function in vineyard soil ecosystems.

A "love match" score to compare root exudate attraction and feeding of the plant growth-promoting rhizobacteria Bacillus subtilis, Pseudomonas fluorescens, and Azospirillum brasilense.

The rhizosphere is the zone of soil surrounding plant roots that is directly influenced by root exudates released by the plant, which select soil microorganisms. The resulting rhizosphere microbiota plays a key role in plant health and development by enhancing its nutrition or immune response and protecting it from biotic or abiotic stresses. In particular, plant growth-promoting rhizobacteria (PGPR) are beneficial members of this microbiota that represent a great hope for agroecology, since they could be used as bioinoculants for sustainable crop production. Therefore, it is necessary to decipher the molecular dialog between roots and PGPR in order to promote the establishment of bioinoculants in the rhizosphere, which is required for their beneficial functions. Here, the ability of root exudates from rapeseed (Brassica napus), pea (Pisum sativum), and ryegrass (Lolium perenne) to attract and feed three PGPR (Bacillus subtilis, Pseudomonas fluorescens, and Azospirillum brasilense) was measured and compared, as these responses are directly involved in the establishment of the rhizosphere microbiota. Our results showed that root exudates differentially attracted and fed the three PGPR. For all beneficial bacteria, rapeseed exudates were the most attractive and induced the fastest growth, while pea exudates allowed the highest biomass production. The performance of ryegrass exudates was generally lower, and variable responses were observed between bacteria. In addition, P. fluorescens and A. brasilense appeared to respond more efficiently to root exudates than B. subtilis. Finally, we proposed to evaluate the compatibility of each plant-PGPR couple by assigning them a "love match" score, which reflects the ability of root exudates to enhance bacterial rhizocompetence. Taken together, our results provide new insights into the specific selection of PGPR by the plant through their root exudates and may help to select the most effective exudates to promote bioinoculant establishment in the rhizosphere.

Combined Effects of Nitrogen Addition and Warming on Shrub Growth and Nutrient Uptake through Microbially Mediated Soil Fertility

Plant restoration strategies are ubiquitously employed for the purposes of soil and water conservation and ecological improvement in forest ecosystems. Despite N and temperature being acknowledged as pivotal factors affecting plant restoration outcomes, their effects on soil fertility, microbial communities, and shrub biomass remain underexplored, particularly in the loess hilly regions of China. Here, we examined the growth patterns and nutrient acquisition abilities of three shrub species, Periploca sepium, Amorpha fruticosa, and Vitex negundo, along with the attendant alterations in soil properties and microbial community composition under controlled greenhouse conditions. Specifically, we imposed three levels of N fertilization (200, 400, and 600 kg ha−1; designated as N1, N2, and N3, respectively) and temperature regimes (18–23, 25–30, and 32–37 °C; labeled T1, T2, and T3, respectively). The results indicated a significant interplay between the combination of N fertilization and temperature significantly affecting shrub growth. Optimal growth conditions, as evidenced by the highest dry biomass accumulation, were identified as N3T1 for A. fruticosa, N1T1 for P. sepium, and N2T2 for V. negundo, with these conditions differentially influencing roots, stems, and leaves. Furthermore, soil microorganisms also responded significantly to the N fertilization and temperature. However, this was largely dependent on shrub species and soil nutrients. For A. fruticosa under N3T1 conditions, Actinobacteria and Basidiomycota abundances correlated strongly with soil C, N, and P contents, while leaf N uptake significantly correlated with the structure of both bacterial and fungal communities. For P. sepium at N1T1, Acidobacteriota was dominant in response to soil N and C, while leaf C uptake and leaf and stem N uptake positively correlated with bacterial and fungal communities, respectively. For V. negundo at N2T2, Chloroflexi had the greatest abundance, responding to the greatest variation in soil N and C, while its stem N uptake was significantly related to the structure of the fungal communities. Thus, our findings underscored the intricate interplay between abiotic factors, shrub growth, soil fertility, and microbial community dynamics, providing insights into the optimization of plant restoration efforts in ecologically sensitive regions.