Specific microbiome signatures under the canopy of Mediterranean shrubs

Impact of soil legacy on plant-soil feedback in grasses and legumes through beneficial and pathogenic microbiota accumulation

Plants shape their surrounding soil, influencing subsequent plant growth in a phenomenon known as plant-soil feedback (PSF). This feedback is driven by chemical and microbial legacies. Here, we cultivated six crops from two functional groups, i.e., three grasses (Lolium, Triticum, and Zea) and three legumes (Glycine, Lens, and Medicago), to condition a living soil. Subsequently, the same species were sown as response plants on conspecific and heterospecific soils. We employed high-throughput sequencing in tandem with soil chemistry, including total organic matter, pH, total nitrogen, electrical conductivity, phosphorus, and macro and micro-nutrients. Our results showed that Glycine exhibited the strongest negative PSF, followed by Triticum and Zea, while Lolium displayed low feedback. Conversely, Lens demonstrated robust positive PSF, with Medicago exhibiting slight positive feedback. Soil chemistry significance indicated only higher Cl content in Triticum soil, while Lens displayed higher Zn and Mn contents. Microbial diversity exhibited no significant variations among the six soils. Although conditioning influenced the abundance of functionally important microbial phyla associated with each plant, no specificity was observed between the two functional groups. Moreover, each crop conditioned its soil with a substantial proportion of fungal pathogens. However, co-occurrence analysis revealed a strong negative correlation between all crop's biomass and fungal pathogens, except Glycine, which exhibited a strong negative correlation with mutualists such as Arthrobacter and Bacillus. This underscores the complexity of predicting PSFs, emphasizing the need for a comprehensive understanding of plant interactions with both pathogens and mutualists, rather than focusing solely on host-specific pathogens.

Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA

Nutrient deficiency, natural enemies and litter autotoxicity have been proposed as possible mechanisms to explain species-specific negative plant-soil feedback (PSF). Another potential contributor to negative PSF is the plant released extracellular self-DNA during litter decay. In this study, we sought to comprehensively investigate these hypotheses by using Arabidopsis thaliana (L.) Heynh as a model plant in a feedback experiment. The experiment comprised a conditioning phase and a response phase in which the conditioned soils underwent four treatments: (i) addition of activated carbon, (ii) washing with tap water, (iii) sterilization by autoclaving, and (iv) control without any treatment. We evaluated soil chemical properties, microbiota by shotgun sequencing and the amount of A. thaliana extracellular DNA in the differently treated soils. Our results showed that washing and sterilization treatments mitigated the negative PSF effect. While shifts in soil chemical properties were not pronounced, significant changes in soil microbiota were observed, especially after sterilization. Notably, plant biomass was inversely associated with the content of plant self-DNA in the soil. Our results suggest that the negative PSF observed in the conditioned soil was associated to increased amounts of soilborne pathogens and plant self-DNA. However, fungal pathogens were not limited to negative conditions, butalso found in soils enhancing A.thaliana growth. In-depth multivariate analysis highlights that the hypothesis of negative PSF driven solely by pathogens lacks consistency. Instead, we propose a multifactorial explanation for the negative PSF buildup, in which the accumulation of self-DNA weakens the plant's root system, making it more susceptible to pathogens.

Shrub expansion raises both aboveground and underground multifunctionality on a subtropical plateau grassland: coupling multitrophic community assembly to multifunctionality and functional trade-off

Introduction

Shrubs have expanded into grasslands globally. However, the relative importance of aboveground and underground diversity and the relative importance of underground community assembly and diversity in shaping multifunctionality and functional trade-offs over shrub expansion remains unknown.

Methods

In this study, aboveground and underground multitrophic communities (abundant and rare archaea, bacteria, fungi, nematodes, and protists) and 208 aboveground and underground ecosystem properties or indicators were measured at three stages (Grass, Mosaic, Shrub) of shrub expansion on the Guizhou subtropical plateau grassland to study multifunctionality and functional trade-offs.

Results

The results showed that shrub expansion significantly enhanced aboveground, underground, and entire ecosystem multifunctionality. The functional trade-off intensities of the aboveground, underground, and entire ecosystems showed significant V-shaped changes with shrub expansion. Shrub expansion improved plant species richness and changed the assembly process and species richness of soil abundant and rare subcommunities. Plant species diversity had a greater impact on multifunctionality than soil microbial diversity by more than 16%. The effect of plant species diversity on functional trade-offs was only one-fifth of the effect of soil microbial diversity. The soil microbial species richness did not affect multifunctionality, however, the assembly process of soil microbial communities did. Rather than the assembly process of soil microbial communities, the soil microbial species richness affected functional trade-offs.

Discussion

Our study is the first to couple multitrophic community assemblies to multifunctionality and functional trade-offs. Our results would boost the understanding of the role of aboveground and underground diversity in multifunctionality and functional trade-offs.

Potential of Biochar as a Peat Substitute in Growth Media for Lavandula angustifolia, Salvia rosmarinus and Fragaria × ananassa

Peat has long been the primary substrate for the production of ornamental and horticultural plants in pots. Today, peat is no longer considered a renewable resource due to its very lengthy regeneration time. Biochar, a solid by-product of biomass pyrolysis, has been proposed as an agricultural soil amendment. We investigated the effects of two types of biochar, namely biochar from pruning wood waste and biochar activated with wood vinegar ("smoked biochar"), on two ornamental plants (Lavandula angustifolia and Salvia rosmarinus) and on strawberries (Fragaria × ananassa). For both types of biochar, we measured the following parameters: the pH, density, electrical conductivity, humidity, calcium carbonate, total carbon, nitrogen, potassium, calcium, magnesium, sodium, and water retention. For peat, we measured the following parameters: the pH, electrical conductivity, total carbon, and total nitrogen. Our results showed an overall increase in plant growth, particularly in L. angustifolia when using 10% and 50% biochar concentrations and a 10% concentration of biochar activated with wood vinegar. In S. rosmarinus, we observed a slight increase in the total plant weight with the application of 10% smoked biochar (biochar activated with wood vinegar). Finally, in F. × ananassa, we observed an increase in the plant weight and fruit production when 10% biochar was applied. On the other hand, when high concentrations of biochar (50% and 100%) and especially smoked biochar were applied, we observed a significant reduction in the growth of all plants. We concluded that biochar and biochar activated with wood vinegar showed remarkable biological activity with marked phytotoxicity at high concentrations. They promoted plant growth when applied diluted and their use as partial peat substitutes could help support more sustainable horticultural practices.

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.

Changes in grassland soil types lead to different characteristics of bacterial and fungal communities in Northwest Liaoning, China

Introduction

Soil microbial communities are critical in regulating grassland biogeochemical cycles and ecosystem functions, but the mechanisms of how environmental factors affect changes in the structural composition and diversity of soil microbial communities in different grassland soil types is not fully understood in northwest Liaoning, China.

Methods

We investigated the characteristics and drivers of bacterial and fungal communities in 4 grassland soil types with 11 sites across this region using high-throughput Illumina sequencing.

Results and Discussion

Actinobacteria and Ascomycota were the dominant phyla of bacterial and fungal communities, respectively, but their relative abundances were not significantly different among different grassland soil types. The abundance, number of OTUs, number of species and diversity of both bacterial and fungal communities in warm and temperate ecotone soil were the highest, while the warm-temperate shrub soil had the lowest microbial diversity. Besides, environmental factors were not significantly correlated with soil bacterial Alpha diversity index. However, there was a highly significant negative correlation between soil pH and Shannon index of fungal communities, and a highly significant positive correlation between plant cover and Chao1 index as well as Observed species of fungal communities. Analysis of similarities showed that the structural composition of microbial communities differed significantly among different grassland soil types. Meanwhile, the microbial community structure of temperate steppe-sandy soil was significantly different from that of other grassland soil types. Redundancy analysis revealed that soil total nitrogen content, pH and conductivity were important influencing factors causing changes in soil bacterial communities, while soil organic carbon, total nitrogen content and conductivity mainly drove the differentiation of soil fungal communities. In addition, the degree of connection in the soil bacterial network of grassland was much higher than that in the fungal network and soil bacterial and fungal communities were inconsistently limited by environmental factors. Our results showed that the microbial community structure, composition and diversity of different grassland soil types in northwest Liaoning differed significantly and were significantly influenced by environmental factors. Microbial community structure and the observation of soil total nitrogen and organic carbon content can predict the health changes of grassland ecosystems to a certain extent.

Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns

Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU.

Effects of Cinnamomum camphora coppice planting on soil fertility, microbial community structure and enzyme activity in subtropical China

Cinnamomum camphora (C. camphora) is a broad-leaved evergreen tree cultivated in subtropical China. Currently, the use of C. camphora clonal cuttings for coppice management has become popular. However, the effects of C. camphora coppice planting on soil abiotic and biotic variances remained unclear. In this study, we collected soil from three points in the seven-year C. camphora coppice planting land: under the tree canopy (P15), between trees (P50), and abandoned land (Control) to investigate the effects of C. camphora coppice planting on soil fertility, microbial community structure and enzyme activity. The results revealed that C. camphora coppice planting significantly increased soil fertility in the point under the tree canopy (P15) and point between trees (P50), and P15 had more significant effects than P50. Meanwhile, in P15 and P50, soil bacterial, fungal alpha-diversity were improved and microbial community structures were also changed. And the changes of soil organic carbon and total nitrogen promote the transformation of soil bacterial, fungal community structures, respectively. In addition, C. camphora coppice planting significantly (p < 0.05) increased soil urease (UE), polyphenol oxidase, and peroxidase activities, while significantly decreased soil ACP activity. This study demonstrated that the C. camphora coppice planting could improve soil fertility in subtropical China, which promoted the transformation of soil microbial community from oligotrophs (K-strategist) to copiotrophs (r-strategist). Thus, this work can provide a theoretical basis for soil nutrient variation and productive management of C. camphora coppice plantation in subtropical China.

Impact of prescribed burning, mowing and abandonment on a Mediterranean grassland: A 5-year multi-kingdom comparison

Mediterranean grasslands are semi-natural, fire-prone, species-rich ecosystems that have been maintained for centuries through a combination of fire, grazing, and mowing. Over the past half century, however, grasslands have faced numerous threats, including the abandonment of traditional agro-pastoral practices. Our hypothesis was that mowing and prescribed burning are management practices potentially effective in counteracting the reduction of plant diversity triggered by land abandonment. However, the long-term effects of such management practices on plant communities and soil microbiota in Mediterranean grassland remain poorly studied. Here, we conducted a 5-year field experiment comparing prescribed fire, vegetation mowing, and abandonment in a fire-prone Mediterranean grassland in southern Italy in order to evaluate the capability of such management strategies to counteract the detrimental impacts of land abandonment on plant diversity and the associated increase of wildfire. We combined vegetation analysis and soil chemical characterization and several microbiota analyses, including microbial biomass and respiration, arthropod community, and high-throughput sequencing of bacterial and eukaryotic rRNA gene markers. Burning and mowing significantly increased plant species richness and diversity compared to abandonment plots, reducing the abundance of perennial tall grasses in favour of short-lived species. Standing litter followed the same trend, being 3.8-fold greater and largely composed of grass remains in the abandoned compared to burnt and mowed plots. In the soil, prescribed burning caused significant increase in pH, a reduction in organic carbon, total N, and cation exchange capacity. Diversity and taxonomic composition of bacterial and fungal microbiota was affected by burning and mowing treatments. Abandonment caused shifts of microbiota towards a fungal-dominated system, composed of late successional fungi of the Basidiomycota. Fast-growing and putative fungal pathogens were more abundant under burnt and mowed treatments. Soil arthropods were influenced by vegetation and microbiota changes, being strongly reduced in mowed plots. Our study demonstrated that grassland abandonment promotes the spread of tall grasses, reducing plant diversity and increasing the risk of wildfire, while prescribed burning and mowing are effective in counteracting such negative effects.