Organic agricultural practice enhances arbuscular mycorrhizal symbiosis in correspondence to soil warming and altered precipitation patterns

The stress history of soil bacteria under organic farming enhances the growth of wheat seedlings

The effects of stress factors associated with climate change and agricultural management practices on microorganisms are often studied separately, and it remains to be determined how these factors impact the soil microbiome and, subsequently, plant growth characteristics. The aim of this study was to understand how the historical climate and agriculture to which soil microbes have been exposed can influence the growth characteristics of wheat seedlings and their associated bacterial communities. We collected soil from organic and conventional fields with different histories of climate conditions to extract microbes to inoculate wheat seeds under agar-based cultivation conditions. Within a growth period of 8 days, we monitored germination rates and time as well as seedling above-ground biomass and their associated bacterial communities. The results showed a positive interaction between conventional farming practices and an ambient climate for faster and higher germination rates. We demonstrate that soil microbial extracts from organic farming with experience of the future climate significantly enhanced above-ground biomass along with the diversity of bacterial communities associated with seedlings than other treatments. Such findings support the idea that organic agricultural practices not only mitigate the adverse effects of climate change but also promote the diversity of seedling-associated bacteria.

Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation

Open-cast mining leads to the loss of naturally developed soils and their ecosystem functions and services. Soil restoration after mining aims to restore the agricultural productivity in which the functions of the fungal community play a crucial role. Whether fungi reach a comparable functional state as in the soil before mining within half a century of recultivation is still unanswered. Here, we characterised the soil fungal community using ITS amplicon Illumina sequencing across a 52-year chronosequence of agricultural recultivation after open-cast mining in northern Europe. Both taxonomic and functional community composition showed profound shifts over time, which could be attributed to the changes in nutrient status, especially phosphorus availability. However, taxonomic composition did not reach the pre-mining state, whereas functional composition did. Importantly, we identified a positive development of arbuscular mycorrhizal root fungal symbionts after the initial three years of alfalfa cultivation, followed by a decline after conversion to conventional farming, with arbuscular mycorrhizal fungi being replaced by soil saprobes. We conclude that appropriate agricultural management can steer the fungal community to its functional pre-mining state despite stochasticity in the reestablishment of soil fungal communities. Nonetheless, conventional agricultural management results in the loss of plant symbionts, favouring non-symbiotic fungi.

Elevated CO2 and temperature increase arbuscular mycorrhizal fungal diversity, but decrease root colonization, in maize and wheat

Anthropogenic climate change threatens ecosystem multifunctionality. Arbuscular mycorrhizal (AM) fungi are important symbionts that participate in mediating many ecosystem processes, and thus being potentially essential link in the chain of responses to climate change. Yet, how climate change affect the abundance and community structure of AM fungi associated with different crops remains elusive. Here, we investigated the changes in rhizosphere AM fungal communities and growth performance of maize and wheat grown in Mollisols under experimentally elevated CO2 (eCO2, +300 ppm), temperature (eT, +2 °C) and both in-combination (eCT) with open-top chambers, representing a scenario likely to occur by this century's end. The results showed that eCT significantly shifted AM fungal communities in both rhizospheres compared with control, but with no remarkable variation of the overall communities in maize rhizosphere, suggesting their greater resistance to climate change. Both eCO2 and eT increased rhizosphere AM fungal diversity, and conversely they reduced mycorrhizal colonization of both crops, probably since AM fungi had distinct adaptive strategies to climate change in rhizospheres (i.e., r-strategy) and roots (K-strategy), while the colonization intensity positively correlated with a decreased phosphorus (P)-uptake in two crops. Furthermore, co-occurrence network analysis showed that eCO2 strongly decreased the modularity and betweenness centrality of network structure than that of eT and eCT in both rhizospheres, along with the reduced network robustness, implied their destabilized communities under eCO2, while root stoichiometry (C:N and C:P ratio) was the most important factor associating with taxa in networks regardless of climate change. Overall, those findings suggest that rhizosphere AM fungal communities in wheat appear to be more sensitive to climate change than that in maize, further highlighting the importance of effective monitoring and managing AM fungi, which may allow crops to maintain critical levels of mineral nutrients (at least P) under future global change.

Development of rapid and precise approach for quantification of bacterial taxa correlated with soil health

The structure and dynamic of soil bacterial community play a crucial role in soil health and plant productivity. However, there is a gap in studying the un-/or reclaimed soil bacteriome and its impact on future plant performance. The 16S metagenomic analysis is expensive and utilize sophisticated pipelines, making it unfavorable for researchers. Here, we aim to perform (1) in silico and in vitro validation of taxon-specific qPCR primer-panel in the detection of the beneficial soil bacterial community, to ensure its specificity and precision, and (2) multidimensional analysis of three soils/locations in Egypt ('Q', 'B', and 'G' soils) in terms of their physicochemical properties, bacteriome composition, and wheat productivity as a model crop. The in silico results disclosed that almost all tested primers showed high specificity and precision toward the target taxa. Among 17 measured soil properties, the electrical conductivity (EC) value (up to 5 dS/m) of 'Q' soil provided an efficient indicator for soil health among the tested soils. The 16S NGS analysis showed that the soil bacteriome significantly drives future plant performance, especially the abundance of Proteobacteria and Actinobacteria as key indicators. The functional prediction analysis results disclosed a high percentage of N-fixing bacterial taxa in 'Q' soil compared to other soils, which reflects their positive impact on wheat productivity. The taxon-specific qPCR primer-panel results revealed a precise quantification of the targeted taxa compared to the 16S NGS analysis. Moreover, 12 agro-morphological parameters were determined for grown wheat plants, and their results showed a high yield in the 'Q' soil compared to other soils; this could be attributed to the increased abundance of Proteobacteria and Actinobacteria, high enrichment in nutrients (N and K), or increased EC/nutrient availability. Ultimately, the potential use of a taxon-specific qPCR primer-panel as an alternative approach to NGS provides a cheaper, user-friendly setup with high accuracy.

Fungal communities in soils under global change

Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO₂ concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology 103: 1-24. doi: 10.3114/sim.2022.103.01.

Distinct effects of host and neighbour tree identity on arbuscular and ectomycorrhizal fungi along a tree diversity gradient

Plant diversity and plant-related ecosystem functions have been important in biodiversity-ecosystem functioning studies. However, biotic interactions with mycorrhizal fungi have been understudied although they are crucial for plant-resource acquisition. Here, we investigated the effects of tree species richness and tree mycorrhizal type on arbuscular (AMF) and ectomycorrhizal fungal (EMF) communities. We aimed to understand how dissimilarities in taxa composition and beta-diversity are related to target trees and neighbours of the same or different mycorrhizal type. We sampled a tree diversity experiment with saplings (~7 years old), where tree species richness (monocultures, 2-species, and 4-species mixtures) and mycorrhizal type were manipulated. AMF and EMF richness significantly increased with increasing tree species richness. AMF richness of mixture plots resembled that of the sum of the respective monocultures, whereas EMF richness of mixture plots was lower compared to the sum of the respective monocultures. Specialisation scores revealed significantly more specialised AMF than EMF suggesting that, in contrast to previous studies, AMF were more specialised, whereas EMF were not. We further found that AMF communities were little driven by the surrounding trees, whereas EMF communities were. Our study revealed drivers of mycorrhizal fungal communities and further highlights the distinct strategies of AMF and EMF.

Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes

The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.