Response of the wheat mycobiota to flooding revealed substantial shifts towards plant pathogens

Rainfall extremes are intensifying as a result of climate change, leading to increased flood risk. Flooding affects above- and belowground ecosystem processes, representing a substantial threat to crop productivity under climate change. Plant-associated fungi play important roles in plant performance, but their response to abnormal rain events is unresolved. Here, we established a glasshouse experiment to determine the effects of flooding stress on the spring wheat-mycobiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages, such as tillering, booting and flowering. We assessed the wheat mycobiota response to flooding in three soil-plant compartments (phyllosphere, roots and rhizosphere) using metabarcoding. Key soil and plant traits were measured to correlate physiological plant and edaphic changes with shifts in mycobiota structure and functional guilds. Flooding reduced plant fitness, and caused dramatic shifts in mycobiota assembly across the entire plant. Notably, we observed a functional transition consisting of a decline in mutualist abundance and richness with a concomitant increase in plant pathogens. Indeed, fungal pathogens associated with important cereal diseases, such as Gibberella intricans, Mycosphaerella graminicola, Typhula incarnata and Olpidium brassicae significantly increased their abundance under flooding. Overall, our study demonstrate the detrimental effect of flooding on the wheat mycobiota complex, highlighting the urgent need to understand how climate change-associated abiotic stressors alter plant-microbe interactions in cereal crops.Peer Reviewe

Establishing a new baseline for monitoring the status of EU Spatial Data Infrastructure: Experiences and conclusions from INSPIRE 2019 monitoring and reporting

The INSPIRE Directive, which aims to establish a pan-European Spatial Data Infrastructure for the purposes of EU environmental policies, requires Member States to monitor and report on the implementation status on an annual basis. The way the INSPIRE monitoring and reporting process was performed in 2019 was driven by Commission Implementing Decision (EU) 2019/1372, which introduced the automated calculation of 19 new indicators through the direct use of the INSPIRE Geoportal and the INSPIRE Reference Validator to process the metadata harvested from Member States discovery services. These indicators are grouped into 5 categories: availability of spatial data and services, conformity of metadata, conformity of spatial data sets, accessibility of spatial data sets through view and download services, and conformity of network services. Most indicators are calculated as a percentage, thus providing a direct measure of performance and allowing also country-by-country comparisons. For each indicator, this report provides a detailed description of the calculation method, the values achieved for all Member States and some summary statistics to capture the overall performance trends. The results show that the status of INSPIRE implementation is very heterogeneous across the EU, with some countries performing well and some others still lagging behind. However, after 13 years from the entry into force of the Directive, there is no single country which has yet achieved full implementation according to the roadmap. The accessibility of data sets through view or download services is on average only about 30%, while the conformity of metadata, data sets and network services varies between 30% and 45% on average. In addition to providing an objective snapshot of the current status of INSPIRE implementation, the results of 2019 monitoring and reporting represent a reliable baseline to monitor the evolution of the EU Spatial Data Infrastructure and its contribution to the European Green Deal data space in the years to come.JRC.B.6-Digital Econom

Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota

BACKGROUND: The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. RESULTS: Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group ‘KD4-96’ (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species’ core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae ‘WD2101 soil group’. CONCLUSIONS: Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies

Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology

Soil microorganisms regulate element cycling and plant nutrition, mediate co-existence of neighbors, and stabilize plant communities. Many of these effects are dependent upon environmental conditions and, in particular, on nutrient quality and availability in soils. In this context, we set up a pot experiment in order to examine the combined effects of soil nutrient availability and microbial communities on plant-soil interactions and to investigate assemblage rules for soil bacterial communities under changed nutrient conditions. Four gamma-sterilized soils, strongly differing in their nutrient contents, were obtained from different fertilization treatments of a centenary field experiment and used to grow communities of grassland plants. The sterilized soils were either self- or cross-inoculated with microbial consortia from the same four soils. Molecular fingerprinting analyses were carried out at several time points in order to identify drivers and underlying processes of microbial community assemblage. We observed that the bacterial communities that developed in the inoculated sterilized soils differed from those in the original soils, displaying dynamic shifts over time. These shifts were illustrated by the appearance of numerous OTUs that had not been detected in the original soils. The community patterns observed in the inoculated treatments suggested that bacterial community assembly was determined by both niche-mediated and stochastic-neutral processes, whereby the relative impacts of these processes changed over the course of the vegetation season. Moreover, our experimental approach allowed us not only to evaluate the effects of soil nutrients on plant performance but also to recognize a negative effect of the microbial community present in the soil that had not been fertilized for more than 100 years on plant biomass. Our findings demonstrate that soil inoculation-based approaches are valid for investigating plant-soil-microbe interactions and for examining rules that shape soil microbial community assemblages under variable ecological conditions

Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota

Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.Peer Reviewe

Do soil-borne fungal pathogens mediate plant diversity–productivity relationships? Evidence and future opportunities

From the establishment of the first biodiversity experiments in the 1990s, studies have consistently reported positive relationships between plant diversity and productivity in grasslands. However, the predominant hypotheses that may explain this pattern have changed. Initially, there was a strong focus on plant–plant interactions such as facilitation and resource partitioning, but the results from the first experiments that manipulated soil communities have led to a paradigm shift. In the current view on mechanisms that drive plant diversity–productivity relationships, fungal pathogen-induced reductions of plant productivity at low diversity play an important role. This role rests on two assumptions: the effects of pathogens (a) are plant-species specific (i.e. not all plant species are affected equally by a fungal pathogen) and (b) display negative density dependence (i.e. decrease with decreasing host plant density and hence, with increasing plant species richness). Here, we review the empirical evidence for these two assumptions. In the biodiversity literature, this is mainly based on indirect approaches, such as soil sterilization, plant–soil feedback studies and plant biomass patterns. The identification and functional characterization of the fungal pathogens that actually drive the plant diversity–productivity relationship have only recently started. Synthesis. Nevertheless, these studies, together with studies on plant–pathogen interactions in agricultural crops and forests, clearly suggest host-specific, negative density-dependent effects of fungal pathogens are common. Moreover, recent studies suggest that the reduced impact of pathogens at high plant diversity depends not just on host density but also on effects of neighbouring (non-host) plant species on the pathogen. Understanding how neighbouring plants affect the interactions between a pathogen and its host plants and disentangling the role of plant–pathogen interactions from other mechanisms potentially driving diversity–productivity relationships are important future challenges.</p

Drivers of total and pathogenic soil-borne fungal communities in grassland plant species

Soil-borne fungi are considered important drivers of plant community structure, diversity and ecosystem process in terrestrial ecosystems. Yet, our understanding of their identity and belowground association with different plant species in natural ecosystems such as grasslands is limited. We identified the soil-borne fungal communities in the roots of a range of plant species representing the main families occurring in natural grasslands using next generation sequencing of the ITS1 region, alongside FUNGuild and a literature review to determine the ecological role of the fungal taxa detected. Our results show clear differences in the total and the pathogenic soil-borne fungal communities between the two main plant functional groups in grasslands (grasses and forbs) and between species within both functional groups, which could to a large extent be explained by plant phylogenetic structure. In addition, our results show that drought can increase the relative abundance of pathogenic fungi. These findings on a range of plant species provide a baseline for future studies revealing the importance of belowground plant-fungal interactions in diverse natural grasslands.</p

Effect of plant-related predictors and drought on sixteen grassland communities grown as monocultures

We explored the total and pathogenic fungi community of sixteen grassland species affiliated to two plant functional groups (grass and forb) grown as monocultures to assess which plant-related predictor, such as plant identity, plant functional group and host phylogeny was better in explaining the variation in fungal richness and community structure among the plants studied. Moreover, we investigated the response of the fungal community to drought. Briefly, the experiment consisted of plant communities comprised of the following plant species: the grasses Agrostis stolonifera, Anthoxanthum odoratum, Arrhenatherum elatius, Briza media, Festuca pratensis, Festuca rubra, Phleum pratense, Trisetum flavescens and forbs Achillea millefolium, Centaurea jacea, Galium mollugo, Leontodon hispidus, Leucanthemum vulgare, Prunella vulgaris, Ranunculus repens, and Sanguisorba officinalis. The plant species were grown in plot of 70 cm x 70 cm, with six replicates for each plant species, leading to a total of 96 plots. These plots were distributed in 3 blocks, which contained 2 plots (2 replicates) of each of the sixteen species per block. In the growing season of the fourth year (10 June -14 July 2017) a drought treatment was set up in half of the replicates using rainout shelters and supplementary watering of control plots

Effect of plant-related predictors and drought on sixteen grassland communities grown as monocultures

We explored the total and pathogenic fungi community of sixteen grassland species affiliated to two plant functional groups (grass and forb) grown as monocultures to assess which plant-related predictor, such as plant identity, plant functional group and host phylogeny was better in explaining the variation in fungal richness and community structure among the plants studied. Moreover, we investigated the response of the fungal community to drought. Briefly, the experiment consisted of plant communities comprised of the following plant species: the grasses Agrostis stolonifera, Anthoxanthum odoratum, Arrhenatherum elatius, Briza media, Festuca pratensis, Festuca rubra, Phleum pratense, Trisetum flavescens and forbs Achillea millefolium, Centaurea jacea, Galium mollugo, Leontodon hispidus, Leucanthemum vulgare, Prunella vulgaris, Ranunculus repens, and Sanguisorba officinalis. The plant species were grown in plot of 70 cm x 70 cm, with six replicates for each plant species, leading to a total of 96 plots. These plots were distributed in 3 blocks, which contained 2 plots (2 replicates) of each of the sixteen species per block. In the growing season of the fourth year (10 June -14 July 2017) a drought treatment was set up in half of the replicates using rainout shelters and supplementary watering of control plots