Intermittent water stress favors microbial traits that better help wheat under drought.

Microorganisms can improve plant resistance to drought through various mechanisms, such as the production of plant hormones, osmolytes, antioxidants, and exopolysaccharides. It is, however, unclear how previous exposure to water stress affects the functional capacity of the soil microbial community to help plants resist drought. We compared two soils that had either a continuous or intermittent water stress history (WSH) for almost 40 years. We grew wheat in these soils and subjected it to water stress, after which we collected the rhizosphere soil and shotgun sequenced its metagenome. Wheat growing in soil with an intermittent WSH maintained a higher biomass when subjected to water stress. Genes related to indole-acetic acid and osmolyte production were more abundant in the metagenome of the soil with an intermittent WSH as compared to the soil with a continuous WSH. We suggest that an intermittent WSH selects traits beneficial for life under water stress.

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.

Colorful windows to the dark rhizosphere.

The dynamic and complex interactions between plant and microbiomes in the rhizosphere play a major role in the plant's health and productivities. Using interdisciplinary approaches, Behr et al. studied how farming practices can influence the rhizosphere process, offering an exciting direction for microbial manipulation to enhance agricultural productivity.

Metatranscriptomic response of the wheat holobiont to decreasing soil water content.

Crops associate with microorganisms that help their resistance to biotic stress. However, it is not clear how the different partners of this association react during exposure to stress. This knowledge is needed to target the right partners when trying to adapt crops to climate change. Here, we grew wheat in the field under rainout shelters that let through 100%, 75%, 50% and 25% of the precipitation. At the peak of the growing season, we sampled plant roots and rhizosphere, and extracted and sequenced their RNA. We compared the 100% and the 25% treatments using differential abundance analysis. In the roots, most of the differentially abundant (DA) transcripts belonged to the fungi, and most were more abundant in the 25% precipitation treatment. About 10% of the DA transcripts belonged to the plant and most were less abundant in the 25% precipitation treatment. In the rhizosphere, most of the DA transcripts belonged to the bacteria and were generally more abundant in the 25% precipitation treatment. Taken together, our results show that the transcriptomic response of the wheat holobiont to decreasing precipitation levels is stronger for the fungal and bacterial partners than for the plant.

Early season soil microbiome best predicts wheat grain quality.

Previous studies have shown that it is possible to accurately predict wheat grain quality and yields using microbial indicators. However, it is uncertain what the best timing for sampling is. For optimal usefulness of this modeling approach, microbial indicators from samples taken early in the season should have the best predictive power. Here, we sampled a field every two weeks across a single growing season and measured a wide array of microbial parameters (amplicon sequencing, abundance of N-cycle related functional genes, and microbial carbon usage) to find the moment when the microbial predictive power for wheat grain baking quality is highest. We found that the highest predictive power for wheat grain quality was for microbial data derived from samples taken early in the season (May-June), which coincides roughly with the seedling and tillering growth stages, that are important for wheat N nutrition. Our models based on LASSO regression also highlighted a set of microbial parameters highly coherent with our previous surveys, including alpha- and beta-diversity indices and N-cycle genes. Taken together, our results suggest that measuring microbial parameters early in the wheat growing season could help farmers better predict wheat grain quality.

Conventional vs. Organic Agriculture-Which One Promotes Better Yields and Microbial Resilience in Rapidly Changing Climates?

In recent years, agricultural productivity has been affected dramatically by climate-related events such as drought. On the other hand, agricultural intensification is expected to increase to satisfy the need for increased global food production. Microbes associated with soil and plants produce a range of bioactive natural products that significantly contribute to crop stress tolerance. Therefore, a better understanding of the parallel effects of agricultural management (conventional and organic croplands) and climate conditions on soil-microbe-plant interactions is crucial to maximizing the effort in engineering a plant microbiome that can better support productivity in agroecosystems. This paper provides a general overview of the major current debates on conventional and organic farming performance regarding yields, particularly under ambient and future climate conditions. With the main focus on cropland, the effect of agricultural management on soil and plant microbiomes is discussed. In addition, the advantage of incorporating microbiome-based approaches into current farming practices to ensure agricultural productivity with less adverse environmental impacts is highlighted. To enhance crop production under organic farming without massive land-use changes and expansion of farmland, the microbial-based approach can be used to ensure higher productivity, particularly under a rapidly changing climate.

A Drying-Rewetting Cycle Imposes More Important Shifts on Soil Microbial Communities than Does Reduced Precipitation.

Global changes will result in altered precipitation patterns, among which the increasing frequency of drought events has the highest deleterious potential for agriculture. Soil microbes have shown some promise to help crops adapt to drought events, but it is uncertain how crop-associated microorganisms will respond to altered precipitation patterns. To investigate this matter, we conducted a field experiment where we seeded two wheat cultivars (one resistant to water stress and the other sensitive) that were subjected to four precipitation exclusion (PE) regimes (0%, 25%, 50%, and 75% exclusion). These cultivars were sampled seven times (every 2 weeks, from May to August) within one growing season to investigate short-term microbiome responses to altered precipitation regimes and seasonality using 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. One of the most striking features of the data set was the dramatic shift in microbial community diversity, structure, and composition together with a doubling of the relative abundance of the archaeal ammonia oxidizer genus Nitrososphaera following an important drying-rewetting event. Comparatively small but significant effects of PE and wheat cultivar on microbial community diversity, composition, and structure were observed. Taken together, our results demonstrate an uneven response of microbial taxa to decreasing soil water content, which was dwarfed by drying-rewetting events, to which soil bacteria and archaea were more sensitive than fungi. Importantly, our study showed that an increase in drying-rewetting cycles will cause larger shifts in soil microbial communities than a decrease in total precipitation, suggesting that under climate changes, the distribution of precipitation will be more important than small variations in the total quantity of precipitation. IMPORTANCE Climate change will have a profound effect on the precipitation patterns of global terrestrial ecosystems. Seasonal and interannual uneven distributions of precipitation will lead to increasing frequencies and intensities of extreme drought and rainfall events, which will affect crop productivity and nutrient contents in various agroecosystems. However, we still lack knowledge about the responses of soil microbial communities to reduced precipitation and drying-rewetting events in agroecosystems. Our results demonstrated an uneven response of the soil microbiome and a dramatic shift in microbial community diversity and structure to a significant drying-rewetting event with a large increase in the relative abundance of archaeal ammonia oxidizers. These findings highlight the larger importance of rewetting of dry soils on microbial communities, as compared to decreased precipitation, with potential for changes in the soil nitrogen cycling.

The response of wheat and its microbiome to contemporary and historical water stress in a field experiment.

In a field experiment, we evaluated the impact of 37 years of contrasting water stress history on the microbial response in various plant compartments at two distinct developmental stages when four wheat genotypes were exposed to contemporary water stress. Seeds were collected and sampled at the end of the experiment to characterize endophytic and epiphytic microbial communities. Amplicon sequencing data revealed that plant development stage and water stress history were the main factors shaping the microbiome of the major plant parts in response to contemporary water limitation. Our results indicate that seeds can become colonized by divergent microbial communities within a single generation based on the initial pool of microbes as determined by historical contingencies, which was modulated by the contemporary environmental conditions and the plant genotype. Such information is essential to incorporate microbial-based strategies into conventional plant breeding to enhance plant resistance to stress.

The resistance of the wheat microbial community to water stress is more influenced by plant compartment than reduced water availability.

Drought is a serious menace to agriculture across the world. However, it is still not clear how this will affect crop-associated microbial communities. Here, we experimentally manipulated precipitation in the field for two years and compared the bacterial communities associated with leaves, roots, and rhizosphere soils of two different wheat genotypes. The bacterial 16S rRNA gene was amplified and sequenced, while 542 microorganisms were isolated and screened for their tolerance to osmotic stress. The bacterial community was not significantly affected by the precipitation manipulation treatments but differed drastically from one plant compartment to the other. Forty-four isolates, mostly bacteria, showed high levels of resistance to osmotic stress by growing in liquid medium supplemented with 30% polyethylene glycol. The Actinobacteria were overrepresented among these isolates, and in contrast to our expectation, precipitation treatments did not influence the odds of isolating osmotic stress-resistant bacteria. However, the odds were significantly higher in the leaves as compared to the roots, the rhizosphere, or the seeds. Our results suggest that isolation efforts for wheat-compatible water stress resistant bacteria should be targeted at the leaf endosphere and that short-term experimental manipulation of precipitation does not result in a more resistant community.

Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns.

Next-generation sequencing is one of the most popular and cost-effective ways of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are limited, as they result in relative abundance profiles of microbial taxa, which does not represent actual abundance in the environment. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that changes in the relative abundance of major microbial phyla do not necessarily follow the same pattern as the estimated quantitative abundance. Most of the bacterial phyla linked with the rhizosphere of plants grown in soil with no history of water stress showed enrichment patterns in their estimated absolute abundance, which was in contradiction with the trends observed in the relative abundance data. However, in the case of the fungal groups (except for Basidiomycota), such an enrichment pattern was not observed and the abundance of fungi remained relatively unchanged under different soil water stress history when estimated absolute abundance was considered. Comparing relative and estimated absolute abundances of dominant bacterial and fungal phyla, as well as their correlation with the functional processes in the rhizosphere, our results suggest that the estimated absolute abundance approach gives a different and more realistic perspective than the relative abundance approach. Such a quantification approach provides complementary information that helps to better understand the rhizosphere microbiomes and their associated ecological functional processes.

Four decades of soil water stress history together with host genotype constrain the response of the wheat microbiome to soil moisture.

There is little understanding about how soil water stress history and host genotype influence the response of wheat-associated microbiome under short-term decreases in soil moisture. To address this, we investigated how plant breeding history (four wheat genotypes; two with recognized drought resistance and two without) and soil water stress history (same wheat field soil from Saskatchewan with contrasting long-term irrigation) independently or interactively influenced the response of the rhizosphere, root and leaf bacterial and fungal microbiota to short-term decreases in soil water content (SWC). We used amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) to characterize the wheat microbiome. Fungal and bacterial communities responses to short-term decreases in SWC were mainly constrained by soil water stress history, with some smaller, but significant influence of plant genotype. One exception was the leaf-associated fungal communities, for which the largest constraint was genotype, resulting in a clear differentiation of the communities based on the genotype's sensitivity to water stress. Our results clearly indicate that soil legacy does not only affect the response to water stress of the microbes inhabiting the soil, but also of the microorganisms more closely associated with the plant tissues, and even of the plant itself.

A water stress-adapted inoculum affects rhizosphere fungi, but not bacteria nor wheat.

Here, we tested if inoculating microbial communities adapted to water stress would increase wheat resistance to water stress. Wheat plants were grown for 4 weeks in high and low diversity soils under well-watered conditions, after which they were subjected to a water stress. After another 2 weeks, the rhizospheres were inoculated with microbial communities extracted from soils with or without a history of water stress. The inoculations did not have significant effects on the plant growth, water content and catalase activity, and on the bacterial communities. However, the inoculation did successfully, though modestly, modify the fungal community, shifting the rhizosphere communities toward the inoculated communities. As hypothesized, these shifts were more pronounced and significant in the low diversity soil, and for the inoculum with a water stress history. Whereas the effects of inoculation were relatively subtle, the water stress resulted in large differences in the wheat phenotype and in both the bacterial and fungal communities. Generally, the microbial changes that followed the water stress were in large part due to shifts in the relative abundance of OTUs that were already present before the stress, rather than to the recruitment of microorganisms from the inoculum or the bulk soil.

Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing "Stress-on-Stress" Responses.

Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the "costs" of adaptation to metals affect the responses of metal-tolerant communities to other stress factors ("stress-on-stress"). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors.

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy.

Microbial community structure and functioning along metal pollution gradients.

Toxic effects of heavy metals on soil microorganisms have been confirmed in a number of laboratory studies. However, most real-field studies do not allow for strong general conclusions due to a range of problems, such as pseudoreplication and confounding factors, which are almost impossible to control for with the most commonly used polluted versus unpolluted or random sampling designs. Effects of metal contamination on soil microbial community traits were measured along 2 pollution gradients in southern Poland. Employing an experimental regression design, using 2 separate gradients, the authors aimed to control for effects of soil properties and beta-diversity of microbial communities. General microbial activity was measured as soil basal respiration rate and substrate-induced respiration, while microbial functional and structural diversity were analyzed with community-level physiological profiles and phospholipid fatty acid patterns, respectively. Metal concentrations were normalized to their toxicity and integrated in a toxicity index (TI). Microbial activity (basal and substrate-induced respiration) decreased in both gradients with increasing TI. Community-level physiological profiles for fungi correlated positively with TI, but no impact of TI on the community-level physiological profiles of bacteria was observed. The phospholipid fatty acids a:15 and i:17 were positively correlated with TI, whereas 16:1ω9 and 18:2ω9 were negatively correlated with TI. The use of 2 gradients (Olkusz and Miasteczko Slaskie) allowed the authors to reveal a clear effect of pollution on general microbial structure and activities, even though they were not able to control completely for all confounding factors. Soil pH, organic matter content, and nutrient level appeared to be at least as important as TI in determining microbial community structure and activities.