Engineering the plant microbiota in the context of the theory of ecological communities

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.

Zinc oxide nanoparticles enhance plasmid transfer among growth-promoting endophytes in Arabidopsis thaliana

Nanoparticles (NPs) hold great promise for agricultural applications, yet their potential impact on exogenous gene transfer within plant remains poorly understood. In this study, we utilized the non-conjugative plasmid pCAMBIA1300, harboring the bialaphos resistance (bar) gene expressed in plant and the kanamycin resistance (kanR) gene as selectable marker in bacteria. Our results revealed a significant increase in the transfer of plasmid (via carrier Escherichia coli DH5α), both intra- and inter-species within the endophyte, when Arabidopsis thaliana was exposed to environmentally relevant level of zinc oxide (ZnO) NPs at a concentration of 0.7 μg/mL throughout its lifespan. Intriguingly, the plasmid exhibited selective transfer to growth-promoting endophytes, such as Enterobacter, Serratia, and Achromobacter, with the presence of ZnO NPs expanding the pool of potential recipients. This result is due to the facilitation of an endophytic and mutualistic lifestyle of invasive E. coli DH5α and the enrichment of beneficial bacteria aided by ZnO NPs. The plant's descendant generations did not express the bar gene, and the endophytes carrying the exogenous plasmid did not transmit it to sub sequent generation. This research provides crucial insights for assessing the potential risks associated with gene contamination and ensuring the safe and sustainable use of NPs in agriculture.

From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.

Microbial inoculants with higher capacity to colonize soils improved wheat drought tolerance

Microbial inoculants have gained increasing attention worldwide as an eco-friendly solution for improving agriculture productivity. Several studies have demonstrated their potential benefits, such as enhanced resistance to drought, salinity, and pathogens. However, the beneficial impacts of inoculants remain inconsistent. This variability is attributed to limited knowledge of the mechanisms by which microbial inoculants affect crop growth and a lack of ecological characteristics of these inoculants that limit our ability to predict their beneficial effects. The first important step is believed to be the evaluation of the inoculant's ability to colonize new habitats (soils and plant roots), which could provide crops with beneficial functions and improve the consistency and efficiency of the inoculants. In this study, we aimed to investigate the impact of three microbial inoculants (two bacterial: P1 and P2, and one fungal: P3) on the growth and stress responses of three wheat varieties in two different soil types under drought conditions. Furthermore, we investigated the impact of microbial inoculants on soil microbial communities. Plant biomass and traits were measured, and high-throughput sequencing was used to characterize bulk and rhizosphere soil microbiomes after exposure to drought stress. Under drought conditions, plant shoot weight significantly increased (11.37%) under P1 treatments compared to uninoculated controls. In addition, total nitrogen enzyme activity increased significantly under P1 in sandy soil but not in clay soil. Importantly, network analyses revealed that P1, consisting of Bacillus paralicheniformis and Bacillus subtilis, emerged as the keystone taxa in sandy soil. Conversely, P2 and P3 failed to establish as keystone taxa, which may explain their insignificant impact on wheat performance under drought conditions. In conclusion, our study emphasizes the importance of effective colonization by microbial inoculants in promoting crop growth under drought conditions. Our findings support the development of microbial inoculants that robustly colonize plant roots for improved 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.

Plant species shape the bacterial communities on the phyllosphere in a hyper-arid desert

Microorganisms are an important component of global biodiversity. However, they are vulnerable to hyper-arid climates in desert regions. Xerophytes are desert vegetation with unique biodiversity. However, little is known about the identities and communities of phyllosphere epiphytic microorganisms inhabiting the xerophyte leaf surface in the hot and dry environment. The diversity and community composition of phyllosphere epiphytes on different desert plants in Gansu, China, was investigated using the next-generation sequencing technique, revealing the diversity and community composition of the phyllosphere epiphytic bacteria associated with desert xerophytes. In addition, the ecological functions of the bacterial communities were investigated by combining the sequence classification information and prokaryotic taxonomic function annotation (FAPROTAX). This study determined the phyllosphere bacterial community composition, microbial interactions, and their functions. Despite harsh environments in the arid desert, we found that there are still diverse epiphytic bacteria on the leaves of desert plants. The bacterial communities mainly included Actinobacteria (52.79%), Firmicutes (31.62%), and Proteobacteria (12.20%). Further comparisons revealed different microbial communities, including Firmicutes at the phylum and Paenibacillaceae at the family level, in the phyllosphere among different plants, suggesting that the host plants had strong filter effects on bacteria. Co-occurrence network analysis revealed positive relationships were dominant among different bacterial taxa. The abundance of Actinobacteria and Proteobacteria was positively correlated, demonstrating their mutual relationship. On the other hand, the abundance of Firmicutes was negatively correlated, which suggested that they inhibit the growth of other bacterial taxa. FAPROTAX prediction revealed that chemoheterotrophy (accounting for 39.02% of the community) and aerobic chemoheterotrophy (37.01%) were the main functions of the leaf epiphytic bacteria on desert plants. This study improves our understanding of the community composition and ecological functions of plant-associated microbial communities inhabiting scattered niches in the desert ecosystem. In addition, the study provides insight into the biodiversity assessment in the desert region.

Biological Disease Control by Beneficial (Micro)Organisms: Selected Breakthroughs in the Past 50 Years

Biological control of plant disease by beneficial (micro)organisms is one of the main tools available to preserve plant health within the wider context of One Health and in line with the goals of the Agenda 2030 for Sustainable Development. The commercial development of biocontrol agents, together with a new perspective on the resident microbial community, all supported by innovative "omics" technologies, continues to gain in prominence in plant pathology, addressing the need to feed the increasing world population and to assure safe and secure access to food. The present review considers selected advances within the last 50 years, highlighting those that can be considered as breakthroughs for the biological control research field. Selected examples of successful biocontrol agents and strategies are reported, including the history of the progress in researching Trichoderma isolates as commercial biocontrol agents, the exploitation of mycoviruses to confer hypovirulence to plant pathogenic fungi, the role of microbial communities in the suppressiveness of soils, and evolving approaches including the establishment of synthetic microbial communities.

The forecasting power of the microbiome

Microorganisms are informative biological integrators of past and present environmental abiotic and biotic conditions. At the same time, they are directly involved in ecosystem processes. Unfortunately, the complexity of microbial communities has so far resulted in most studies being descriptive. Here, we suggest that signals in the microbiome data can be used to forecast future ecosystem processes. The combination of omics with various statistical learning approaches, selected based on accuracy-interpretability and bias-variance trade-offs, will be key to attain this goal, as exemplified by recent studies. The time is ripe for microbial ecologists to fully exploit the forecasting power of microbiomes.

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.

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.

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.

Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health

Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.

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.

Exploiting Beneficial Pseudomonas spp. for Cannabis Production

Among the oldest domesticated crops, cannabis plants (Cannabis sativa L., marijuana and hemp) have been used to produce food, fiber, and drugs for thousands of years. With the ongoing legalization of cannabis in several jurisdictions worldwide, a new high-value market is emerging for the supply of marijuana and hemp products. This creates unprecedented challenges to achieve better yields and environmental sustainability, while lowering production costs. In this review, we discuss the opportunities and challenges pertaining to the use of beneficial Pseudomonas spp. bacteria as crop inoculants to improve productivity. The prevalence and diversity of naturally occurring Pseudomonas strains within the cannabis microbiome is overviewed, followed by their potential mechanisms involved in plant growth promotion and tolerance to abiotic and biotic stresses. Emphasis is placed on specific aspects relevant for hemp and marijuana crops in various production systems. Finally, factors likely to influence inoculant efficacy are provided, along with strategies to identify promising strains, overcome commercialization bottlenecks, and design adapted formulations. This work aims at supporting the development of the cannabis industry in a sustainable way, by exploiting the many beneficial attributes of Pseudomonas spp.

Predictive microbial-based modelling of wheat yields and grain baking quality across a 500km transect in Québec

Crops yield and quality are difficult to predict using soil physico-chemical parameters. Because of their key roles in nutrient cycles, we hypothesized that there is an untapped predictive potential in the soil microbial communities. To test our hypothesis, we sampled soils across 80 wheat fields of the province of Quebec at the beginning of the growing season in May-June. We used a wide array of methods to characterize the microbial communities, their functions, and activities, including: 1) amplicon sequencing, 2) real-time PCR quantification, and 3) community-level substrate utilization. We also measured grain yield and quality at the end of the growing season, and key soil parameters at sampling. The diversity of fungi, the abundance of nitrification genes, and the use of specific organic carbon sources were often the best predictors for wheat yield and grain quality. Using 11 or less parameters, we were able to explain 64 to 90% of the variation in wheat yield and grain and flour quality across the province of Quebec. Microbial-based regression models outperformed basic soil-based models for predicting wheat quality indicators. Our results suggest that the measurement of microbial parameters early in the season could help predict accurately grain quality and quantity.

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.