Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana

History of a model plant growth-promoting rhizobacterium, Bacillus velezensis GB03: from isolation to commercialization

Bacillus velezensis strain GB03 is a Gram-positive rhizosphere bacterium known for its ability to promote plant growth and immunity. This review provides a comprehensive overview of the research on GB03 from its initial discovery in Australian wheat fields in 1971 to its current applications. Recognized as a model plant growth-promoting rhizobacterium (PGPR), GB03 has exhibited outstanding performance in enhancing the growth and protection of many crop plants including cucumber, pepper, wheat, barley, soybean, and cotton. Notably, GB03 has been reported to elicit plant immune response, referred to as induced systemic resistance (ISR), against above-ground pathogens and insect pests. Moreover, a pivotal finding in GB03 was the first-ever identification of its bacterial volatile compounds, which are known to boost plant growth and activate ISR. Research conducted over the past five decades has clearly demonstrated the potential of GB03 as an eco-friendly substitute for conventional pesticides and fertilizers. Validating its safety, the U.S. Environmental Protection Agency endorsed GB03 for commercial use as Kodiak® in 1998. Subsequently, other compounds, such as BioYield™, were released as a biological control agent against soil-borne pathogens and as a biofertilizer, utilizing a durable spore formulation. More recently, GB03 has been utilized as a keystone modulator for engineering the rhizosphere microbiome and for eliciting microbe-induced plant volatiles. These extensive studies on GB03 underscore its significant role in sustainable agriculture, positioning it as a safe and environmentally-friendly solution for crop protection.

Inoculation with Plant Growth-Promoting Bacteria and Nitrogen Doses Improves Wheat Productivity and Nitrogen Use Efficiency

Wheat is one of the staple foods of the global population due to its adaptability to a wide range of environments. Nitrogen is one of the crucial limiting factors in wheat production and is considered a challenge to food security. Therefore, sustainable agricultural technologies such as seed inoculation with plant growth-promoting bacteria (PGPBs) can be adopted to promote biological nitrogen fixation (BNF) for higher crop productivity. In this context, the objective of the current study was to evaluate the effects of nitrogen fertilization and seed inoculations with Azospirillum brasilense, Bacillus subtilis and A. brasilense + B. subtilis on agronomic and yield attributes, grain yield, grain N accumulation, N use efficiency and applied N recovery in Brazilian Cerrado, which consists of gramineous woody savanna. The experiment was carried out in two cropping seasons in Rhodic Haplustox soil under a no-tillage system. The experiment was designed in a randomized complete block in a 4 × 5 factorial scheme, with four replications. The treatments consisted of four seed inoculations (control-without inoculation, inoculation with A. brasilense, B. subtilis and A. brasilense + B. subtilis) under five N doses (0, 40, 80, 120 and 160 kg ha^-1, applied from urea) at the wheat tillering stage. Seed co-inoculation with A. brasilense + B. subtilis increased grain N accumulation, number of spikes m^-1, grains spike^-1 and grain yield of wheat in an irrigated no-tillage system of tropical savannah, regardless of the applied N doses. Nitrogen fertilization at a dose of 80 kg ha^-1 significantly increased grain N accumulation and number of grains spikes^-1 and nitrogen use efficiency. Recovery of applied N was increased with inoculation of B. subtilis and co-inoculation of A. brasilense + B. subtilis at increasing N doses. Therefore, N fertilization can be reduced by the inclusion of co-inoculation with A. brasilense + B. subtilis in the cultivation of winter wheat under a no-tillage system of Brazilian Cerrado.

Microbes to support plant health: understanding bioinoculant success in complex conditions

A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for plant performance and health. When applied in agriculture to improve crop yield and performance, these microbes are commonly referred to as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically in the field, hampering their applicability. Invasion of the rhizosphere microbiome is a critical determinant for bioinoculant success. Invasion is a complex phenomenon that is shaped by interactions with the local, resident microbiome and the host plant. Here, we explore all of these dimensions by cross-cutting ecological theory and molecular biology of microbial invasion in the rhizosphere. We refer to the famous Chinese philosopher and strategist Sun Tzu, who believed that solutions for problems require deep understanding of the problems themselves, to review the major biotic factors determining bioinoculant effectiveness.

The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions

As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.

Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads

Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera.

IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.

Impact of biocontrol microbes on soil microbial diversity in ginger (Zingiber officinale Roscoe)

BACKGROUND

Bacteria are the most diverse and abundant group of soil organisms that influence plant growth and health. Bacillus and Trichoderma are commonly used as biological control agents (BCA) that directly or indirectly act on soil bacteria. Therefore, it is essential to understand how the applied microbes impact the indigenous microbial community before exploring their activity in the control of soilborne diseases.

RESULTS

MiSeq sequencing of the 16S rRNA gene was used to decipher the shift of rhizosphere bacterial community in ginger (Zingiber officinale Roscoe) treated with Bacillus subtilus and Trichoderma harzianum at different concentrations. The dominant phyla in treated and nontreated samples were Proteobacteria, Actinobacteria, Acidobacteria and comprised up to 54.7% of the total sequences. There were significant differences between BCA treated and nontreated samples in the bacteria community. BCA treated plants presented higher bacterial diversity than nontreated and higher dosage of BCA had a larger impact on rhizosphere microbiota, but the 'dose-response relationship' varied in different bacterial groups. Potential biomarkers at genus level were found, such as RB41, Pseudomonas, Nitrospira, Candidatus_Udaeobacter.

CONCLUSION

The combined use of Bacillus subtilus and Trichoderma harzianum could alter bacterial community structure and diversity in rhizosphere soil. BCA-microbes interactions as well as soil microbial ecology should be noticed in plant disease management. © 2021 Society of Chemical Industry.

Rhizobacteria Impact Colonization of Listeria monocytogenes on Arabidopsis thaliana Roots

In spite of its relevance as a foodborne pathogen, we have limited knowledge about Listeria monocytogenes in the environment. L. monocytogenes outbreaks have been linked to fruits and vegetables; thus, a better understanding of the factors influencing its ability to colonize plants is important. We tested how environmental factors and other soil- and plant-associated bacteria influenced L. monocytogenes' ability to colonize plant roots using Arabidopsis thaliana seedlings in a hydroponic growth system. We determined that the successful root colonization of L. monocytogenes 10403S was modestly but significantly enhanced by the bacterium being pregrown at higher temperatures, and this effect was independent of the biofilm and virulence regulator PrfA. We tested 14 rhizosphere-derived bacteria for their impact on L. monocytogenes 10403S, identifying one that enhanced and 10 that inhibited the association of 10403S with plant roots. We also characterized the outcomes of these interactions under both coinoculation and invasion conditions. We characterized the physical requirements of five of these rhizobacteria to impact the association of L. monocytogenes 10403S with roots, visualizing one of these interactions by microscopy. Furthermore, we determined that two rhizobacteria (one an inhibitor, the other an enhancer of 10403S root association) were able to similarly impact 10 different L. monocytogenes strains, indicating that the effects of these rhizobacteria on L. monocytogenes are not strain specific. Taken together, our results advance our understanding of the parameters that affect L. monocytogenes plant root colonization, knowledge that may enable us to deter its association with and, thus, downstream contamination of, food crops. IMPORTANCE Listeria monocytogenes is ubiquitous in the environment, being found in or on soil, water, plants, and wildlife. However, little is known about the requirements for L. monocytogenes' existence in these settings. Recent L. monocytogenes outbreaks have been associated with contaminated produce; thus, we used a plant colonization model to investigate factors that alter L. monocytogenes' ability to colonize plant roots. We show that L. monocytogenes colonization of roots was enhanced when grown at higher temperatures prior to inoculation but did not require a known regulator of virulence and biofilm formation. Additionally, we identified several rhizobacteria that altered the ability of 11 different strains of L. monocytogenes to colonize plant roots. Understanding the factors that impact L. monocytogenes physiology and growth will be crucial for finding mechanisms (whether chemical or microbial) that enable its removal from plant surfaces to reduce L. monocytogenes contamination of produce and eliminate foodborne illness.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.