Rhizosphere Protists Change Metabolite Profiles in Zea mays

Acanthamoeba castellanii alone is not a growth promoter for Hordeum vulgare

Protists are important key players in the microbial loop and influence their environment by grazing, which leads to the return of nutrients into the soil and reduces pathogen pressure on plants. Specifically, protists on and around plant roots are important for plants' development and growth. For this study, the fourth most important crop in the world, Hordeum vulgare, was selected. Seeds of H. vulgare were inoculated with Acanthamoeba castellanii alone or with additional soil bacteria at the beginning and during the experiment. The germination of the seeds and the growth of the plants in pouches were monitored over 3 weeks. No differences were found in leaf growth, root growth, root and leaf nitrogen content or ammonia content of the liquid from the pouches. In contrast, the relative increase in root and leaf dry weight showed a small difference compared to the controls. The results of this experiment demonstrated that seed inoculation with A. castellanii alone or with additional unidentified soil bacteria did not have a major effect on the growth and development of barley. Nevertheless, small changes in plant development were detected, indicating that A. castellanii should be considered for further investigation of co-inoculations with plant growth-promoting bacteria and additional nutrients.

Differential regulation of belowground rhizospheric ecosystem by biological and chemical nitrogen supplies: implications for maize yield enhancement mechanisms

Nitrogen (N) content affects aboveground maize growth and nutrient absorption by altering the belowground rhizospheric ecosystem, impacting both yield and quality. However, the mechanisms through which different N supply methods (chemical and biological N supplies) regulate the belowground rhizospheric ecosystem to enhance maize yield remain unclear. To address this issue, we conducted a field experiment in northeast China, comprising three treatments: maize monocropping without N fertilizer application (MM), maize/alfalfa intercropping without N fertilizer application (BNF), and maize monocropping with N fertilizer application (CNS). The MM treatment represents the control, while the BNF treatment represents the biological N supply form, and CNS treatment represents the chemical N supply form. In the autumn of 2019, samples of maize and rhizospheric soil were collected to assess parameters including yield, rhizospheric soil characteristics, and microbial indicators. Both BNF and MM significantly increased maize yield and different yield components compared with MM, with no statistically significant difference in total yield between BNF and CNS. Furthermore, BNF significantly improved N by 12.61% and available N (AN) by 13.20% compared with MM. Furthermore, BNF treatment also significantly increased the Shannon index by 1.90%, while the CNS treatment significantly increased the Chao1 index by 28.1% and ACE index by 29.49%, with no significant difference between CNS and BNF. However, CNS had a more pronounced impact on structure of the rhizosphere soil bacterial community compared to BNF, inducing more significant fluctuations within the microbial network (modularity index and negative cohesion index). Regarding N transformation pathways predicted by bacterial functions, BNF significantly increased the N fixation pathway, while CNS significantly increased assimilatory nitrate reduction. In CNS, AN, NO3-N, NH4-N, assimilatory nitrate reduction, and community structure contributed significantly to maize yield, whereas in BNF, N fixation, community structure, community stability, NO3-N, and NH4-N played significant roles in enhancing maize yield. While CNS and BNF can achieve comparable maize yields in practical agricultural production, they have significantly different impacts on the belowground rhizosphere ecosystem, leading to different mechanisms of yield enhancement.

Factors driving the halophyte rhizosphere bacterial communities in coastal salt marshes

Introduction

Root-associated microorganisms promote plant growth and provide protection from stresses. Halophytes are the fundamental components maintaining ecosystem functions of coastal salt marshes; however, it is not clear how their microbiome are structured across large spatial scales. Here, we investigated the rhizosphere bacterial communities of typical coastal halophyte species (Phragmites australis and Suaeda salsa) in temperate and subtropical salt marshes across 1,100 km in eastern China.

Methods

The sampling sites were located from 30.33 to 40.90°N and 119.24 to 121.79°E across east China. A total of 36 plots were investigated in the Liaohe River Estuary, the Yellow River Estuary, Yancheng, and Hangzhou Bay in August 2020. We collected shoot, root, and rhizosphere soil samples. the number of pakchoi leaves, total fresh and dry weight of the seedlings was counted. The soil properties, plant functional traits, the genome sequencing, and metabolomics assay were detected.

Results

The results showed that soil nutrients (total organic carbon, dissolved organic carbon, total nitrogen, soluble sugars, and organic acids) are high in the temperate marsh, while root exudates (measured by metabolite expressions) are significantly higher in the subtropical marsh. We observed higher bacterial alpha diversity, more complex network structure, and more negative connections in the temperate salt marsh, which suggested intense competition among bacterial groups. Variation partitioning analysis showed that climatic, edaphic, and root exudates had the greatest effects on the bacteria in the salt marsh, especially for abundant and moderate subcommunities. Random forest modeling further confirmed this but showed that plant species had a limited effect.

Conclutions

Taken together, the results of this study revealed soil properties (chemical properties) and root exudates (metabolites) had the greatest influence on the bacterial community of salt marsh, especially for abundant and moderate taxa. Our results provided novel insights into the biogeography of halophyte microbiome in coastal wetlands and can be beneficial for policymakers in decision-making on the management of coastal wetlands.

Plant Microbiome Engineering: Hopes or Hypes

Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.

The impact of protozoa addition on the survivability of Bacillus inoculants and soil microbiome dynamics

Protists' selective predation of bacterial cells is an important regulator of soil microbiomes, which might influence the success of bacterial releases in soils. For instance, the survival and activity of introduced bacteria can be affected by selective grazing on resident communities or the inoculant, but this remains poorly understood. Here, we investigated the impact of the introduction in the soil of two protozoa species, Rosculus terrestris ECOP02 and/or Cerocomonas lenta ECOP01, on the survival of the inoculants Bacillus mycoides M2E15 (BM) or B. pumilus ECOB02 (BP). We also evaluated the impact of bacterial inoculation with or without protozoan addition on the abundance and diversity of native soil bacterial and protist communities. While the addition of both protozoa decreased the survival of BM, their presence contrarily increased the BP abundance. Protists' selective predation governs the establishment of these bacterial inoculants via modifying the soil microbiome structure and the total bacterial abundance. In the BP experiment, the presence of the introduced protozoa altered the soil community structures and decreased soil bacterial abundance at the end of the experiment, favouring the invader survival. Meanwhile, the introduced protozoa did not modify the soil community structures in the BM experiment and reduced the BM + Protozoa inoculants' effect on total soil bacterial abundance. Our study reinforces the view that, provided added protozoa do not feed preferentially on bacterial inoculants, their predatory behaviour can be used to steer the soil microbiome to improve the success of bacterial inoculations by reducing resource competition with the resident soil microbial communities.

Microbe-Mediated Thermotolerance in Plants and Pertinent Mechanisms- A Meta-Analysis and Review

Microbial symbionts can mediate plant stress responses by enhancing thermal tolerance, but less attention has been paid to measuring these effects across plant-microbe studies. We performed a meta-analysis of published studies as well as discussed with relevant literature to determine how the symbionts influence plant responses under non-stressed versus thermal-stressed conditions. As compared to non-inoculated plants, inoculated plants had significantly higher biomass and photosynthesis under heat stress conditions. A significantly decreased accumulation of malondialdehyde (MDA) and hydrogen peroxide (H2O2) indicated a lower oxidation level in the colonized plants, which was also correlated with the higher activity of catalase, peroxidase, glutathione reductase enzymes due to microbial colonization under heat stress. However, the activity of superoxide dismutase, ascorbate oxidase, ascorbate peroxidase, and proline were variable. Our meta-analysis revealed that microbial colonization influenced plant growth and physiology, but their effects were more noticeable when their host plants were exposed to high-temperature stress than when they grew under ambient temperature conditions. We discussed the mechanisms of microbial conferred plant thermotolerance, including at the molecular level based on the available literature. Further, we highlighted and proposed future directions toward exploring the effects of symbionts on the heat tolerances of plants for their implications in sustainable agricultural production.

Is the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement?

The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.

An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness

Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root-soil-microbiome interactions creates emerging properties that impact plant nutrition and health. As a consequence, the rhizosphere can be considered an extended root phenotype, a manifestation of the effects of plant genes on their environment inside and/or outside of the organism. Here, we review current understanding of how plants shape the rhizosphere and the benefits it confers to plant fitness. We discuss future research challenges and how applying their solutions in crops will enable us to harvest the benefits of the extended root phenotype.

Plant-associated and soil microbiota composition as a novel criterion for the environmental risk assessment of genetically modified plants

The impact of genetically modified plants on plant-associated and surrounding soil microorganisms is an uninvestigated area of environmental risk assessment. Biological markers such as lysine racemase, phosphomannose isomerase, and sulfadiazine are in use or suggested for use in plant genetic transformation technologies to confirm that the uptake of DNA has occurred. Similar to the effects of antibiotic-resistance genes, these markers might change the host plant's microbiota. Taking into account the importance of the microbiota in plant growth and protection from pathogens as well as in the lives of both humans and animals, we propose novel criteria for the environmental risk assessment of genetically modified plants: the composition of the plant microbiota and plant-associated soil microbiota. In addition to the possible impact of genetic transformation technologies on the plant microbiota highlighted in this report, the microbiota of genetically modified plants (and/or plant-associated soil microbiota) should be investigated in a comparative study of genetically modified and unmodified plant-derived microbiotas. This could potentially provide important information to farmers when considering the adoption of genetically modified plants.

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.

Protists: Puppet Masters of the Rhizosphere Microbiome

The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Here we review the importance of protists, a paraphyletic group of unicellular eukaryotes, as a key regulator of microbiome assembly. Protists can promote plant-beneficial functions within the microbiome, accelerate nutrient cycling, and remove pathogens. We conclude that protists form an essential component of the rhizosphere microbiome and that accounting for predator-prey interactions would greatly improve our ability to predict and manage microbiome function at the service of plant growth and health.