Exploring stress-tolerant plant growth-promoting rhizobacteria from groundnut rhizosphere soil in semi-arid regions of Ethiopia

The potential of rhizobacteria with plant growth promoting (PGP) traits in alleviating abiotic stresses, especially drought, is significant. However, their exploitation in the semi-arid regions of Ethiopian soils remains largely unexplored. This research aimed to isolate and evaluate the PGP potential of bacterial isolates collected from groundnut cultivation areas in Ethiopia. Multiple traits were assessed, including phosphate solubilization, indole-3-acetic acid (IAA) production, ammonia production, salt and heavy metal tolerance, drought tolerance, enzyme activities, hydrogen cyanide production, antibiotic resistance, and antagonistic activity against fungal pathogens. The identification of potent isolates was carried out using MALDI-TOF MS. Out of the 82 isolates, 63 were gram-negative and 19 were gram-positive. Among them, 19 isolates exhibited phosphate solubilization, with AAURB 34 demonstrating the highest efficiency, followed by AURB 12. Fifty-six isolates produce IAA in varying amounts and all isolates produce ammonia with AAURB12, AAURB19, and AAURB34 displaying strong production. Most isolates demonstrated tolerance to temperatures up to 40°C and salt concentrations up to 3%. Notably, AAURB12 and AAURB34 exhibited remarkable drought tolerance at an osmotic potential of -2.70 Mpa. When subjected to levels above 40%, the tested isolates moderately produced lytic enzymes and hydrogen cyanide. The isolates displayed resistance to antibiotics, except gentamicin, and all isolates demonstrated resistance to zinc, with 81-91% showing resistance to other heavy metals. AAURB34 and AAURB12 exhibited suppression against fungal pathogens, with percent inhibition of 38% and 46%, respectively. Using MALDI-TOF MS, the promising PGP isolates were identified as Bacillus megaterium, Bacillus pumilus, and Enterobacter asburiae. This study provides valuable insights into the potential of rhizobacteria as PGP agents for mitigating abiotic stresses and contribute to the understanding of sustainable agricultural practices in Ethiopia and similar regions facing comparable challenges.

The microbial-driven nitrogen cycle and its relevance for plant nutrition

Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids and proteins. Microorganisms are major drivers of N-cycling processes in all ecosystems, including the soil and plant environment. The availability of N is a major growth-limiting factor for plants and it is significantly affected by the plant microbiome. Plants and microorganisms form complex interaction networks resulting in molecular signaling, nutrient exchange, and other distinct metabolic responses. In these networks, microbial partners influence growth and N use efficiency of plants either positively or negatively. Harnessing the beneficial effects of specific players within crop microbiomes is a promising strategy to counteract the emerging threats to human and planetary health due to the overuse of industrial N fertilizers. However, in addition to N-providing activities (e.g. the well-known symbiosis of legumes and Rhizobium spp.), other plant-microorganism interactions must be considered to obtain a complete picture of how microbial-driven N transformations might affect plant nutrition. For this, we review recent insights into the tight interplay between plants and N-cycling microorganisms, focusing on microbial N-transformation processes representing N sources and sinks that ultimately shape plant N acquisition.

Effects of Trichoderma harzianum and Bacillus subtilis on the root and soil microbiomes of the soybean plant INTACTA RR2 PRO™

Introduction

Soybean is a significant export product for several countries, including the United States and Brazil. There are numerous varieties of soybean. Among them, a genetically modified type known as INTACTA RR2 PRO™ has been designed to demonstrate resistance to glyphosate and to produce toxins that are lethal to several species of caterpillars. Limited information is available on the use of Trichoderma harzianum and Bacillus subtilis to promote plant growth and their impact on the plant microbiome.

Methods

This study aimed to evaluate the effects of these microorganisms on this soybean cultivar by analyzing parameters, such as root and shoot dry matter, nutritional status, and root and soil microbial diversity.

Results

The results indicated that treatments with B. subtilis alone or in combination with T. harzianum as seed or seed and soil applications significantly enhanced plant height and biomass compared to the other treatments and the control. No significant differences in phosphorus and nitrogen concentrations were detected across treatments, although some treatments showed close correlations with these nutrients. Microbial inoculations slightly influenced the soil and root microbiomes, with significant beta diversity differences between soil and root environments, but had a limited overall impact on community composition.

Discussion

The combined application of B. subtilis and T. harzianum particularly enhanced plant growth and promoted plant-associated microbial groups, such as Rhizobiaceae, optimizing plant-microbe interactions. Furthermore, the treatments resulted in a slight reduction in fungal richness and diversity.

A comprehensive review of soybean RNL and TIR domain proteins

Both prokaryotic and eukaryotic organisms use the nucleotide-binding domain/leucine-rich repeat (NBD/LRR)-triggered immunity (NLR-triggered immunity) signaling pathway to defend against pathogens. Plant NLRs are intracellular immune receptors that can bind to effector proteins secreted by pathogens. Dicotyledonous plants express a type of NLR known as TIR domain-containing NLRs (TNLs). TIR domains are enzymes that catalyze the production of small molecules that are essential for immune signaling and lead to plant cell death. The activation of downstream TNL signaling components, such as enhanced disease susceptibility 1 (EDS1), phytoalexin deficient 4 (PAD4), and senescence-associated gene 101 (SAG101), is facilitated by these small molecules. Helper NLRs (hNLRs) and the EDS1-PAD4/SAG101 complex associate after activation, causing the hNLRs to oligomerize, translocate to the plasma membrane (PM), and produce cation-selective channels. According to a recent theory, cations enter cells through pores created by oligomeric hNLRs and trigger cell death. Occasionally, TNLs can self-associate to create higher-order oligomers. Here, we categorized soybean TNLs based on the protein domains that they possess. We believe that TNLs may help soybean plants effectively fight pathogens by acting as a source of genetic resistance. In summary, the purpose of this review is to elucidate the range of TNLs that are expressed in soybean.

Trichoderma koningiopsis fermentation in airlift bioreactor for bioherbicide production

During scaling of fermentations, choosing a bioreactor is fundamental to ensure the product's quality. This study aims to produce bioherbicides using Trichoderma koningiopsis fermentation, evaluating process parameters in an Airlift bioreactor. As a response, we quantified the production of enzymes involved in the bioherbicide activity (amylase, cellulase, laccase, lipase, and peroxidase). In addition, it evaluated the agronomic efficiency of the fermented extract optimized through tests that promoted soybean growth and nodulation, soybean seed germination, and in vitro phytopathogen control. As a result of optimizing the scaling bioprocess, it was possible to obtain an adequate fermentation condition, which, when applied to soybean seeds, had beneficial effects on their growth. It allowed the production of an enzyme cocktail. These results add a crucial biotechnological potential factor for the success of the optimized formulation in the Airlift bioreactor, in addition to presenting relevant results for the scientific community.

Enhancing Soybean Yield: The Synergy of Sulfur and Rhizobia Inoculation

Sulfur deficiency severely limits soybean growth, inhibiting the rhizobia nitrogenase and soybean protein synthesis. This study assessed the impact of sulfur fertilization and rhizobia inoculation on soybean growth and nitrogen fixation through bacterial culture and hydroponic experiments. We selected three rhizobia strains for bacterial cultures and used six sulfur levels. The test demonstrated severe inhibition of Rhizobium USDA110 growth without sulfur. In hydroponic experiment, we employed five sulfur levels with USDA110 as the inoculum strain. Soybean growth, nitrogen fixation, yield, and root morphology-related parameters, and root nodule growth, were significantly inhibited without sulfur. Following Rhizobium inoculation, low sulfur concentrations (0.15-0.60 mM) stimulated early-stage (V9) root growth and increased shoot nitrogen accumulation, but inhibited root growth at R5 stage. Furthermore, Rhizobium inoculation notably enhanced soybean growth, nitrogen fixation, and yield, especially within the recommended low sulfur concentration range (0.15-0.30 mM). The maximum nodule nitrogenase activity at R5 stage and highest yield was recorded at a 0.3 mM sulfur concentration with Rhizobium inoculation, which was 9.51-1222.07% higher than other treatments. These findings highlight that low sulfur concentration and rhizobia inoculation enhance soybean growth, nitrogen fixation, and yield but reduce soybean root efficacy, increasing reliance on root nodules.

The calcium connection: exploring the intricacies of calcium signaling in plant-microbe interactions

The process of plant immune response is orchestrated by intracellular signaling molecules. Since plants are devoid of a humoral system, they develop extensive mechanism of pathogen recognition, signal perception, and intricate cell signaling for their protection from biotic and abiotic stresses. The pathogenic attack induces calcium ion accumulation in the plant cells, resulting in calcium signatures that regulate the synthesis of proteins of defense system. These calcium signatures induct different calcium dependent proteins such as calmodulins (CaMs), calcineurin B-like proteins (CBLs), calcium-dependent protein kinases (CDPKs) and other signaling molecules to orchestrate the complex defense signaling. Using advanced biotechnological tools, the role of Ca2+ signaling during plant-microbe interactions and the role of CaM/CMLs and CDPKs in plant defense mechanism has been revealed to some extent. The Emerging perspectives on calcium signaling in plant-microbe interactions suggest that this complex interplay could be harnessed to improve plant resistance against pathogenic microbes. We present here an overview of current understanding in calcium signatures during plant-microbe interaction so as to imbibe a future direction of research.

Lemnaceae as Novel Crop Candidates for CO2 Sequestration and Additional Applications

Atmospheric carbon dioxide (CO2) is projected to be twice as high as the pre-industrial level by 2050. This review briefly highlights key responses of terrestrial plants to elevated CO2 and compares these with the responses of aquatic floating plants of the family Lemnaceae (duckweeds). Duckweeds are efficient at removing CO2 from the atmosphere, which we discuss in the context of their exceptionally high growth rates and capacity for starch storage in green tissue. In contrast to cultivation of terrestrial crops, duckweeds do not contribute to CO2 release from soils. We briefly review how this potential for contributions to stabilizing atmospheric CO2 levels is paired with multiple additional applications and services of duckweeds. These additional roles include wastewater phytoremediation, feedstock for biofuel production, and superior nutritional quality (for humans and livestock), while requiring minimal space and input of light and fertilizer. We, furthermore, elaborate on other environmental factors, such as nutrient availability, light supply, and the presence of a microbiome, that impact the response of duckweed to elevated CO2. Under a combination of elevated CO2 with low nutrient availability and moderate light supply, duckweeds' microbiome helps maintain CO2 sequestration and relative growth rate. When incident light intensity increases (in the presence of elevated CO2), the microbiome minimizes negative feedback on photosynthesis from increased sugar accumulation. In addition, duckweed shows a clear propensity for absorption of ammonium over nitrate, accepting ammonium from their endogenous N2-fixing Rhizobium symbionts, and production of large amounts of vegetative storage protein. Finally, cultivation of duckweed could be further optimized using hydroponic vertical farms where nutrients and water are recirculated, saving both resources, space, and energy to produce high-value products.

Nodulation number tempers the relative importance of stochastic processes in the assembly of soybean root-associated communities

Identifying the ecological forces that structure root-associated microbial communities is an essential step toward more sustainable agriculture. Legumes are widely utilized as model plants to study selective forces and their functioning in plant-microbial interactions owing to their ability to establish mutualism with rhizobia. Root nodules act as symbiotic organs to optimize the cost-benefit balance in this mutualistic relationship by modulating the number of nodules. However, it is not known whether the number of nodules is related to the structure of root-associated bacterial communities. Here, the root-associated bacterial communities of soybean grown in native soil by means of soybean cultivars with super- or normal nodulation were investigated across four developmental stages. We compared ecological processes between communities and found decreased relative importance of neutral processes for super-nodulating soybean, although the overall structures resembled those of normal-nodulating soybean. We identified the generalist core bacterial populations in each root-associated compartment, that are shared across root-associated niches, and persist through developmental stages. Within core bacterial species, the relative abundances of bacterial species in the rhizosphere microbiome were linked to host-plant functional traits and can be used to predict these traits from microbes using machine learning algorithms. These findings broaden the comprehensive understanding of the ecological forces and associations of microbiotas in various root-associated compartments and provide novel insights to integrate beneficial plant microbiomes into agricultural production to enhance plant performance.

Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean

Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.

Preliminary symbiotic performance of indigenous soybean (Glycine max)-nodulating rhizobia from agricultural soils of Tanzania

Globally, the increase in human population continues to threaten the sustainability of agricultural systems. Despite the fast-growing population in Sub-Saharan Africa (SSA) and the efforts in improving the productivity of crops, the increase in the yield of crops per unit area is still not promising. The productivity of crops is primarily constrained by inadequate levels of soil nutrients to support optimum crop growth and development. However, smallholder farmers occasionally use fertilizers, and the amount applied is usually small and does not meet plant requirements. This is due to the unaffordability of the cost of fertilizers, which is enough to suffice the crop requirement. Therefore, there is a need for alternative affordable and effective fertilization methods for sustainable intensification and improvement of the smallholder farming system's productivity. This study was designed to evaluate the symbiotic performance of indigenous soybean nodulating rhizobia in selected agricultural soils of Tanzania. In total, 217 rhizobia isolates were obtained from three agroecological zones, i.e., eastern, northern, and southern highlands. The isolates collected were screened for N2 fixing abilities under in vitro (nitrogen-free medium) and screen house conditions. The results showed varying capabilities of isolates in nitrogen-fixing both under in vitro and screen house conditions. Under in vitro experiment, 22% of soybean rhizobia isolates were identified to have a nitrogen-fixing capability on an N-free medium, with the highest N2-fixing diameter of 1.87 cm. In the screen house pot experiment, results showed that soybean rhizobia isolate significantly (P < 0.001) influenced different plant growth and yield components, where the average shoot dry weight ranged from 2.49 to 10.98 g, shoot length from 41 to 125.27 cm whilst the number of leaves per plant ranged from 20 to 66. Furthermore, rhizobia isolates significantly (P = 0.038) increased root dry weight from 0.574 to 2.17 g. In the case of symbiotic parameters per plant, the number of nodules was in the range of 0.33–22, nodules dry weight (0.001–0.137 g), shoot nitrogen (2.37–4.97%), total nitrogen (53.59–6.72 g), and fixed nitrogen (46.878–0.15 g) per plant. In addition, the results indicated that 51.39% of the tested bacterial isolates in this study were ranked as highly effective in symbiosis, suggesting that they are promising as potential alternative biofertilizers for soybean production in agricultural soils of Tanzania to increase productivity per unit area while reducing production cost.

Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa

The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal–Wallis test was used to test samples’ diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.