Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect

Variability of microbiomes in winter rye, wheat, and triticale affected by snow mold: predicting promising microorganisms for the disease control

BACKGROUND

Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.

RESULTS

The variability of microbiomes between different crops within a particular agrocenosis was largely determined by fungal communities, whereas the variability of microbiomes of a particular crop in different agrocenoses was largely determined by bacterial communities. The snow mold pathocomplex was the most "constant" in rye, with the lowest level of between-replicate variability and between-agrocenoses variability and (similar to the triticale snow mold pathocomplex) strong dominance of Microdochium over other snow mold fungi. The wheat snow mold pathocomplex was represented by different snow mold fungi, including poorly investigated Phoma sclerotioides. To predict snow mold-control microorganisms, a conveyor of statistical methods was formed and applied; this conveyor enables considering not only the correlation between the abundance of target taxa and a phytopathogen but also the stability and fitness of taxa within plant-associated communities and the reproducibility of the predicted effect of taxa under different conditions. This conveyor can be widely used to search for biological agents against various plant infectious diseases.

CONCLUSIONS

The top indicator microbial taxa for winter wheat and rye following the winter period were Ph. sclerotioides and Microdochium, respectively, both of which are causal agents of snow mold disease. Bacteria from the Cellulomonas, Lechevalieria, and Pseudoxanthomonas genera and fungi from the Cladosporium, Entimomentora, Pseudogymnoascus, and Cistella genera are prime candidates for testing their plant-protective properties against Microdochium-induced snow mold disease and for further use in agricultural practice.

Bacterial consortium amendment effectively reduces Pb/Cd bioavailability in soil and their accumulation in wheat

Microbial remediation can maintain the sustainability of farmlands contaminated with heavy metals (HMs). However, the effects of bacterial consortium on crop growth and potential risks under HM stress, as well as its mechanisms, are still unclear compared with a single microorganism. Here, we investigated the effect of a bacterial consortium consisting of some HMs-resistant bacteria, including Bacillus cereus, Bacillus thuringiensis, and Herbaspirillum huttiense, on plant growth promotion and inhibition of Pb/Cd accumulation within different contaminated soil-wheat systems through pot experiments. The results showed that microbial inoculation alleviated HMs-induced growth inhibition by activating antioxidant enzymes and inhibiting lipid peroxidation, and enhanced plant growth in the bacterial consortium. Compared to a single strain (Bacillus cereus, Bacillus thuringiensis, or Herbaspirillum huttiense), the bacterial consortium was more conducive to improving root development and reducing the content of available HMs in soil (4.5-10.3%) and its transfer to shoot (4.3-8.4%). Moreover, bacterial consortium significantly increased soil enzyme activities and available nutrients, resulting in nearly twice that of a single strain on the effect of soil quality and plant growth. Correlation analysis and least square path analysis showed that the bacterial consortium could significantly reduce the HMs-enrichment/transport from soil to shoot than a single strain by regulating soil available HMs and biochemical properties, as well as the parameters for plant growth. This study emphasizes that bacterial consortium promotes the growth of the crop wheat and reduces the risk of HMs entering human food chain, further providing an effective strategy for the safe production of food crops in contaminated soils.

National-scale distribution of protists associated with sorghum leaves and roots

Protists, as integral constituents of the plant microbiome, are posited to confer substantial benefits to plant health and performance. Despite their significance, protists have received considerably less attention compared to other constituents of the plant microbiome, such as bacteria and fungi. To investigate the diversity and community structure of protists in sorghum leaves and roots, we employed amplicon sequencing of the eukaryotic 18S rRNA gene in 563 leaf and root samples collected from 57 locations across China. We found significant differences in the diversity and community structure of protists in sorghum leaves and roots. The leaf was taxonomically dominated by Evosea, Cercozoa and Ciliophora, while the root was dominated by Endomyxa, Cercozoa and Oomycota. The functional taxa of protists exhibited notable differences between leaves and roots, with the former being predominantly occupied by consumers and the latter by parasites. The community composition of protists in the leaf was predominantly influenced by mean annual precipitation, whereas soil pH played a more significant role in the root. The present study identified the most abundant and distributed protists in sorghum leaves and roots and elucidated the underlying factors that govern their community structure. The present study offers a novel perspective on the factors that shape plant-associated protist communities and their potential roles in enhancing the functionality of plant ecosystems.

Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane

Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.

Changes in the Microbiome of Sugarcane (Saccharum spp. Hybrids.) Rhizosphere in Response to Manganese Toxicity

Manganese toxicity has limited sugarcane (Saccharum spp. hybrid.) growth and production in acidic soils in south China. The rhizosphere plays an irreplaceable role in plant adaptation to soil abiotic stress, but the responses of the sugarcane rhizosphere to manganese toxicity are still unknown. We designed pot experiments in Mn-rich acidic soil, collected the sugarcane rhizosphere and bulk soil samples, and then investigated the changes in Mn-related soil parameters and microbiome. The results indicated that the water-soluble and exchangeable manganese concentrations in the sugarcane rhizosphere were significantly lower than that in the bulk soil, which was not associated with soil pH changes. In contrast, the number of bacteria and the activity of peroxidase, sucrase, urease, and laccase in the rhizosphere were significantly higher. The 16S rDNA sequencing results showed that the bacterial diversity and quantity along with the abundance of Proteobacteria in the rhizosphere were significantly higher than in the bulk soil, while the abundance of Acidobacteria was lower than in the bulk soil. The soil laccase activity and the number of bacteria decreased significantly with the increase in the manganese toxicity stress. Finally, the relative abundance of proteins associated with manganese transportation and oxidation was significantly higher in the rhizosphere soil. In summary, the Mn-induced response of the rhizosphere is an important mechanism in sugarcane adaptation to manganese toxicity in acidic soil.

Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production

Oilcane is a metabolically engineered sugarcane (Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI1 transgene. The WRI1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.

Earthworm Aporrectodea molleri (oligochaeta)'s coelomic fluid-associated bacteria modify soil biochemical properties and improve maize (Zea mays L.) plant growth under abiotic stress conditions

This study evaluated the impact of Aporrectodea molleri's coelomic fluid-associated bacteria (CFB) on Zea mays L. growth and soil biochemical characteristics under abiotic stress conditions, including alkaline soil (pH = 8) and nitrogen (N), phosphate (P), and potassium (K) deficit. Compared to maize cultivated in uninoculated soil, the effect of CFB on boosting plant growth under abiotic stress was notably exceptional. Different CFB treatments increased significantly root and shoot length by 50% and 21%, respectively. Furthermore, the presence of isolates in soil resulted in a significant increase in plant fresh and dry weights (of up to 113% and 91% for roots, and up to 173% and 44% for shoots), leaf surface (78%), and steam diameter (107%). Overall, soil inoculation with CFB significantly (P < 0.05) enhanced chlorophyll and water content in the plant compared to the untreated soil. Despite the soil's alkaline condition, CFB drastically boosted soil quality by increasing nutrient availability (up to 30 ppm for N, 2 ppm for P, and 60 ppm for K) and enzyme activity (up to 1.14 μg p-NP h^-1 g^-1 for acide phosphatase, 9 μg p-NP h^-1 g^-1 for alkaline phosphatase and 40 μg NH₄-N 2 h^-1 g^-1 for urease), throughout the early stages of the growth period. Interestingly, alkaline phosphatase concentrations were substantially greater in treatments with different isolates than acid phosphatase. Furthermore, the principal component analysis showed that the inoculation with bacteria strains CFB1 Buttiauxella gaviniae and CFB3 Aeromonas hydrophila had a significantly better stimulatory stimulatory and direct influence on maize growth than the other isolates had a substantial effect on soil's biochemical features. Thus, we assumed that the beneficial contribution of earthworms in the rhizosphere might be attributed in large part to associated microorganisms.

Plant growth promoting activities and effect of fermented panchagavya isolate Klebsiella sp. PG-64 on Vigna radiata

A natural bacterial isolate from fermented panchagavya named as PG-64, exhibits multiple plant growth-promoting traits. This Gram-negative bacteria was identified as Klebsiella sp. PG-64 by 16S rRNA gene sequencing. The Klebsiella sp. PG-64 has shown production of indole acetic acid (106.0 µg/ml), gibberellic acid (20.0 µg/ml), ammonia (7.12 µmol/ml), exopolysaccharide (2.04% w/v) and phosphate solubilization (106.0 µg/ml). It produced 437 µg/ml IAA with 0.75% (w/v) L-tryptophan supplementation and was increased to 575 µg/ml in a laboratory-scale fermenter. The PG-64 has shown tolerance to abiotic stress conditions like pH (5.0-12.0), temperature (28-46 °C), salt (0.5-10.0% w/v NaCl) and osmotic resistance (1-10% w/v PEG-6000). The PG-64 also produced 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (0.3 ng α-ketobutyrate/mg protein/h) indicating its potential for drought tolerance. Owing to its diverse properties, the effect of Klebsiella sp. PG-64 on Vigna radiata (Mung bean) was examined. The seeds treated with PG-64 culture showed 92% germination with a good seedling vigour index (202). In the pot study, Vigna radiata growth showed 2.23, 1.55, 2.00, 1.65, 1.73, 1.88, 5.00, 5.00, 1.57 times increase in primary root length, dry root weight, root hair numbers, leaf width, leaf numbers, leaf area, fruits number, flower number and chlorophyll content, respectively after 75 days. The application of Klebsiella sp. PG-64 culture resulted in substantial growth enhancement of Vigna radiata. The Klebsiella sp. PG-64 has multiple plant growth-promoting properties along with capabilities to tolerate abiotic stresses, making it a promising liquid biofertilizer contender for various crops.

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure

Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.

Microbiota Communities of Healthy and Bacterial Pustule Diseased Soybean

Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.

Synergistic effects of Cd-loving Bacillus sp. N3 and iron oxides on immobilizing Cd and reducing wheat uptake of Cd

Iron oxides and microorganisms are important soil components that profoundly affect the transformation and bioavailability of heavy metals in soils. Here, batch and pot experiments were conducted to investigate the immobilization mechanisms of Cd by Cd-loving Bacillus sp. N3 and ferrihydrite (Fh) as well as their impacts on Cd uptake by wheat and bacterial community composition in wheat rhizospheric soil. The results showed that the combination of strain N3 with Fh could immobilize more Cd compared to strain N3 and Fh, respectively. Furthermore, strain N3 facilitated Cd retention on Fh, which synergistically reduced the concentration of DTPA extracted Cd in the soil and decreased Cd content (57.1%) in wheat grains. Moreover, inoculation with strain N3 increased the complexity of the co-occurrence network of the bacterial community in rhizospheric soil, and the abundance of beneficial bacteria with multipel functions including heavy metal immobilization, dissimilatory iron reduction, and plant growth promotion. Overall, this study demonstrated the enrichment of strain N3 and iron oxides, together with increased soil pH, synergistically immobilized soil Cd, which strongly suggested inoculation with Cd-loving strains could be a promising approach to immobilize Cd and reduce wheat uptake of Cd, particular for soils rich in iron oxides.

Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome

Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.