Microbes - friends and foes of sugarcane

Sugarcane productivity and economic viability in response to planting density

Planting with higher density in sugarcane is one of the practices used to overcome low productivity. However, this planting material is equivalent to 25% of the total cost of production, being one of the main expenses for cultivation. In this sense, the present work aims to evaluate the productivity and economic viability of sugarcane as a function of planting density. The experiment was carried out at Usina Monte Alegre in the municipality of Mamanguape, Paraíba, Brazil, from March 2021 to January 2022 with the variety RB92579. Seven planting density were studied: T1: 7 gems m-1, T2: 10 gems m-1, T3: 12 gems m-1, T4: 11 gems m-1, T5: 15 gems m-1, T6: 17 gems m-1, T7: 24 gems m-1, in randomized blocks with four replications. Growth, productivity and economic viability were evaluated. The highest productivity of cane and sugar, 77.69 ton ha-1 and 10.390 ton ha-1, respectively, was with planting density of 17 and 24 gems-1. While the minimum productivity of cane (61.313 ton ha-1) and sugar (7.924 ton ha-1) was recorded at sowing density of 7 and 11 gems-1. However, cultivation density with 7 and 10 gems m-1 were the ones that provided the highest profitability around 50%, followed by density of 12, 15 and 17 gems m-1 with an average of 45% profit and 11 and 24 gems m-1 with the lowest proportion of profit on average 38%. The cultivation with 17 gems m-1 of cane provides in cane-plant, variety RB92579, greater productivity with a profit rate of 45%, being the most suitable.

Adaptation of rhizosphere bacterial communities of drought-resistant sugarcane varieties under different degrees of drought stress

Sugarcane is highly sensitive to changes in moisture, and increased drought severely restricts its growth and productivity. Recent studies have shown that plant growth-promoting microorganisms are essential to reduce the adverse effects of environmental stresses, especially drought. However, our knowledge about the dynamics of rhizosphere microbial community structure in sugarcane under varying degrees of drought stress is limited. We analyzed the effects of different degrees of drought stress on the rhizosphere microbial communities of Zhongzhe 1(ZZ1) and Zhongzhe 6(ZZ6) with differences in drought resistance, by combining soil enzyme activity, nutrient content, and physiological and morphological characteristics of sugarcane roots. The results showed that rhizosphere bacterial community began to change at a field capacity of 50%, enriching the sugarcane rhizosphere with drought-resistant bacteria. The core strains of ZZ1 and ZZ6 rhizosphere enrichment were mainly Streptomycetales, Sphingomonadales, and Rhizobiales. However, compared to ZZ1, the changes in rhizosphere bacterial abundance in ZZ6 were primarily associated with the abundance of Streptomycetales as drought levels increased. Rhizobiales and Streptomycetales, enriched in the rhizosphere of ZZ6 under drought, were positively correlated with root tip number and total root length (TRL), increasing the distribution area of roots and, thus, improving water and nutrient uptake by the roots thereby enhancing the resistance of sugarcane to drought stress. This research enhances our understanding of the composition of the rhizosphere microbial community in sugarcane under different levels of drought stress and its interaction with the roots, thereby providing valuable insights for enhancing drought resistance in sugarcane. IMPORTANCE Drought stress is expected to further increase in intensity, frequency, and duration, causing substantial losses in sugarcane yields. Here, we exposed sugarcane to varying degrees of drought treatment during growth and quantified the eventual composition of the resulting sugarcane rhizosphere bacterial community groups. We found that sugarcane rhizosphere under mild drought began to recruit specific bacterial communities to resist drought stress and used the interactions of root tip number, total root length, and drought-resistant strains to improve sugarcane survival under drought. This research provides a theoretical basis for the rhizosphere microbiome to help sugarcane improve its resistance under different levels of drought stress.

Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems

Soil microbiomes play important roles in supporting agricultural ecosystems. However, it is still not well-known how soil microbiomes and their functionality respond to fertilization in various cropping systems. Here we examined the effects of 36 years of phosphorus, nitrogen, and manure application on soil bacterial communities, functionality and crop productivity in three contrasting cropping systems (i.e., continuous leguminous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation of winter wheat + millet - pea - winter wheat (GLR)) in a highland region of China's Loess Plateau. We showed that long-term fertilization significantly affected soil bacterial communities and that the effects varied with cropping system. Compared with the unfertilized control, fertilization increased soil bacterial richness and diversity in the leguminous AC system, whereas it decreased those in the GLR system. Fertilization, particularly manure application, enlarged the differences in soil bacterial communities among cropping systems. Soil bacterial communities were mostly affected by the soil organic carbon and nitrogen contents in the WC and GLR systems, but by the soil available phosphorous content in the AC system. Crop productivity was closely associated with the abundance of fertilization-responsive taxa in the three cropping systems. Our study highlights that legume and non-legume cropping systems should be disentangled when assessing the responses of soil microbial communities to long-term fertilizer application.

Correlation of microbiomes in "plant-insect-soil" ecosystem

Introduction

Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance.

Methods

Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters.

Results and Discussion

Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control.

Influence of Sugarcane Variety on Rhizosphere Microbiota Under Irrigated and Water-Limiting Conditions

Drought is one of the main problems linked to climate change that is faced by agriculture, affecting various globally important crops, including sugarcane. Environmentally sustainable strategies have been sought to mitigate the effects of climate change on crops. Among them, the use of beneficial microorganisms offers a promising approach. However, it is still necessary to understand the mechanisms that regulate plant-microorganism interactions, in normal situations and under stress. In this work, the rhizosphere metagenomes of two sugarcane varieties, one resistant and the other susceptible to drought, were compared under normal conditions and under water-limiting conditions. The results showed that for the drought-resistant sugarcane variety, bacteria belonging to the order Sphingomonadales and the family Xanthomonadaceae presented increased activities in terms of mobility, colonization, and cell growth. In contrast, the rhizosphere associated with the drought-sensitive variety exhibited increases of bacteria belonging to the family Polyangiaceae, and the genus Streptomyces, with modifications in DNA metabolism and ribosome binding proteins. The results pointed to variation in the rhizosphere microbiota that was modulated by the host plant genotype, revealing potential bacterial candidates that could be recruited to assist plants during water-limiting conditions.

Functional Investigation of Plant Growth Promoting Rhizobacterial Communities in Sugarcane

Plant microbiota are of great importance for host nutrition and health. As a C₄ plant species with a high carbon fixation capacity, sugarcane also associates with beneficial microbes, though mechanisms underlying sugarcane root-associated community development remain unclear. Here, we identify microbes that are specifically enriched around sugarcane roots and report results of functional testing of potentially beneficial microbes propagating with sugarcane plants. First, we analyzed recruitment of microbes through analysis of 16S rDNA enrichment in greenhouse cultured sugarcane seedlings growing in field soil. Then, plant-associated microbes were isolated and assayed for beneficial activity, first in greenhouse experiments, followed by field trials for selected microbial strains. The promising beneficial microbe SRB-109, which quickly colonized both roots and shoots of sugarcane plants, significantly promoted sugarcane growth in field trials, nitrogen and potassium acquisition increasing by 35.68 and 28.35%, respectively. Taken together, this report demonstrates successful identification and utilization of beneficial plant-associated microbes in sugarcane production. Further development might facilitate incorporation of such growth-promoting microbial applications in large-scale sugarcane production, which may not only increase yields but also reduce fertilizer costs and runoff.

Smarter cures to combat COVID-19 and future pathogens: a review

Prevention is better than cure. A milestone of the anthropocene is the emergence of a series of epidemics and pandemics often characterized by the transmission of a pathogen from animals to human in the past two decades. In particular, the coronavirus disease 2019 (COVID-19) has made a profound impact on emergency responding and policy-making in a public health crisis. Classical solutions for controlling the virus, such as travel restrictions, lockdowns, repurposed drugs and vaccines, are socially unpopular and medically limited by the fast mutation and adaptation of the virus. This is exacerbated by microbial resistance to therapeutic drugs and the slowness of vaccine development. In other words, microbial pathogens are somehow 'smarter' and faster than us, thus calling for more intelligent cures to combat future pandemics. Here, we compare therapeutics for COVID-19 such as synthetic drugs, vaccines, antibodies and phages. We present the strength and limitations of antibiotic and antiviral drugs, vaccines, and antibody-based therapeutics. We describe smarter, cheaper and preventive cures such as bacteriophages, food medicine using probiotics and prebiotics, sports, healthy diet, music, yoga, Tai Chi, dance, reading, knitting, cooking and outdoor activities. Some of these preventive cures have been intuitively developed since thousands of years ago, as illustrated by the fascinating similarity of the Chinese characters for 'music' and 'herbal medicine.'

Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling

Beneficial plant–microbe interactions lead to physiological and biochemical changes that may result in plant-growth promotion. This study evaluated the effect of the interaction between sugarcane and endophytic bacterial strains on plant physiological and biochemical responses under two levels of nitrogen (N) fertilization. Six strains of endophytic bacteria, previously selected as plant growth-promoting bacteria (PGPB), were used to inoculate sugarcane mini stalks, with and without N fertilization. After 45 days, biomass production; shoot nutrient concentrations; foliar polyamine and free amino acid profiles; activities of nitrate reductase and glutamine synthase; and the relative transcript levels of the GS1, GS2, and SHR5 genes in sugarcane leaves were determined. All six endophytic strains promoted sugarcane growth, increasing shoot and root biomass, plant nutritional status, and the use efficiency of most nutrients. The inoculation-induced changes at the biochemical level altered the foliar free amino acid and polyamine profiles, mainly regarding the relative concentrations of citrulline, putrescine, glycine, alanine, glutamate, glutamine, proline, and aspartate. The transcription of GS1, GS2, and SHR5 was higher in the N fertilized seedlings, and almost not altered by endophytic bacterial strains. The endophytic strains promoted sugarcane seedlings growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acid and polyamine composts, or GS1, GS2, and SHR5, showing that complex interactions may be associated with enhancement of the sugarcane seedlings’ performance by endophytic bacteria. The strains demonstrated biotechnological potential for sugarcane seedling production.

Osmo- and cryotherapy of sugarcane (Saccharum spp. L.) shoot-tips infected with sugarcane mosaic virus (SCMV)

In this work, we investigated the effect of different osmoprotective treatments and of cryopreservation using a droplet-vitrification (D-V) protocol to eliminate sugarcane mosaic virus (SCMV) of shoot-tips excised from in vitro propagated infected plantlets. Shoot-tips of sugarcane (Saccharum spp. L.) were precultured on semisolid MS medium supplemented with 0.3 M sucrose for 1 day, loaded in solution with 0.4 M sucrose and 2 M glycerol for 30 min and exposed to plant vitrification solution 2 for 15 min at room temperature prior to ultra-rapid cooling in liquid nitrogen. Virus indexing was performed by the DAS-ELISA immunoenzymatic test. The presence of SCMV was confirmed in the donor-plantlets derived of infected field material. No virus was detected in the regenerated plantlets from shoot-tips subjected to cryopreservation protocol. The progressive decrease in absorbances occurred from the first preculture treatment and no significant differences (P ≤ 0.05) were found with respect to following steps of D-V protocol. These results indicate that the osmotic dehydration treatments (osmotherapy) and cryopreservation (cryotherapy) may be potentially effective strategies to remove the SCMV from infected plants.

Dark Septate Endophytic Fungi Associated with Sugarcane Plants Cultivated in São Paulo, Brazil

Dark septate endophytes (DSEs) constitute a polyphyletic group within the Ascomycota, with global distribution and a wide range of host plant species. The present study evaluated the diversity of DSE in sugarcane roots of the varieties RB867515, RB966928, and RB92579, and four varieties of not commercialized energy cane. A total of 16 DSE strains were isolated, mostly from the varieties RB966928 and RB867515, with six and five isolates, respectively. Just one of the four energy cane varieties had fungi with DSE appearance. The analyses of the DNA sequences from the internal transcribed spacer (ITS) and the large subunit (LSU), in association with the micromorphology of the isolates, allowed the differentiation of the 16 isolates in at least five species, within the families Periconiaceae, Pleosporaceae, Lentitheciaceae, Vibrisseaceae, and Apiosporaceae and the orders Pleosporales, Helotiales, and Xylariales. The order Pleosporales represented 80% of the isolates, and the species Periconia macrospinosa, with six isolates, accounted for the highest isolation frequency. The results confirm the natural occurrence of the DSE symbiosis in sugarcane varieties and the generalist character of these fungi as some of the detected species have already been reported associated with other host plants, ecosystems, and regions of the world.

Prospecting Plant Growth-Promoting Bacteria Isolated from the Rhizosphere of Sugarcane Under Drought Stress

In the rhizosphere, the soil bacteria and the plants are closely related, with the plant-associated microbiota playing an important role in promoting plant growth under both normal and stress conditions. In this study, the cultivable bacteria in the sugarcane rhizosphere under different levels of drought stress were characterized and screened for plant growth activities. The results suggested that the microbial community associated with the sugarcane rhizosphere was strongly affected by drought, but some important genera of bacteria such as Arthrobacter, Pseudomonas, Microbacterium, and Bacillus remained present during the entire experiment, indicating the adaptability of these organisms and their importance in the rhizosphere community. Many isolates exhibited positive results for one or more plant growth activity, and they were also capable of growing under simulated drought stress, suggesting that the microorganisms isolated from the sugarcane rhizosphere could be explored for uses such as biofertilizers or biocontrol agents in agriculture.

Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system

BACKGROUND

Sugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causing severe losses to the sugarcane industry. The use of PCR reference genes is essential to the normalization of data on gene expression involving the sugarcane-S. scitamineum interaction system; however, no report that addresses criteria in selecting these reference genes has been published to date.

RESULTS

In this study, 10 sugarcane genes and eight S. scitamineum genes were selected as candidate PCR reference genes in the sugarcane-S. scitamineum interaction system. The stability and reliability of these 18 candidate genes were analyzed in smut-resistant (NCo376) and -susceptible (YC71-374) genotypes using the statistical algorithms geNorm, NormFinder, BestKeeper, and deltaCt method. Subsequently, the relative expression levels of the sugarcane chitinase I-3 gene and S. scitamineum chorismate mutase gene were determined to validate the applicability of these sugarcane and S. scitamineum PCR reference genes, respectively. We finally found that the acyl-CoA dehydrogenase gene (ACAD), serine/arginine repetitive matrix protein 1 gene (SARMp1), or their combination (ACAD + SARMp1) could be utilized as the most suitable reference genes for normalization of sugarcane gene expression in sugarcane bud tissues after S. scitamineum infection. Similarly, the inosine 5'-monophosphate dehydrogenase gene (S10), the SEC65-signal recognition particle subunit gene (S11), or their combination (S10 + S11) were suitable for normalization of S. scitamineum gene expression in sugarcane bud tissues.

CONCLUSIONS

The PCR reference genes ACAD, SARMp1, S10, and S11 may be employed in gene transcriptional studies involving the sugarcane-S. scitamineum interaction system.

The Systematic Investigation of the Quorum Sensing System of the Biocontrol Strain Pseudomonas chlororaphis subsp. aurantiaca PB-St2 Unveils aurI to Be a Biosynthetic Origin for 3-Oxo-Homoserine Lactones

The shoot endophytic biocontrol strain Pseudomonas chlororaphis subsp. aurantiaca PB-St2 produces a wide range of exoproducts, including enzymes and antibiotics. The production of exoproducts is commonly tightly regulated. In order to get a deeper insight into the regulatory network of PB-St2, the strain was systematically investigated regarding its quorum sensing systems, both on the genetic and metabolic level. The genome analysis of PB-St2 revealed the presence of four putative acyl homoserine lactone (AHL) biosynthesis genes: phzI, csaI, aurI, and hdtS. LC-MS/MS analyses of the crude supernatant extracts demonstrated that PB-St2 produces eight AHLs. In addition, the concentration of all AHL derivatives was quantified time-resolved in parallel over a period of 42 h during the growth of P. aurantiaca PB-St2, resulting in production curves, which showed differences regarding the maximum levels of the AHLs (14.6 nM– 1.75 μM) and the production period. Cloning and heterologous overexpression of all identified AHL synthase genes in Escherichia coli proved the functionality of the resulting synthases PhzI, CsaI, and AurI. A clear AHL production pattern was assigned to each of these three AHL synthases, while the HdtS synthase did not lead to any AHL production. Furthermore, the heterologous expression study demonstrated unequivocally and for the first time that AurI directs the synthesis of two 3-oxo-AHLs.