Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach.

Understanding the functions carried out by rhizosphere microbiomes will further explore their importance in biotechnological improvement and agricultural sustainability. This study presents one of the foremost attempts to understand the functional diversity of the rhizosphere microbiome in mono-cropping and crop rotation farming sites using shotgun metagenomic techniques. We hypothesized that the functional diversity would vary in the cropping sites and more abundant in the rotational cropping site. Hence, we carried out complete DNA extraction from the bulk and rhizospheric soils associated with maize plant cultivated on the mono-cropping farm (LT and LTc) and the crop rotation farm (VD and VDc), respectively, and sequenced employing shotgun approach. Using the SEED subsystem, our result revealed that a total of 24 functional categories dominated the rotational cropping site, while four functional categories dominated the mono-cropping sites. Alpha diversity assessment showed that no significant difference (p > 0.05) was observed across the cropping sites, while beta diversity assessment revealed a significant difference. Going by the high abundance of functional groups observed in the samples from the crop rotational site, it is evident that cropping systems influenced the functions of soil microbiomes. Worthy of note is the high abundance of unknown functions associated with these maize rhizosphere microbiomes. This is an indication that there are still some under-investigated functional genes associated with the maize rhizosphere microbiome. It is, therefore, imperative that further studies explore these functional genes for their agricultural and biotechnological potentials.

Metagenomic profiling of rhizosphere microbial community structure and diversity associated with maize plant as affected by cropping systems.

Soil microbial diversity is believed to be vital in maintaining soil quality and health. Limited knowledge exists on the impact of cropping systems (mono-cropping and crop rotation) on the diversity of the whole soil microbiome. In this study, we investigated the effects of two cropping systems, namely crop rotation and mono-cropping, on the community structure and diversity of rhizosphere microbiome in the rhizosphere and bulk soil associated with maize plant using shotgun metagenomics. Whole DNA was extracted from bulk, and rhizosphere soils associated with maize plant from the mono-cropping (LT and LTc) and crop rotation (VD and VDc) sites, respectively, and sequenced employing shotgun metagenomics. The results obtained via the Subsystem database showed 23 bacteria, 2 fungi, and 3 archaea most abundant phyla. The major bacterial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Cyanobacteria, Spirochaetes, Aquificae, Verrucomicrobia, Chloroflexi, Planctomycetes, and Chlorobi. The major fungi phyla observed were Ascomycota and Basidiomycota, while the dominant archaea phyla are Euryarchaeota, Thaumarchaeota, and Crenarchaeota. Our diversity assessment showed that the rhizosphere microbial community was more abundant in the samples from the rotational crop site following VD>VDc>LT>LTc. Alpha diversity showed that there was no significant difference (P>0.05) in the soil microbial communities (P>0.05), while better diversity indicated that a significant difference (P = 0.01) occurred. Taken together, crop rotational practice was found to positively influence the rhizosphere microbial community associated with the maize plant.

Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plant.

This study investigated the diversity, structure and nutrient pathways of the root-associated bacterial endophytes of maize plant cultivated using different fertilizers to verify the claim that inorganic fertilizers have some toxic effects on plant microbiome and not are ecofriendly. Whole DNA was extracted from the roots of maize plants cultivated with organic fertilizer, inorganic fertilizer and maize planted without any fertilizer at different planting sites in an experimental field and sequenced using shotgun metagenomics. Our results using the Subsystem database revealed a total of 28 phyla and different nutrient pathways in all the samples. The major phyla observed were Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, Tenericutes, Planctomycetes, Cyanobacteria, and Chlorobi. Bacteroidetes dominated maize from organic fertilizer sites, Firmicutes dominated the no fertilizers site while Proteobacteria dominated Inorganic fertilizer. The diversity analysis showed that the abundance of endophytic bacteria in all the sites is in the order organic fertilizer (FK) > no fertilizer (CK) > inorganic fertilizer (NK). Furthermore, the major nutrient cycling pathways identified are linked with nitrogen and phosphorus metabolism which were higher in FK samples. Going by the results obtained, this study suggests that organic fertilizer could be a boost to sustainable agricultural practices and should be encouraged. Also, a lot of novel endophytic bacteria groups were identified in maize. Mapping out strategies to isolate and purify this novel endophytic bacteria could help in promoting sustainable agriculture alongside biotechnological applications in future.

Anthropogenic fertilization influences a shift in barley rhizosphere microbial communities.

Background: Anthropogenic mediations contribute a significant role in stimulating positive reactions in soil-plant interactions; however, methodical reports on how anthropogenic activities impact soil microorganism-induced properties and soil health are still inadequate. In this study, we evaluated the influence of anthropogenic fertilization of farmland soil on barley rhizosphere microbial community structure and diversity, and the significant impacts on agro-ecosystem productivity. This will help validate the premise that soil amendment with prolonged synthetic fertilizers can lead to a significant reduction in bacterial abundance and diversity, while soils amended with organic fertilizers elicit the succession of the native soil microbial community and favor the growth of copiotrophic bacteria. Methods: The total metagenomic DNA was extracted from soils obtained from the barley rhizosphere under chemical fertilization (CB), organic fertilization (OB), and bulk soil (NB). Subsequently, these samples were sequenced using an amplicon-based sequencing approach, and the raw sequence dataset was examined using a metagenomic rast server (MG-RAST). Results: Our findings showed that all environments (CB, OB, and NB) shared numerous soil bacterial phyla but with different compositions. However, Bacteroidetes, Proteobacteria, and Actinobacteria predominated in the barley rhizosphere under chemical fertilization, organic fertilization, and bulk soils, respectively. Alpha and beta diversity analysis showed that the diversity of bacteria under organic barley rhizosphere was significantly higher and more evenly distributed than bacteria under chemical fertilization and bulk soil. Conclusion: Understanding the impact of conventional and organic fertilizers on the structure, composition, and diversity of the rhizosphere microbiome will assist in soil engineering to enhance microbial diversity in the agroecosystem.

Isolation and Characterization of Plant-Growth-Promoting, Drought-Tolerant Rhizobacteria for Improved Maize Productivity.

Drought is one of the main abiotic factors affecting global agricultural productivity. However, the application of bioinocula containing plant-growth-promoting rhizobacteria (PGPR) has been seen as a potential environmentally friendly technology for increasing plants' resistance to water stress. In this study, rhizobacteria strains were isolated from maize (Zea mays L.) and subjected to drought tolerance tests at varying concentrations using polyethylene glycol (PEG)-8000 and screened for plant-growth-promoting activities. From this study, 11 bacterial isolates were characterized and identified molecularly, which include Bacillus licheniformis A5-1, Aeromonas caviae A1-2, A. veronii C7_8, B. cereus B8-3, P. endophytica A10-11, B. halotolerans A9-10, B. licheniformis B9-5, B. simplex B15-6, Priestia flexa B12-4, Priestia flexa C6-7, and Priestia aryabhattai C1-9. All isolates were positive for indole-3-acetic acid (IAA), siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, ammonia production, nitrogen fixation, and phosphate solubilization, but negative for hydrogen cyanide production. Aeromonas strains A1-2 and C7_8, showing the highest drought tolerance of 0.71 and 0.77, respectively, were selected for bioinoculation, singularly and combined. An increase in the above- and below-ground biomass of the maize plants at 100, 50, and 25% water-holding capacity (WHC) was recorded. Bacterial inoculants, which showed an increase in the aerial biomass of plants subjected to moderate water deficiency by up to 89%, suggested that they can be suitable candidates to enhance drought tolerance and nutrient acquisition and mitigate the impacts of water stress on plants.

Dataset of shotgun metagenomic evaluation of lettuce (Lactuta sativa L.) rhizosphere microbiome.

Lettuce (Lactuca sativa L.) is an important vegetable grown and consumed across the world, including South Africa and its rhizosphere constitutes a dynamic community of root associated microbes. Dataset of the microbial community profile of the lettuce rhizospheric soils obtained from Talton, Gauteng Province of South Africa was subjected to metagenomic evaluation using the shotgun approach. The whole DNA isolated from the community was sequenced using NovaSeq 6000 system (Illumina). The raw data obtained consists of 129,063,513.33 sequences with an average length of 200 base pairs and 60.6% Guanine + Cytosine content. The metagenome data has been deposited to the National Centre for Biotechnology Information SRA under the bioproject number PRJNA763048. The downstream analysis alongside taxonomical annotation carried out using an online server MG-RAST, showed the community analysis as being made up of archaea (0.95%), eukaryotes (1.36%), viruses (0.04%), while 97.65% of the sequences were classified as bacteria. A sum of 25 bacteria, 20 eukaryotic and 4 archaea phyla were identified. The predominant genera were Acinetobacter (4.85%), Pseudomonas (3.41%), Streptomyces (2.79%), Candidatus solibacter (1.93%), Burkholderia (1.65%), Bradyrhizobium (1.51%) and Mycobacterium (1.31%). Annotation using Cluster of Orthologous Group (COG) showed 23.91% of the sequenced data were for metabolic function, 33.08% for chemical process and signaling while 6.42% were poorly characterized. Furthermore, the subsystem annotation method showed that sequences were majorly associated with carbohydrates (12.86%), clustering-based subsystems (12.68%), and genes coding for amino acids and derivatives (10.04%), all of which could serve in growth promotion and plant management.

Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum.

The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.

A Potential Draft Sequence Analysis of Enterobacter asburiae Strain B6_18 of an Endophytic Bacterium.

The work presented here describes the genomic analysis of the maize plant-isolated endophytic strain Enterobacter asburiae B6_18 from Northwest Province, South Africa, for potential maize plant growth-promoting traits.

Draft Genome Sequence of Citrobacter freundii AYS58, a Potential Plant Growth-Promoting Endophyte.

Here, we report the draft genome sequence of Citrobacter freundii AYS58, an endophyte isolated from the roots of a maize plant in Mafikeng, South Africa. The genome was 5,569,547 bp and exhibited a GC content of 50.5% and 5,904 genes, with 5,658 coding sequences, 3 rRNAs, 82 tRNAs, and 1 CRISPR.

Communication between Plants and Rhizosphere Microbiome: Exploring the Root Microbiome for Sustainable Agriculture.

Plant roots host numerous microorganisms around and inside their roots, forming a community known as the root microbiome. An increasing bulk of research is underlining the influences root-associated microbial communities can have on plant health and development. However, knowledge on how plant roots and their associated microbes interact to bring about crop growth and yield is limited. Here, we presented (i) the communication strategies between plant roots and root-associated microbes and (ii) the applications of plant root-associated microbes in enhancing plant growth and yield. This review has been divided into three main sections: communications between root microbiome and plant root; the mechanism employed by root-associated microbes; and the chemical communication mechanisms between plants and microbes and their application in plant growth and yield. Understanding how plant root and root-associated microbes communicate is vital in designing ecofriendly strategies for targeted disease suppression and improved plant growth that will help in sustainable agriculture. Ensuring that plants become healthy and productive entails keeping plants under surveillance around the roots to recognize disease-causing microbes and similarly exploit the services of beneficial microorganisms in nutrient acquisition, stress mitigation, and growth promotion.

Maize rhizosphere modulates the microbiome diversity and community structure to enhance plant health.

Metagenomic has been explored in investigating microbiome diversity. However, there is limited available information on its application towards securing plant health. Hence, this study adopts the metagenomic approach to unravel the microbiome diversity associated with healthy (LI and MA) and Northern corn leaf blight (NCLB) infected (LID and MAD) maize rhizosphere in the maize growing field at Lichtenburg and Mafikeng, North-West province of South Africa. The extraction of whole DNA from the respective healthy and diseased rhizosphere soils was conducted and sequenced using shotgun metagenomics. A total of 12 bacteria, 4 archaea and 2 fungal phyla were found as predominant across the fields with the use of the SEED subsystem database. The most predominant bacteria phyla included Proteobacteria, Dienococcus-Thermus, Gemmatimonadetes, Chlorobi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Acidobacteria, Firmicutes, Chloroflexi and Bacteroidetes. Archaea consisted of Euryarchaeota, Thaumarchaeota, Crenarchaeota and Korachaeota, while Ascomycota and Basidiomycota were the dominant fungal phyla. Microbial abundance and diversity were higher in the rhizosphere of healthy maize (LI and MA) rhizosphere as compared to the NCLB diseased (LID and MAD), in the order LI > MA > LID > MAD. At phylum and genus level, alpha diversity index showed no significant (p > 0.05) difference in the abundance of the microbial community of healthy and NCLB infected maize rhizosphere, while beta analysis produced a significant (p = 0.01) difference in the microbial diversity in the soil. Taken together, the study revealed that the abundance of microbial diversity in the maize rhizosphere influences the efficacy of the rhizosphere microbiome to modulate microbial functions towards managing and sustaining plant health.

Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview.

Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth and development. Abiotic stressors like drought and excessive heat are expected to occur more frequently in the future due to climate change, which would reduce the yields of important crops like maize, wheat, and rice which may jeopardize the food security of human populations. The plant microbiomes are a varied and taxonomically organized microbial community that is connected to plants. By supplying nutrients and water to plants, and regulating their physiology and metabolism, plant microbiota frequently helps plants develop and tolerate abiotic stresses, which can boost crop yield under abiotic stresses. In this present study, with emphasis on temperature, salt, and drought stress, we describe current findings on how abiotic stresses impact the plants, microbiomes, microbe-microbe interactions, and plant-microbe interactions as the way microorganisms affect the metabolism and physiology of the plant. We also explore crucial measures that must be taken in applying plant microbiomes in agriculture practices faced with abiotic stresses.

Draft genome sequence of Acinetobacter sp. AYS6, a potential plant growth-promoting endophyte.

Here, we report the draft genome sequence of Acinetobacter sp. AYS6, an endophyte isolated from the roots of maize plant in Mafikeng, South Africa. The genome was 7,072,605 bp and exhibited a GC content of 45.6% and 3,654 genes with 3,539 coding sequences, 64 rRNA, 60 tRNAs, and 2 CRISPR.

Agroecological Management of the Grey Mould Fungus Botrytis cinerea by Plant Growth-Promoting Bacteria.

Botrytis cinerea is the causal agent of grey mould and one of the most important plant pathogens in the world because of the damage it causes to fruits and vegetables. Although the application of botrycides is one of the most common plant protection strategies used in the world, the application of plant-beneficial bacteria might replace botrycides facilitating agroecological production practices. Based on this, we reviewed the different stages of B. cinerea infection in plants and the biocontrol mechanisms exerted by plant-beneficial bacteria, including the well-known plant growth-promoting bacteria (PGPB). Some PGPB mechanisms to control grey mould disease include antibiosis, space occupation, nutrient uptake, ethylene modulation, and the induction of plant defence mechanisms. In addition, recent studies on the action of anti-Botrytis compounds produced by PGPB and how they damage the conidial and mycelial structures of the pathogen are reviewed. Likewise, the advantages of individual inoculations of PGPB versus those that require the joint action of antagonist agents (microbial consortia) are discussed. Finally, it should be emphasised that PGPB are an excellent option to prevent grey mould in different crops and their use should be expanded for environmentally friendly agricultural practices.

Trichoderma Species: Our Best Fungal Allies in the Biocontrol of Plant Diseases-A Review.

Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers.

Decrypting the multi-functional biological activators and inducers of defense responses against biotic stresses in plants.

Plant diseases are still the main problem for the reduction in crop yield and a threat to global food security. Additionally, excessive usage of chemical inputs such as pesticides and fungicides to control plant diseases have created another serious problem for human and environmental health. In view of this, the application of plant growth-promoting rhizobacteria (PGPR) for controlling plant disease incidences has been identified as an eco-friendly approach for coping with the food security issue. In this review, we have identified different ways by which PGPRs are capable of reducing phytopathogenic infestations and enhancing crop yield. PGPR suppresses plant diseases, both directly and indirectly, mediated by microbial metabolites and signaling components. Microbial synthesized anti-pathogenic metabolites such as siderophores, antibiotics, lytic enzymes, hydrogen cyanide, and several others act directly on phytopathogens. The indirect mechanisms of reducing plant disease infestation are caused by the stimulation of plant immune responses known as initiation of systemic resistance (ISR) which is mediated by triggering plant immune responses elicited through pathogen-associated molecular patterns (PAMPs). The ISR triggered in the infected region of the plant leads to the development of systemic acquired resistance (SAR) throughout the plant making the plant resistant to a wide range of pathogens. A number of PGPRs including Pseudomonas and Bacillus genera have proven their ability to stimulate ISR. However, there are still some challenges in the large-scale application and acceptance of PGPR for pest and disease management. Further, we discuss the newly formulated PGPR inoculants possessing both plant growth-promoting activities and plant disease suppression ability for a holistic approach to sustaining plant health and enhancing crop productivity.

Metagenomic Survey of Tomato Rhizosphere Microbiome Using the Shotgun Approach.

Food sustainability, e.g., fruit and vegetables, is a major agricultural problem that requires monitoring. Rhizosphere microbiomes' abundance and functionality are essential in promoting tomato plants' growth and health. We selected farms in South Africa's North West Province and present the metagenomes of their tomato rhizospheres and associated functional potentials.

Draft Genome Sequence of Aeromonas caviae Strain A1-2, a Potential Plant Growth-Promoting Rhizospheric Bacterium.

The genomic analysis of the plant growth-promoting rhizospheric Aeromonas caviae strain A1-2, which was isolated from a maize plant in Northwest Province, South Africa, is presented in this paper. Aeromonas caviae strain A1-2 demonstrates its potential to promote plant growth and enhance the tolerance of maize plants to drought stress.

Efforts towards overcoming drought stress in crops: Revisiting the mechanisms employed by plant growth-promoting bacteria.

Globally, agriculture is under a lot of pressure due to rising population and corresponding increases in food demand. However, several variables, including improper mechanization, limited arable land, and the presence of several biotic and abiotic pressures, continually impact agricultural productivity. Drought is a notable destructive abiotic stress and may be the most serious challenge confronting sustainable agriculture, resulting in a significant crop output deficiency. Numerous morphological and physiological changes occur in plants as a result of drought stress. Hence, there is a need to create mitigation techniques since these changes might permanently harm the plant. Current methods used to reduce the effects of drought stress include the use of film farming, super-absorbent hydrogels, nanoparticles, biochar, and drought-resistant plant cultivars. However, most of these activities are money and labor-intensive, which offer limited plant improvement. The use of plant-growth-promoting bacteria (PGPB) has proven to be a preferred method that offers several indirect and direct advantages in drought mitigation. PGPB are critical biological elements which have favorable impacts on plants' biochemical and physiological features, leading to improved sugar production, relative water content, leaf number, ascorbic acid levels, and photosynthetic pigment quantities. This present review revisited the impacts of PGPB in ameliorating the detrimental effects of drought stress on plants, explored the mechanism of action employed, as well as the major challenges encountered in their application for plant growth and development.

Draft Genome Sequence of Enterobacter mori AYS9, a Potential Plant Growth-Promoting Rhizobacterium.

Here, we report the draft genome sequence of Enterobacter mori AYS9, a rhizobacterium isolated from the rhizosphere of sorghum plants in South Africa. The genome sequence comprised 4,852,175 bp and exhibited a GC content of 55.5% and 4,567 genes, with 4,453 coding sequences, 3 rRNAs, 64 tRNAs, and 1 CRISPR.