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

Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil

Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the "biosynthesis process". Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.

Metagenomics reveals the variations in functional metabolism associated with greenhouse gas emissions during legume-vegetable rotation process

Legume-based rotation is commonly recognized for its mitigation efficiency of greenhouse gas (GHG) emissions. However, variations in GHG emission-associated metabolic functions during the legume-vegetable rotation process remain largely uncharacterized. Accordingly, a soybean-radish rotation field experiment was designed to clarify the responses of microbial communities and their GHG emission-associated functional metabolism through metagenomics. The results showed that the contents of soil organic carbon and total phosphorus significantly decreased during the soybean-radish process (P < 0.05), while soil total potassium content and bacterial richness and diversity significantly increased (P < 0.05). Moreover, the predominant bacterial phyla varied, with a decrease in the relative abundance of Proteobacteria and an increase in the relative abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi. Metagenomics clarified that bacterial carbohydrate metabolism substantially increased during the rotation process, whereas formaldehyde assimilation, methanogenesis, nitrification, and dissimilatory nitrate reduction decreased (P < 0.05). Specifically, the expression of phosphate acetyltransferase (functional methanogenesis gene, pta) and nitrate reductase gamma subunit (functional dissimilatory nitrate reduction gene, narI) was inhibited, indicating of low methane production and nitrogen metabolism. Additionally, the partial least squares path model revealed that the Shannon diversity index was negatively correlated with methane and nitrogen metabolism (P < 0.01), further demonstrating that the response of the soil bacterial microbiome responses are closely linked with GHG-associated metabolism during the soybean-radish rotation process. Collectively, our findings shed light on the responses of soil microbial communities to functional metabolism associated with GHG emissions and provide important insights to mitigate GHG emissions during the rotational cropping of legumes and vegetables.

Influence of rice-wheat and sugarcane-wheat rotations on microbial diversity and plant growth promoting bacteria: Insights from high-throughput sequencing and soil analysis

Wheat is a staple food crop, primarily grown in India's Indo-Gangetic plains, crucial for sustaining the region. Soil quality, vitality, and microbial inhabitants' interplay are pivotal. However, very little information is available on the impacts of agricultural practices, such as crop rotation and cropping systems, on the diversity of both bulk soil (BS) and rhizospheric soil (RS) microbiota. The impact of two different cropping systems, rice-wheat (RW) and sugarcane-wheat (SW) on soil properties, microbial diversity, and plant growth-promoting bacteria (PGPB) in wheat cultivation was investigated in the Indo-Gangetic plains of India. Microbial richness and diversity were analyzed using 16S rRNA sequencing, which reveals distinct clustering patterns between RS and BS, with higher diversity in BS of RW and higher richness in RS of SW. Notably, Proteobacteria dominated across all samples, along with Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Firmicutes, Planctomycetes, candidate division TM7, Cyanobacteria, and Nitrospirae. Intriguingly, the RS associated with the SW system exhibited the presence of 67 distinct genera, whereas the RS under the RW system showed 48 such genera. Within the realm of specific microbial genera exhibiting plant growth-promoting (PGP) activity, a higher abundance was noted in the RS (17.48%), as opposed to the BS (15.21%). Moreover, certain genera such as Haliangium, Iamia, Bacillus, Gaiella, Candidatus_Entotheonella, Anaerolinea, and Anaeromyxobacter, were found to be positively correlated with the availability of nitrogen, phosphorus, potassium, iron, and sulfur. The study sheds light on the intricate relationships between cropping practices, soil properties, and microbial dynamics, contributing to the development of sustainable agricultural practices for wheat cultivation.

Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields

Over the years, the microbial community of maize (Zea mays) rhizosphere has been extensively studied; however, the role of microdiversity sustain rhizosphere-associated microbial species distribution from root surface to bulk soil in mature maize is still unclear. Although operational taxonomic units (OTUs) have been used to classify species, amplicon sequence variants (ASVs) have been shown to be effective in representing microdiversity within OTUs at a finer genetic scale. Therefore, the aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients from root surface to bulk soil at the OTU and ASV levels. Here, the microbial community structures of bulk, loosely bound, and tightly bound soil samples from maize rhizosphere were examined at OTU and ASV levels. The results showed that OTU and ASV methods exhibited similar microbial community structures in rhizosphere. Additionally, different ecotypes with varying distributions and habitat preferences were observed within the same bacterial OTU at the ASV level, indicating a rich bacterial microdiversity. In contrast, the fungal community exhibited low microdiversity, with no significant relationship between fungal microdiversity and persistence and variability. Moreover, the ecotypes observed within the bacterial OTUs were found to be positively or negatively associated with environmental factors, such as soil organic carbon (SOC), NO3 --N, NH4 +-N contents, and pH. Overall, the results showed that the rich microdiversity could sustain the distribution of rhizosphere-associated bacterial species across environmental gradients from root surface to bulk soil. Further genetic analyses of rhizosphere-associated bacterial species could have considerable implications for potential mediation of microdiversity for sustainable crop production.

Rare rhizo-Actinomycetes: A new source of agroactive metabolites

Numerous biotic and abiotic stress in some geographical regions predisposed their agricultural matrix to challenges threatening plant productivity, health, and quality. In curbing these threats, different customary agrarian principles have been created through research and development, ranging from chemical inputs and genetic modification of crops to the recently trending smart agricultural technology. But the peculiarities associated with these methods have made agriculturists rely on plant rhizospheric microbiome services, particularly bacteria. Several bacterial resources like Proteobacteria, Firmicutes, Acidobacteria, and Actinomycetes (Streptomycetes) are prominent as bioinoculants or the application of their by-products in alleviating biotic/abiotic stress have been extensively studied, with a dearth in the application of rare Actinomycetes metabolites. Rare Actinomycetes are known for their colossal genome, containing well-preserved genes coding for prolific secondary metabolites with many agroactive functionalities that can revolutionize the agricultural industry. Therefore, the imperativeness of this review to express the occurrence and distributions of rare Actinomycetes diversity, plant and soil-associated habitats, successional track in the rhizosphere under diverse stress, and their agroactive metabolite characteristics and functionalities that can remediate the challenges associated with agricultural productivity.

Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize-cabbage rotation

Crop rotation is an important agricultural practice for homeostatic crop cultivation. Here, we applied high-throughput sequencing of ribosomal RNA gene amplicons to investigate soil biota in two fields of central Japan with different histories of maize-cabbage rotation. We identified 3086 eukaryotic and 17,069 prokaryotic sequence variants (SVs) from soil samples from two fields rotating two crops at three different growth stages. The eukaryotic and prokaryotic communities in the four sample groups of two crops and two fields were clearly distinguished using β-diversity analysis. Redundancy analysis showed the relationships of the communities in the fields to pH and nutrient, humus, and/or water content. The complexity of eukaryotic and prokaryotic networks was apparently higher in the cabbage-cultivated soils than those in the maize-cultivated soils. The node SVs (nSVs) of the networks were mainly derived from two eukaryotic phyla: Ascomycota and Cercozoa, and four prokaryotic phyla: Pseudomonadota, Acidobacteriota, Actinomycetota, and Gemmatimonadota. The networks were complexed by cropping from maize to cabbage, suggesting the formation of a flexible network under crop rotation. Ten out of the 16 eukaryotic nSVs were specifically found in the cabbage-cultivated soils were derived from protists, indicating the potential contribution of protists to the formation of complex eukaryotic networks.

Effects of the dual inoculation of dark septate endophytes and Trichoderma koningiopsis on blueberry growth and rhizosphere soil microorganisms

Blueberry is a shallow root plant in which the absorption of nutrients is inefficient, resulting in slow growth under artificial cultivation conditions. Endophytes play an important role in promoting plant growth; however, the effects of Trichoderma spp. and dark septate endophytes (DSEs) on host plant growth and soil microorganisms are still debatable. We isolated two endophytic fungal species, Trichoderma koningiopsis (TK) and a DSE (Amesia nigricolor; AN), from blueberry roots, which can solubilize insoluble phosphorus and produce amylase and cellulase to promote plant growth. We found that under dual inoculation, the colonization rate and colonization intensity of TK were higher than they were under single inoculation with TK, while the colonization rate and colonization intensity of AN were lower under dual inoculation than under single inoculation with AN. The plant nutrients, root activity, available potassium, and parts of soil phosphatase activities were highest under dual inoculation. TK inoculation resulted in the highest diversity and richness in the soil fungi and bacteria, followed by dual inoculation. The abundance of Ascomycota, Acidobacteriae, Firmicutes, and Actinobacteriota increased significantly, resulting in Trichoderma and Vicinamibacteria inoculated with TK, Chaetomium and Alicyclobacillales inoculated with AN, and Hypocreales and Burkholderiaceae with dual inoculation enriched in the soil.

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.

The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with Solanum lycopersicum

Powdery mildew disease caused by Oidium neolycopersici is one of the major diseases affecting tomato production in South Africa. Interestingly, limited studies exist on how this disease affects the community structure microbial communities associated with tomato plants employing shotgun metagenomics. In this study, we assess how the health status of a tomato plant affects the diversity of the rhizosphere microbial community. We collected soil samples from the rhizosphere of healthy (HR) and diseased (DR; powdery mildew infected) tomatoes, alongside bulk soil (BR), extracted DNA, and did sequencing using shotgun metagenomics. Our results demonstrated that the rhizosphere microbiome alongside some specific functions were abundant in HR followed by DR and bulk soil (BR) in the order HR > DR > BR. We found eighteen (18) bacterial phyla abundant in HR, including Actinobacteria, Acidobacteria, Aquificae, Bacteroidetes, etc. The dominant fungal phyla include; Ascomycota and Basidiomycota, while the prominent archaeal phyla are Thaumarchaeota, Crenarchaeota, and Euryarchaeota. Three (3) bacteria phyla dominated the DR samples; Bacteroidetes, Gemmatimonadetes, and Thermotoga. Our result also employed the SEED subsystem and revealed that the metabolic pathways involved were abundant in HR. The α-diversity demonstrates that there is no significant difference among the rhizosphere microbiomes across the sites, while β-diversity demonstrated a significant difference.

Recent Developments in the Study of Plant Microbiomes

To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions.