Elucidating mechanisms of endophytes used in plant protection and other bioactivities with multifunctional prospects

Endophytes are abundant in plants and studies are continuously emanating on their ability to protect plants from pathogens that cause diseases especially in the field of agriculture. The advantage that endophytes have over other biocontrol agents is the ability to colonize plant's internal tissues. Despite this attributes, a deep understanding of the mechanism employed by endophytes in protecting the plant from diseases is still required for both effectiveness and commercialization. Also, there are increasing cases of antibiotics resistance among most causative agents of diseases in human beings, which calls for an alternative drug discovery using natural sources. Endophytes present themselves as a storehouse of many bioactive metabolites such as phenolic acids, alkaloids, quinones, steroids, saponins, tannins, and terpenoids which makes them a promising candidate for anticancer, antimalarial, antituberculosis, antiviral, antidiabetic, anti-inflammatory, antiarthritis, and immunosuppressive properties among many others, even though the primary function of bioactive compounds from endophytes is to make the host plants resistant to both abiotic and biotic stresses. Endophytes still present themselves as a peculiar source of possible drugs. This study elucidates the mechanisms employed by endophytes in protecting the plant from diseases and different bioactivities of importance to humans with a focus on endophytic bacteria and fungi

Isolation and characterization of beneficial indigenous endophytic bacteria for plant growth promoting activity in Molelwane Farm, Mafikeng, South Africa

Plant-associated bacteria that live inside plant tissues without causing any damage to plants are defined as endophytic bacteria. The present study was carried out to analyze the phenotypic and genotypic diversity of endophytic bacteria associated with Amaranthus hybridus, Solanum lycopersicum and Cucurbita maxima. A total of 50 bacteria were isolated from the roots of the plants. All the isolates were screened for morphological features (Gram reaction, pigmentation, odour, colour, motility and sharp). Isolates exhibiting difference in morphological features were selected for molecular identification. Eight isolates that exhibited differences in phenotypic aspect were subjected to partial 16S-rDNA gene sequencing using polymerase chain reaction (PCR) for phylogenetic analysis. Sequence analysis using Clustal-X version 1.83 software identified the following isolated bacteria: Stenotrophomonas maltophilia KC010525, Pseudomonas putida KC010526, P. putida KC010527, P. putida KC010528, S. maltophilia KC010529, Achromobacter xylosoxidans KC010530, A. xylosoxidans KC010531 and Achromobacte sp. KC010532. Further evaluation of the bacterial isolates for phosphate solubilization capacity, indole acetic acid (IAA), hydrogen cyanide (HCN) and ammonium gas production, showed all eight bacterial isolates were able to produce IAA (0.32-2.42 mg/mgl-1). However, seven isolates excluding S. maltophilia KC010525 showed ability to produce ammonium. HCN was observed in six isolates: A. xylosoxidans KC010530, A. xylosoxidans KC010531, A. KC010532, P. putida KC010526, P. putida KC010527, and P. putida KC010528. When determining the phosphate solubilizing capacity, it was observed that seven solubilized insoluble phosphate in Pikovskya’s agar plates produced halo zones (1 to 4 mm). Seven tested bacteria were active against Fusarium oxysporum. Therefore, the results indicate that the bacteria isolates may be used as a promising microbial inoculant for plant growth and productivity.Keywords: Plant growth promoting rhizobacteria (PGPR), 16S-rDNA sequencing, HCN production, indole acetic acid (IAA), phosphate solubilization, antifungal activity.African Journal of Biotechnology Vol. 12(26), pp. 4105-411

Genomic mechanisms of plant growth-promoting bacteria in the production of leguminous crops

Legumes are highly nutritious in proteins and are good food for humans and animals because of their nutritional values. Plant growth-promoting bacteria (PGPR) are microbes dwelling in the rhizosphere soil of a plant contributing to the healthy status, growth promotion of crops, and preventing the invasion of diseases. Root exudates produced from the leguminous plants’ roots can lure microbes to migrate to the rhizosphere region in other to carry out their potential activities which reveals the symbiotic association of the leguminous plant and the PGPR (rhizobia). To have a better cognition of the PGPR in the rhizosphere of leguminous plants, genomic analyses would be conducted employing various genomic sequences to observe the microbial community and their functions in the soil. Comparative genomic mechanism of plant growth-promoting rhizobacteria (PGPR) was discussed in this review which reveals the activities including plant growth promotion, phosphate solubilization, production of hormones, and plant growth-promoting genes required for plant development. Progress in genomics to improve the collection of genotyping data was revealed in this review. Furthermore, the review also revealed the significance of plant breeding and other analyses involving transcriptomics in bioeconomy promotion. This technological innovation improves abundant yield and nutritional requirements of the crops in unfavorable environmental conditions

Unravelling the endophytic virome inhabiting maize plant

Endophytes are well-known for their symbiotic interaction with plants and their ability to promote plant growth by producing various metabolites. The most well-studied endophytes are bacteria and fungi. For generations, viruses were misnamed, and their symbiotic associations were ambiguous. Recent advances in omics techniques, particularly next-generation sequencing, have given rise to novel developments in the mutualistic relationships that exist between plants and viruses. Endogenous viruses have received a lot of attention in the animal world, but limited information exists on their functions and importance to plants. Therefore, endophytic viral populations inhabiting the root of a maize plant were assessed in this study for the first time using shotgun metagenomics. Complete DNA was extracted and sequenced using shotgun metagenomics from the maize roots in farming sites where organic fertilization (FZ), inorganic fertilization (CZ), and maize planted with no fertilization (NZ) are being practised in an experimental field. Our results identified 2 orders namely: Caudovirales (67.5%) and Herpesvirales (28.5%) which dominated the FZ site, although they do not show any significant difference (p > 0.05) across the sites. At the class level Microviridae, Phycodnaviridae, Podoviridae, Phycodnaviridae, and Poxviridae dominated the FZ site. Myoviridae and Podoviridae were more abundant in the CZ site, while only Siphoviridae predominated the inorganic fertiliser site (NZ). Diversity analysis revealed that viral populations were more abundant in organic fertilization (FZ). Taken together, this research adds to our understanding of the symbiotic integration of endophytic viruses with maize plants and that their abundance is affected by farming practices. In addition, their potential can be exploited to solve a variety of agronomic issues

Shotgun metagenomics reveals the functional diversity of root-associated endophytic microbiomes in maize plant

In this study, we used shotgun metagenomics to analyze the whole DNA from maize root planted with different fertilization and without fertilization in a bid to profile the impact of fertilizer applications on the functional diversity of endophytic microbiomes. Complete DNA extraction from roots of maize plant grown on different farming sites such as organic (FK), inorganic (NK) and no fertilizer (CK) sites was carried out, and sequenced using a shotgun metagenomic approach. The raw sequenced data obtained were analyzed using an online database called MG-RAST. Through MG-RAST analysis, endophytic microbiome sequences were identified while sequences of maize origin were discarded. The prediction of the functions of the endophytic microbiomes was done using the SEED subsystem. Our results revealed that no significant difference (P > 0.05) exist in the relative abundance of the 28 functional groups identified within the endophytic microbiomes across the sites. Also, some functional groups and metabolic pathways associated with plant growth promotion such as carbohydrate, secondary metabolism, nitrogen metabolism, iron acquisition and metabolism alongside phosphorus metabolism were observed in the endophytes across the sites. Alpha diversity study revealed no significant difference exist among the functional groups of the endophytes across the sites, while beta diversity study indicated that there was a significant difference (P = 0.01) among the functional groups of the endophytes across the fertilizer sites. Going by the high abundance of functional groups observed in this study, especially in FK samples, it is evident that different farming practices influenced the functions of endophytic microbiomes. We recommend that further studies should explore the functional genes in endophytic microbiomes with the aim of assessing their usefulness in promoting sustainable agriculture

Forest plantations reduce soil functioning in terrestrial ecosystems from South Africa

The role of forest plantations in regulating soil ecosystem functions remains poorly understood in terrestrial ecosystems from Africa. Here, we evaluated the importance of forest plantations in regulating soil microbial functional profiles, community-level physiological profiles (CLPPs) and activities of soil microbial communities compared with native forests in two contrasting seasons. We found that forest plantations consistently reduced the rates of multiple soil functions associated with soil nutrient and carbon (C) cycling and shifted the activity and functional profile of microbial communities in two contrasting seasons and two independent regions from South Africa. Our results suggest land use changes from natural forests to plantations to maintain a continuously growing human population will have important negative consequences for soil functions in forest ecosystems from Africa with implications for ecosystem functioning under changing environments

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

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

The potential role of microbial biostimulants in the amelioration of climate change-associated abiotic stresses on crops

4openInternationalInternational coauthor/editorCrop plants are more often exposed to abiotic stresses in the current age of fast-evolving climate change. This includes exposure to extreme and unpredictable changes in climatic conditions, phytosanitary hazards, and cultivation conditions, which results in drastic losses in worldwide agricultural productions. Plants coexist with microbial symbionts, some of which play key roles in the ecosystem and plant processes. The application of microbial biostimulants, which take advantage of symbiotic relationships, is a long-term strategy for improving plant productivity and performance, even in the face of climate change-associated stresses. Beneficial filamentous fungi, yeasts, and bacteria are examples of microbial biostimulants, which can boost the growth, yield, nutrition and stress tolerance in plants. This paper highlights recent information about the role of microbial biostimulants and their potential application in mitigating the abiotic stresses occurring on crop plants due to climate change. A critical evaluation for their efficient use under diverse climatic conditions is also made. Currently, accessible products generally improve cultural conditions, but their action mechanisms are mostly unknown, and their benefits are frequently inconsistent. Thus, further studies that could lead to the more precisely targeted products are discussedopenFadiji, Ayomide Emmanuel; Babalola, Olubukola Oluranti; Santoyo, Gustavo; Perazzolli, MicheleFadiji, A.E.; Babalola, O.O.; Santoyo, G.; Perazzolli, M

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