Composting is the controlled conversion of degradable organic products and wastes into stable products with the aid of microorganisms. Composting is a long-used technology, though it has some shortcomings that have reduced its extensive usage and efficiency. The shortcomings include pathogen detection, low nutrient status, long duration of composting, long mineralization duration, and odor production. These challenges have publicized the use of chemical fertilizers produced through the Haber–Bosch process as an alternative to compost over time. Chemical fertilizers make nutrients readily available to plants, but their disadvantages outweigh their advantages. For example, chemical fertilizers contribute to greenhouse effects, environmental pollution, death of soil organisms and marine inhabitants, ozone layer depletion, and human diseases. These have resulted in farmers reverting to the application of composts as a means of restoring soil fertility. Composting is a fundamental process in agriculture and helps in the recycling of farm wastes. The long duration of composting is a challenge; this is due to the presence of materials that take a longer time to compost, especially during co-composting. This review discusses the proper management of wastes through composting, different composting methods, the factors affecting composting, long-duration composting, the mechanism behind it, the present trends in composting and prospects. The extraction of mono-fertilizers from compost, development of strips to test for the availability of heavy metals and pathogens as well as an odor-trapping technique can go a long way in enhancing composting techniques. The addition of activators to raw materials can help to improve the nutritional quality of compost. This review further recommends that degradable organic material in which composts slowly should be assessed for their ability to mineralize slowly, which could make them advantageous to perennial or biennial crops. Viricides, fungicides, anti-nematodes, and anti-bacterial of plant or organic sources could as well be added to improve compost quality. The enhancement of composting duration will also be useful.

Soil degradation remains an ongoing process that is exacerbated by the effects of climate change. Consequently, these processes decrease soil organic matter and nutrient contents, soil biological functions, and plant productivity. The addition of organic amendments (OAs) to the soil is a widespread practice to enhance soil quality and the health of agricultural soils. One of the most significant microbial hotspots controlling the processes, dynamics, and cycling of nutrients, carbon and water in terrestrial ecosystems is the rhizosphere. Understanding the continuing transformations of OAs and the distribution of different factors (C, nutrients, and microbial activities) across and along roots is crucial in the rhizosphere. The application of OAs to soil increases soil organic matter and nutrients, water holding capacity, improves soil structure and stimulates soil microbial activity and biomass. This review evaluates the role of the rhizosphere microbial community in organically amended soils for promoting plant growth and health. The diversity of the rhizosphere microbiome and the mechanisms used in plant protection are discussed.

The findings on the strategies employed by endophytic microbes have provided salient information to the researchers on the need to maximally explore them as bio-input in agricultural biotechnology. Biotic and abiotic factors are known to influence microbial recruitments from external plant environments into plant tissues. Endophytic microbes exhibit mutualism or antagonism association with host plants. The beneficial types contribute to plant growth and soil health, directly or indirectly. Strategies to enhance the use of endophytic microbes are desirable in modern agriculture, such that these microbes can be applied individually or combined as bioinoculants with bioprospecting in crop breeding systems. Scant information is available on the strategies for shaping the endophytic microbiome; hence, the need to unravel microbial strategies for yield enhancement and pathogen suppressiveness have become imperative. Therefore, this review focuses on the endophytic microbiome, mechanisms, factors influencing endophyte recruitment, and strategies for possible exploration as bioinoculants.

Bacillusspecies genomes are rich in plant growth-promoting genetic elements.Bacillus subtilisandBacillus velezensisare important plant growth promoters; hence, to further improve their abilities, the genetic elements responsible for these traits were characterized and reported. Genetic elements reported include those of auxin, nitrogen fixation, siderophore production, iron acquisition, volatile organic compounds, and antibiotics. Furthermore, the presence of phages and antibiotic-resistant genes in the genomes are reported. Pan-genome analysis was conducted using tenBacillusspecies. From the analysis, pan-genome ofBacillus subtilisandBacillus velezensisare still open. Ultimately, this study brings an insight into the genetic components of the plant growth-promoting abilities of these strains and shows their potential biotechnological applications in agriculture and other relevant sectors.

The uncontrolled use of chemicals, urban wastes, nuclear resources, mining, petrochemicals and disposal of sewage sludge only a few anthropogenic activities that have contributed to the rapid industrialization and severe heavy metal contamination of soils and waterways. Both inorganic and organic pollutants, such as heavy metals, pesticides, petroleum hydrocarbons, and polycyclic aromatic hydrocarbons, can impact the composition and functionality of soils. Soils and plants are affected by pollution, thus, pose a dire threat to food security. This directly renders the soil unuseful for agricultural purposes, destroys the beneficial microbes in the soil, reduces the soil organic matter content, causes the imbalance of soil nutrients, affects plant growth and the interaction between the plants and microbes, subsequently affecting the soil and crop productivity. In addition, environmental pollutants affect human health, leading to different illnesses such as headaches, allergies, coughs, depression, chest pain, nausea, diabetes, liver problems, cancers, eye problems, and so on. Remediation (physical, chemical or biological) is therefore necessary to reduce the impacts of these pollutants in the environment. Bioremediations involve using natural products from plants, microbes, and so on, to detoxify the environment and make it useful or productive again. A key type of remediation is the Remediation by Enhanced Natural Attenuation (RENA) which involves the turning of soil to promote microbial proliferation, aeration, nutrient availability, moisture and consequently, the degradation of pollutants. This review discusses the technology of RENA, the associated microbes, the mechanism of its action, challenges associated with its usage and recommendations to advance the use of RENA for a sustainable environment.

The extreme conditions linked with abiotic stresses have greatly affected soil and plant health. The diverse biochemical activities occurring in the soil environment have been attributed to shaping the dynamics of plant–soil microbiomes by contributing to microbial lifestyles and enhancing microbial functional properties to boost plant tolerance to abiotic-induced stresses. Soil microbiomes play crucial roles in enhancing plant nutrition and abiotic stress management through diverse mechanisms. With the current insights into the use of engineered soil microbes as single or combined inoculants, their use has contributed to plant fitness and stability under different environmental stress conditions by activating plant defense mechanisms, enzyme production (lowering free radicals resulting in plant oxidative stress), protein regulation, and the production of growth factors. The detection of certain genes involved in the growth factors can underline microbial functions in mitigating plant stress. Hence, the projections for sustainable eco-friendly agriculture with the possible exploration of beneficial rhizosphere microbes to manage the effect of abiotic stress on plant nutrition remain critical points of discussion recently, with prospects for ensuring food security. Therefore, this review focuses on the impacts of soil microbiomes in abiotic stress mitigation for enhancing plant nutrition.