Prospect and Challenges for Sustainable Management of Climate Change-Associated Stresses to Soil and Plant Health by Beneficial Rhizobacteria

Chapter 1 - Mechanisms of the phytomicrobiome for enhancing soil fertility and health

Organic Farming, Soil Health, and Food Quality: Considering Possible Links

Microplastic contamination poses a significant threat to agroecosystem functioning, provoking a move away from the use of conventional oil-based plastics in agriculture, to biodegradable alternatives that may be degraded over a shorter timescale. The impact of these bioplastics on plant and soil health, however, has received relatively little attention. Here, we investigated the effect of soil loading (0.01%, 0.1%, 1% and 10%) of biobased microplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) on soil and plant ( Zea mays L.) health and function. We showed that PHBV caused a dose-dependent reduction in plant growth and foliar nitrogen (N) content while untargeted metabolite analysis revealed significant shifts in foliar metabolic function. These results were also reflected in soil, where PHBV led to reduced plant availability of both ammonium and nitrate. Soil 14 C-isotope tracing and 16 S metabarcoding revealed that PHBV supressed microbial activity, reduced bacterial diversity and shifted microbial community structure, inducing a major shift in soil metabolic pathways, and thus functioning. Overall, our data suggests that the bioplastic PHBV is not environmentally benign and that contamination levels as low as 0.01% (0.01 mg kg -1 ) can induce significant short-term changes in both plant and soil microbial functioning, with potential implications for long term agroecosystem health. • Effect of biopolymer PHBV microplastic on soil and plant health was investigated • PHBV addition caused a dose-dependent negative effect on soil and plant health • PHBV addition altered foliar metabolism and reduced plant growth and foliar N • PHBV reduced soil microbial activity and changed the bacterial community structure • Bioplastics may not be environmentally benign

Numerous factors, such as the soil’s low organic content and the inaccessibility of phosphorus nutrients in acidic soil conditions, restrict the growth of crops and the health of the soil. In the 21st century, crop production and soil health need attention for food security in order to enhance soil fertility and vigorous crop production. The objective of the study was to investigate how biodynamic farming affects on soil health and plant biomass production as phosphorus can react with aluminum and iron in acidic soil to generate insoluble compounds that are unavailable to plants. Phosphorus availability in acidic soil might be a problem and less available to plant roots as a result of the precipitation. By lowering the solubility of aluminum and iron in acidic soils, nano-black carbon increases the availability of phosphorus to plants. Experimental findings revealed that grain phytate concentration and fertilizer use-efficiency were significantly improved with agronomic interventions. The highest GPC and TPU were noted with nano-black carbon tretament. However, SPU was increased with muck compost application. The maximum GPC, SPU, and TPU were recorded at 100 kg P ha−1. Maximum GPC, SPU, and TPU were recorded with Trichoderma achlamydosporum than Pseudomonas. Highest FUE was recorded with 75 kg-P-ha−1. AE and PFPp altered with treatments and highest AE and PFP were noted with nano-black carbon. Conclusively, PAE, PFPp, and FUE were higher with integration of nano-black carbon+achlamydosporum along with inorganic P (75 kg per hac) can improve soil health and nutrients status along with yield and productivity on a sustainable basis.

Soil fungi are key component of soil biota having an important role in many ecological processes. As pathogens, decomposers and plant mutualists they can affect plant and soil health in agro-ecosystems significantly. The impact of crop management practices on soil fungal communities is diverse and still poorly studied. The lack of knowledge is mainly related to their hidden life mode, high phenotypic diversity, the great heterogeneity of soil microhabitats, difficulty for culturing and species identification. Collecting data with high accuracy to detect effects relevant to ecosystem management is an ongoing challenge for soil ecological studies and biomonitoring. However, the combination of DNA-based identification methods and Next Generation Sequencing technology was recognized as a powerful tool to evaluate biodiversity in environmental samples, especially soil biodiversity. In the frame of the National Research Program "Healthy Foods for a Strong Bio-Economy and Quality of Life", soil microbiome diversity (fungi, prokaryotes and archaea) will be used as indicator for assessing soil and plant health, and ecosystem services in several agricultural ecosystems. Four crop types (apple, lavender, rose and pea) located in southern Bulgaria, and managed by conventional and organic farming have been selected. Two general objectives related to soil biodiversity study were envisaged: to examine the impact of cropping systems on microbiome structural and functional diversity, and to propose management measures and agronomic practices improving soil and plant health. to examine the impact of cropping systems on microbiome structural and functional diversity, and to propose management measures and agronomic practices improving soil and plant health. Here we present some preliminary results on soil fungal communities evaluated by using amplicon DNA sequencing of the internal transcribed spacer 2 (ITS2) rDNA region. Multiple core soil samples were collected from 18 sampling plots in June 2019. Fungal diversity and community structure were evaluated at different taxonomic levels. The most common and abundant taxa at all sites were Fusarium Link 1809, Solicoccozyma X.Z.Liu, F.Y.Bai, M.Groenew. & Boekhout 2015, Cladosporium Link 1816, Alternaria Nees ex Wallroth 1816, and Mortierella E.Coemans 1863. The multivariate statistics (PCA) comparing the overall microbial composition revealed loose clusters linked to crops and localities. The study provides a new comprehensive overview of soil fungal communities (composition and diversity) from Bulgarian agro-ecosystems using high-throughput DNA sequencing.

The sub‐mountainous tea gardens of the Dooars region of West Bengal, which contribute approximately 25% of the national tea yield, are constantly fighting with diminishing soil fertility. Inorganic alternatives like chemical fertilizers can provide easier yet short‐term solutions, as their prolonged and indiscriminate usage leaches the soil, devouring its productivity, increasing the soil's heavy metal contents, and subsequently accumulating those heavy metals in leaves. A plausible substitution in this scenario could be the use of organic alternatives like composting or biofertilizer. Although references to such alternative means are found in the literature, a holistic approach targeting plant growth promotion along with mitigating soil metal toxicity is lacking. Keeping this background in mind, this pilot study was designed to optimize the dosage of novel biofertilizers (using resident and alien flora) that can reduce heavy metal loads and residual toxicity in soil, thereby improving overall soil health and tea production. Two potential metallophilic plant growth‐promoting strains of Bacillus sp. (previously reported) were selected and applied to potted tea plants of two different varieties of tea: TV9 and TV25. Among the two modes of treatment tested: solid treatment (compost amended with bacterial culture) and liquid treatment (cell pellets mixed in water suspension), the water suspension‐based direct application of resident soil bacteria showed the highest physiological growth with reduced metal toxicity. Based on physiological data and physico‐chemical data collected, it was observed that direct application of bacteria showed better results in both plant and soil health improvement in comparison to regular compost amended with beneficial microflora. Therefore, this small‐scale pilot study aimed to optimize the dosage and mode of application of novel biofertilizers for improved soil and plant health.

The human eye does not have sufficient resolution to unravel the mysteries of soil and plant health. Corn is one of the major grains grown in Canada. The proposed maximum theoretical yield of corn is 450-500 bu/acre, but average growers are producing 150 bu/acre. The main aim of this study is to understand the factors associated with soil health and plant productivity beyond the cropping system and practices. We measure the aspects of soil physical, chemical properties and differences in microorganism communities will be related to yield responses collected from plants harvested from 40 diverse sites across Ontario using aerial infrared photography to identify sections of fields where plants appear healthy or stressed (as we discovered that when corn plants were randomly selected for testing, their microbiomes were quite similar). In this way, we hope to identify some of the primary reasons that confer the unevenness in crop yield seen across the same field when the same farm inputs had been applied. Such findings will be used to improve low production sites, thereby increasing overall yields significantly. Based on results from our previous studies we hypothesized that the difference in the plant productivity at different sites are due the abundance and diversity of microbial communities, and the impacts of their specific activities such as nitrogen fixation, phosphorous solubilisation, root growth promotion, and suppression of plant pathogens. The ratio of different soil chemical parameters affects microbial community richness and diversity in many ways. The study results will be integral in our understanding of the microbial community structures that influence crop productivity either negatively or positively. We expect to find out who are the key microorganisms and their roles in corn growth and productivity. Our initial analysis of data generated through TRFLP and next generation based sequencing of microbial communities showed, the endophytic microbial communities were distinct between low and high producing sites across most of the field sites tested. The high producing area had significantly higher bacterial richness and less diversity than the low producing area. Initial correlation analysis revealed potential positive interactions between the general fertility index, potassium to magnesium ratio, the gram negative and nitrogen fixer bacterial communities with yield and yield related parameters. Taken together, the corn sap bacterial community composition and richness was greatly influenced by soil chemical properties, which may indicate shifts in their functionality despite equal levels of total bacterial loads. The talk will identify factors associated with high and poor yielding sites and how this relates to soil and crop health.

Soil, a natural four‐dimensional body at the atmosphere–lithosphere interface, is organic‐carbon‐mediated realm in which solid, liquid, and gaseous phases interact at a range of scales and generate numerous ecosystem goods and services. Soil organic carbon (SOC) strongly impacts soil quality, functionality and health. Terms soil quality and soil health should not be used interchangeable. Soil quality is related to what it does (functions), whereas soil health treats soil as a living biological entity that affects plant health. Through plant growth, soil health is also connected with the health of animals, humans, and ecosystems within its domain. Through supply of macro‐ and micronutrients, soil health, mediated bySOCdynamics is a strong determinant of global food and nutritional security. Soil C pool consists of two related but distinct components:SOCand soil inorganic C (SIC). TheSICpool comprises of primary and secondary carbonates, and the latter consists of calcitic (no net sequestration of atmosphericCO2) and silicatic (net sequestration). WhileSOCis highly dynamic, its mean residence time depends on the degree of protection (physical, chemical, biological, and ecological) within the soil matrix. Formation of stable microaggregates and of organo–mineral complexes can protectSOCagainst microbial processes for millennia. In addition to formation of silicatic type of secondary carbonates, leaching of bicarbonates into the subsoil or shallow water table is also an important mechanism of sequestration ofCO2asSIC. Numerous soil functions and ecosystem services depend onSOCand its dynamics. Improvements in soil health, along with increase in availability of water and nutrients, increases soil's resilience against extreme climate events (e.g., drought, heat wave) and imparts disease‐suppressive attributes. Enhancing and sustaining soil health is also pertinent to advancing Sustainable Development Goals of the U.N. such as alleviating poverty, reducing hunger, improving health, and promoting economic development.

A participatory approach was used to improve smallholder tomato farmers’ understanding of and access to soil health monitoring in the Morogoro Region of Tanzania. Baseline soil characteristics were gathered from 50 tomato fields in the region, local soil knowledge was elicited from farmers and used to develop a soil health card to qualitatively assess soil health, and farmers (n = 32) were trained on the use of a low-cost soil test kit to quantitatively assess soil health. Farmers most often described local indicators of soil health in terms of soil texture and tilth, soil color, soil water relations, and soil fertility. Following use of the soil test kit, farmers indicated increased awareness of soil testing services (Wilcoxon signed rank Z = –3.0, P = 0.001), more agreed they had access to soil testing services (Z = –2.7, P = 0.004), and more agreed that soil management recommendations were easy to understand (Z = –3.4, P < 0.0001) compared with pre-exposure results. Farmers continued to use the soil health test kit and soil health card based on a follow-up survey administered 1 year after project completion. Participatory soil health monitoring projects can improve farmers’ ability to monitor and manage soil health, potentially impacting sustained soil and plant health.

The interactions of plants with different microorganisms in the rhizosphere have varied effects on plant health, productivity, and soil fertility. Numerous types of bacteria play certain vital roles in agriculture production systems by way of establishing different types of relationships that are commonly called as plant growth-promoting rhizobacteria (PGPRs). These PGPRs have multiple roles that have positive impact on plant physiological activities and defense mechanism against biotic and abiotic stresses. Such effects may include symbiotic and asymbiotic N fixation and mobilization; production of siderophores, phytohormones, and antibiotics; counteracting the effect on various pathogenic fungi; solubilization of soil phosphate; and production of growth-promoting indole acetic acid (IAA). Besides, under various stress situations (such as drought, salinity, and metal toxicity), these PGPRs not only halt the deleterious effects of such stresses but also make the plant grow and develop normally. PGPRs through production of ACC (1-aminocyclopropane-1-carboxylate) deaminase can successfully deter the detrimental stress effect of ethylene, enabling the plants to grow normally by alleviating the harmful effect of this. The toxic effects of higher concentration of heavy metals can also be counteracted through PGPRs. These favorable microorganisms reduce the chemical load in rhizosphere and also have multiple synergistic effects on the plant growth and efficacy of other microorganism. Recently, PGPRs have become the most important tool for use as biofertilizers because they provide sustainability of agroecosystems. As the understanding of these PGPRs is increasing, it has become quite evident that apart from legumes, these are also contributing cereals and other nonlegume host crops in a variety of ways. Eco-friendly PGPRs have now become a very important supplement for agriculture production and soil health with involvement of minimal cost. In the light of this background, various aspects of PGPRs biotechnology with special reference to legumes are reviewed and discussed in this chapter.

Chapter 35 - Plant growth promoting Rhizobacteria and their biofilms in promoting sustainable agriculture and soil health

An increasing trend for the use of microbial bioinoculants to accomplish sustainable agriculture has been witnessed across the globe. Bacterial inoculants, mostly composed of beneficial bacteria including the plant growth-promoting rhizobacteria (PGPRs), exhibit tremendous metabolic versatility for carrying out processes such as nitrogen fixation, phosphate, potassium, zinc, silica, and other substrate solubilization or mineralization, release of plant growth-promoting substances (PGPSs), antibiotic synthesis, and biodegradation of soil organic matter. These processes contribute toward maintenance of soil health. Appropriately screened and applied bacterial inoculants can be a prodigious tool for increasing crop productivity besides decreasing current intensive use of chemical or synthetic fertilizers. These inoculants can help in achieving the long-desired goal of sustainable productivity with a low eco-footprint such that environmental quality conducive for the health of humans, livestock, plants, and soil can be maintained. Because the soil microbial diversity, enumerated as microbial species richness and number, can be considered as an index of soil health and fertility, bacterial genera in the rhizosphere and endosphere of the plants will indicate the health of the soil and, therefore, have a regulating effect on crop productivity. This chapter discusses various mechanisms of action of these bacteria and the beneficial effects of plant growth-promoting bacterial inoculants to realize the concept of conservation of natural resources, particularly the soil as a natural resource for sustainable crop production.

In the present investigations it is proved that the inoculation of multifunctional microbial formulation to the soil improves soil quality, soil health, plant health, growth, yield, and quality of a broad spectrum of crops reducing chemical fertilizer and pesticide input. These microbial populations consist of selected species including plant growth promoting rhizo-bacteria, N2-fixing bacteria, Phosphate solubilizers, phytohormone producers, plant disease suppressive bacteria and fungi. To make it very simple a different dimension as „Bio Protectant” is given in this presentation to the collective synergistic effects of beneficial microbes stimulating soil, plant and environmental health reducing chemical fertilizer and pesticide application. A healthy plant does not require unwanted, poisonous chemical pesticides. Review of literature is focused in multiple ways on the growth promoting ability along with the biological activity of beneficial microorganisms. The present SumaGrow-F2 formulation contains multi-functional Rhizobium species, Pseudomonas spp., Bacillus, and Trichoderma spp. The recorded novel benefits of SumaGrow-F2 formulation in the Green House and Field are discussed here as microbes increasing plant health, soil health, and root health of a broad spectrum of crops. Not only can it eliminate almost all insect infestations and reduce fungal or bacterial infection, it also creates a healthier environment for plant growth. The result is healthy crops with a corresponding increase in the yield of fruits or vegetables or grains. Modern trend is to look for inspiring intelligent multi-functional microbial Plant protectant or bio protectant for sustainable agriculture.

This chapter aims to demonstrate that agriculture, and specifically crop nutrition, is a key entry point for positive human health outcomes. Potassium has been selected for this review, because it is a mineral element that originates in the soil and the K nutrition of plants and humans largely rely on the transition of K from the soil to the plants and human via the food chain. The initial search focused on individual components, K, and soil health; K and plant health; and K and human health. Quantitative soil health indexes have yet to be applied to potato-production areas. Soil health has been declining along with potato productivity. Comprehensive data sets capturing the fates of nutrients and other quality parameters offer promise to deepen our understanding of how soil, plant, and human health interact to meet the energy and nutritional needs of humans to create desired health outcomes in system.

Soil and plant health are linked with each other, and both are badly affected by the excess application of inorganic fertilizers and pesticides. The negative impact of chemical fertilizers toward the environment forced the scientific community to find out an alternative strategy that can improve crop yield and quality in an eco-friendly manner. The modern agriculture system is well furnished with microbial inoculants and plant defense elicitors. However, the application of microbes to manage plant growth and fitness needs to improve. Microbial inoculants play an important role in soil mineralization, energy mobilization and channelization, and also nitrogen fixation. This chapter aims to review the microbial plant helpers and their interlinks toward plant and human health. Microbial inoculums improve crop quality and yield, plant and soil health, and profit to farmers and reduce pollution. Proper utilization of microbial inoculants could help to improve the economic condition of the farmers and the country.