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Microbiology in agriculture: an introduction
Abstract
Among the biological sciences, microbiology is well established and related with various fields in the present era. Agricultural microbiology is a blooming research field emerging from the intersection of general microbiology and microbial ecology to the agricultural biotechnologies. The ultimate aim of agricultural microbiology is a wide-ranging study of beneficial bacteria and fungi interacting with agriculturally important plants, thereby meeting the global demand of food in an eco-friendly manner. Our aim is to torch the current status and application of microbiology in modern agriculture. The present chapter gives an overall view about the role of microbiology in sustainable agriculture and also discusses effective microorganisms, rhizosphere, mycorrhizal fungi, phosphate solubilizing bacteria, impact of microbes on soil properties, synthetic biology, microbes as elicitors, microbes in stress agriculture, and climate smart agriculture.
... The bacteria perform various functions that are essential for plant growth and soil health, such as nutrient cycling, organic matter decomposition, and abiotic stress tolerance (Berendsen et al. 2012). They may also have antagonistic effects if they compete with plants for soil nutrients or act as one of the causative agents for plant diseases (Suganya et al. 2022;Yamasamit et al. 2023). The existing literature has primarily focused on studying soil water retention and plant parameters for WAP-amended soil (Saha and Sekharan 2021;Rattan et al. 2022). ...
Aims
The use of water-absorbing polymers (WAP) in soils for mitigating water stress is well known. However, the influence of WAP on the soil microbiota and hence, plant growth in soils. The objective of this study is to quantify the combined influence of water absorbing polymer (WAP) amendment and vegetation on the bacterial community of an agricultural soil when subjected to drought conditions.
Methods
In this study, two WAPs along with the plant species Phaseolus vulgaris L. (common bean) were considered to study its impact on the soil bacterial community under controlled environment conditions (greenhouse). The soil bacterial community was assessed using 16 S rRNA gene sequencing at three stages of bean growth. Additionally, energy-dispersive X-ray (EDX) analysis was performed to identify soil constituents and their correlation with bacterial changes.
Results
Results demonstrated significant alterations in bacterial community composition and diversity with WAP application. Notably, the combined effects of WAP and plant species under drought resulted in a synergistic interaction between plant development and treatment. Enrichment of Proteobacteria, Gemmntinonadetes, Verrucomicrobia, and Bacteroidetes was observed, while Actinobacteria, Chloroflexi, and Planctomycetes showed a decreasing trend. Furthermore, WAP amendment in the presence of plants led to increased nitrogen (5.8%), phosphorus (1.9%), and potassium (7.35) (NPK) concentrations in the soil.
Conclusions
These findings highlight the significant positive impact of WAP as a soil amendment on the bacterial community and improved nutrient availability (carbon cycle, nitrogen cycling and fixation, phosphorus availability) in the soil matrix, thereby promoting sustainable agricultural practices.
Microbial inoculants are critical tools for improving soil health and crop growth within sustainable agriculture frameworks. Despite numerous microorganisms being identified as potential candidates, their transition from laboratory efficacy to field application remains constrained by the complex and variable conditions of field environments. This review critically examines the current state of microbial inoculant research, pinpointing key challenges such as the lack of diversity in test environments and the insufficient integration of agronomic practices crucial for practical adoption. We propose the farmer Participatory research (FPR) model as a robust methodology to address these challenges, emphasizing the co-creation of knowledge between researchers and farmers. This approach uses the practical insights of farmers and integrates multidisciplinary scientific advances to ensure that the development of microbial inoculants is scientifically sound and practically viable in diverse agricultural settings. By adopting FPR principles, this review offers a detailed roadmap for future research, emphasizing the importance of farmer-centric approach in integrating advanced technologies like amplicon sequencing, machine learning, synthetic biology, and systems carriers in optimizing microbial inoculant performance. This paradigm shift towards a collaborative, multidisciplinary approach is poised to significantly improve the efficacy of field trials and establish robust agronomic management strategies for microbial inoculants application, ultimately advancing microbial inoculant research.
Chitosan is an effective organic molecule that improve productivity by supplying valuable nutrients to plant and due to site specific action of this nanoparticle it also enhance activity of protective enzymes that enables for biotic and abiotic stress resistance in plants. It acts as a carrier of major and micro nutrients, pesticide, herbicide and increase crop yield in a sustainable manner.
Agricultural production is mainly depends on the health of soil, which is a measure of a
complex set of biological, chemical and physical interactions driven by microorganisms.
Effective microorganism increases the beneficial microbial population in the soil for
sustainable crop production. Effective Microorganisms are mixed cultures of beneficial
naturally-occurring organisms that can be applied as inoculants to increase the microbial
diversity of soil ecosystem. They consist mainly of the photosynthesizing bacteria, lactic
acid bacteria, yeasts, actinomycetes and fermenting fungi. EM will improve the structure
of the soil, increase its fertility and radically improve biological diversity, suppress soilborne
pathogens, fixes the nitrogen in soil and enhances nutrient uptake, accelerates the
decomposition of organic waste, residues and composting, increases beneficial minerals in
organic compound, enhances the activities of indigenous microorganism and boosts the
strength of plants and yield of crops. EM works by being dominant over other soil
microbes. As a result, this encourages the bulk of the other microbes in the soil to follow
them and in doing so suppress the activity of the smaller group of negative or opportunistic microbes. Effective microorganisms can help to improve and maintain the soil chemical and physical properties.
Extreme saline environments represent unique ecosystems for novel microbial biodiversity. The salt-tolerant
microbiomes have been reported from diverse saline habitat. The biodiversity of salt-tolerant microbes showed the presence of different groups of microbes including Actinobacteria, Bacteroidetes, Euryarchaeota, Firmicutes,Proteobacteria, and Spirochaetes. The salt-tolerant plant growth promoting (PGP) microbes such as Ammoniphilus,
Arthrobacter, Azospirillum, Bacillus, Brevibacillus, Brevibacterium, Haloarcula, Halobacillus, Halococcus, Haloferax, Halolamina, Halomonas, Halorubrum, Haloterrigena, Lysinibacillus, Marinobacter, Marinospirillum, Oceanobacillus, Paenibacillus, Penicillium, Pontibacillus, Pseudomonas, Sediminibacillus, Sporosarcina, Streptomyces, Thalassobacillus, and Thermonema have been isolated and characterized for plant growth under the salinity stress. The halophilic microbes have ability to produce phytohormones (indole acetic acids, gibberellic acids, and cytokinin), solubilize and bind nutrients (phosphorus, potassium, zinc, and siderophores), besides eliciting plant defense reactions
against pathogens, also help in plant growth under harsh saline environments. The halophilic PGP microbes increase the plant growth, yields, and nutrient uptake under the saline condition. In the present review, the biodiversity of halophilic microbes from diverse ecosystems, its functional PGP attributes and mechanisms of action for amelioration of salt stress, plant growth, and soil health for sustainable agriculture have been discussed. The salt-tolerant microbes with multifarious PGP attributes could be applied for plant growth and ameliorations of salt stress.
Soils are integral to the function of all terrestrial ecosystems and to food and fibre production. An overlooked aspect of soils is their potential to mitigate greenhouse gas emissions. Although proven practices exist, the implementation of soil-based greenhouse gas mitigation activities are at an early stage and accurately quantifying emissions and reductions remains a substantial challenge. Emerging research and information technology developments provide the potential for a broader inclusion of soils in greenhouse gas policies. Here we highlight 'state of the art' soil greenhouse gas research, summarize mitigation practices and potentials, identify gaps in data and understanding and suggest ways to close such gaps through new research, technology and collaboration.
Harvested fruits, vegetables, nuts and grains harbour a very reach microbiota that influence their shelf-life, quality and safety for human consumption. Spoilage due to fungal or bacterial rot, mycotoxin production and contamination by food-borne human bacterial pathogens are within the main problems of harvest products that are consumed fresh. Control of these problems is currently done by conventional methods of sanitation, disinfection or treatment with chemical fungicides. Biological control of postharvest problems can be achieved with certain strains of antagonistic viruses, bacteria, yeast and fungi. The mechanisms of action are very diverse, and several mechanisms may act simultaneously. Mechanisms include competition for nutrients and niches, antibiosis by means of antimicrobials and lytic enzymes, inhibitory volatile metabolites, pH decrease, parasitism, and induction of defence responses in the harvested plant product. Several commercial products containing strains of biological control agents are available as an alternative or complement to chemicals for postharvest rot control.
We develop a framework that facilitates the study of the causal structure of
spacetimes with a causally preferred foliation. Such spacetimes may arise as
solutions of Lorentz-violating theories, e.g. Horava gravity. Our framework
allows us to rigorously define concepts such as black/white holes and to
formalize the notion of a `universal horizon', that has been previously
introduced in the simpler setting of static and spherically symmetric
geometries. We also touch upon the issue of development and prove that
universal horizons are Cauchy horizons when evolution depends on boundary data
or asymptotic conditions. We establish a local characterisation of universal
horizons in stationary configurations. Finally, under the additional assumption
of axisymmetry, we examine under which conditions these horizons are cloaked by
Killing horizons, which can act like usual event horizons for low-energy
excitations.
Biofertilizers have been used as sources to improve plant nutrients in sustainable agriculture. Experiments were conducted to evaluate the potential of phosphate solubilizing bacteria (PSB) Bacillus megaterium var. phosphaticum and potassium solubilizing bacteria (KSB) Bacillus mucilaginosus inoculated in nutrient limited soil planted with pepper and cucumber. Results showed that rock P and K applied either singly or in combination did not significantly enhance soil availability of P and K, indicating their unsuitability for direct application. PSB was a more potent P-solubilizer than KSB, and co-inoculation of PSB and KSB resulted in consistently higher P and K availability than in the control without bacterial inoculum and without rock material fertilizer. Integrated rock P with inoculation of PSB increased the availability of P and K in soil, the uptake of N, P and K by shoot and root, and the growth of pepper and cucumber. Similar but less pronounced results were obtained when rock K and KSB were added concomitantly. Combined together, rock materials and both bacterial strains consistently increased further mineral availability, uptake and plant growth of pepper and cucumber, suggesting its potential use as fertilizer.
Climate-smart agriculture (CSA) is an approach for transforming and reorienting agricultural systems to support food security under the new realities of climate change. Widespread changes in rainfall and temperature patterns threaten agricultural production and increase the vulnerability of people dependent on agriculture for their livelihoods, which includes most of the world's poor. Climate change disrupts food markets, posing population-wide risks to food supply. Threats can be reduced by increasing the adaptive capacity of farmers as well as increasing resilience and resource use efficiency in agricultural production systems. CSA promotes coordinated actions by farmers, researchers, private sector, civil society and policymakers towards climate-resilient pathways through four main action areas: (1) building evidence; (2) increasing local institutional effectiveness; (3) fostering coherence between climate and agricultural policies; and (4) linking climate and agricultural financing. CSA differs from 'business-as-usual' approaches by emphasizing the capacity to implement flexible, context-specific solutions, supported by innovative policy and financing actions.
Phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. Although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. The P content in average soil is about 0.05% (w/w) but only 0.1% of the total P is available to plant because of poor solubility and its fixation in soil (Illmer and Schinner, Soil Biol Biochem 27:257-263, 1995). An adequate supply of phosphorus during early phases of plant development is important for laying down the primordia of plant reproductive parts. It plays significant role in increasing root ramification and strength thereby imparting vitality and disease resistance capacity to plant. It also helps in seed formation and in early maturation of crops like cereals and legumes. Poor availability or deficiency of phosphorus (P) markedly reduces plant size and growth. Phosphorus accounts about 0.2 - 0.8% of the plant dry weight.
To satisfy crop nutritional requirements, P is usually added to soil as chemical P fertilizer, however synthesis of chemical P fertilizer is highly energy intensive processes, and has long term impacts on the environment in terms of eutrophication, soil fertilility depletion, carbon footprint. Moreover, plants can use only a small amount of this P since 75–90% of added P is precipitated by metal–cation complexes, and rapidly becomes fixed in soils. Such environmental concerns have led to the search for sustainable way of P nutrition of crops. In this regards phosphate-solubilizing microorganisms (PSM) have been seen as best eco-friendly means for P nutrition of crop. Although, several bacterial (pseudomonads and bacilli) and fungal strains (Aspergilli and Penicillium) have been identified as PSM their performance under in situ conditions is not reliable and therefore needs to be improved by using either genetically modified strains or co-inoculation techniques. This review focuses on the diversity of PSM, mechanism of P solubilization, role of various phosphatases, impact of various factors on P solubilization, the present and future scenario of their use and potential for application of this knowledge in managing a sustainable environmental system.
Plant production systems globally must be optimized to produce stable high yields from limited land under changing and variable climates. Demands for food, animal feed, and feedstocks for bioenergy and biorefining applications, are increasing with population growth, urbanization and affluence. Low-input, sustainable, alternatives to petrochemical-derived fertilizers and pesticides are required to reduce input costs and maintain or increase yields, with potential biological solutions having an important role to play. In contrast to crops that have been bred for food, many bioenergy crops are largely undomesticated, and so there is an opportunity to harness beneficial plant-microbe relationships which may have been inadvertently lost through intensive crop breeding. Plant-microbe interactions span a wide range of relationships in which one or both of the organisms may have a beneficial, neutral or negative effect on the other partner. A relatively small number of beneficial plant-microbe interactions are well understood and already exploited; however, others remain understudied and represent an untapped reservoir for optimizing plant production. There may be near-term applications for bacterial strains as microbial biopesticides and biofertilizers to increase biomass yield from energy crops grown on land unsuitable for food production. Longer term aims involve the design of synthetic genetic circuits within and between the host and microbes to optimize plant production. A highly exciting prospect is that endosymbionts comprise a unique resource of reduced complexity microbial genomes with adaptive traits of great interest for a wide variety of applications.
© 2014 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Most eukaryotes develop close interactions with microorganisms that are essential for their performance and survival. Thus, eukaryotes and prokaryotes in nature can be considered as meta-organisms or holobionts. Consequently, microorganisms that colonize different plant compartments contain the plant's second genome. In this respect, many studies in the last decades have shown that plant-microbe interactions are not only crucial for better understanding plant growth and health, but also for sustainable crop production in a changing world. This mini-review acting as editorial presents retrospectives and future perspectives for plant microbiome studies as well as information gaps in this emerging research field. In addition, the contribution of this research topic to the solution of various issues is discussed.
Significance
Biological diversity is the foundation for the maintenance of ecosystems. Consequently it is thought that anthropogenic activities that reduce the diversity in ecosystems threaten ecosystem performance. A large proportion of the biodiversity within terrestrial ecosystems is hidden below ground in soils, and the impact of altering its diversity and composition on the performance of ecosystems is still poorly understood. Using a novel experimental system to alter levels of soil biodiversity and community composition, we found that reductions in the abundance and presence of soil organisms results in the decline of multiple ecosystem functions, including plant diversity and nutrient cycling and retention. This suggests that below-ground biodiversity is a key resource for maintaining the functioning of ecosystems.
The worldwide increases in both environmental damage and human population pressure have the unfortunate consequence that global food production may soon become insufficient to feed all of the world's people. It is therefore essential that agricultural productivity be significantly increased within the next few decades. To this end, agricultural practice is moving toward a more sustainable and environmentally friendly approach. This includes both the increasing use of transgenic plants and plant growth-promoting bacteria as a part of mainstream agricultural practice. Here, a number of the mechanisms utilized by plant growth-promoting bacteria are discussed and considered. It is envisioned that in the not too distant future, plant growth-promoting bacteria (PGPB) will begin to replace the use of chemicals in agriculture, horticulture, silviculture, and environmental cleanup strategies. While there may not be one simple strategy that can effectively promote the growth of all plants under all conditions, some of the strategies that are discussed already show great promise.
The association between plant and plant growth promoting bacteria (PGPB) contributes to the successful thriving of plants in extreme environments featured by water shortage. We have recently shown that, with respect to the non-cultivated desert soil, the rhizosphere of pepper plants cultivated under desert farming hosts PGPB communities that are endowed with a large portfolio of PGP traits. Pepper plants exposed to bacterial isolates from plants cultivated under desert farming exhibited a higher tolerance to water shortage, compared with untreated control. This promotion was mediated by a larger root system (up to 40%), stimulated by the bacteria, that enhanced plant ability to uptake water from dry soil. We provide initial evidence that the nature of the interaction can have a limited level of specificity and that PGPB isolates may determine resistance to water stress in plants others than the one of the original isolation. It is apparent that, in relation to plant resistance to water stress, a feature of primary evolutionary importance for all plants, a cross-compatibility between PGPB and different plant models exists at least on a short-term.
Disease control is largely based on the use of fungicides, bactericides, and insecticides—chemical compounds toxic to plant invaders, causative agents, or vectors of plant diseases. However, the hazardous effect of these chemicals or their degradation products on the environment and human health strongly necessitates the search for new, harmless means of disease control. There must be some natural phenomenon of induced resistance to protect plants from disease. Elicitors are compounds, which activate chemical defense in plants. Various biosynthetic pathways are activated in treated plants depending on the compound used. Commonly tested chemical elicitors are salicylic acid, methyl salicylate, benzothiadiazole, benzoic acid, chitosan, and so forth which affect production of phenolic compounds and activation of various defense-related enzymes in plants. Their introduction into agricultural practice could minimize the scope of chemical control, thus contributing to the development of sustainable agriculture. This paper chiefly highlights the uses of elicitors aiming to draw sufficient attention of researchers to the frontier research needed in this context.
Plant growth-promoting rhizobacteria (PGPR) are free-living bacteria which actively colonize plant roots, exerting beneficial effects on plant development. The PGPR may (i) promote the plant growth either by using their own metabolism (solubilizing phosphates, producing hormones or fixing nitrogen) or directly affecting the plant metabolism (increasing the uptake of water and minerals), enhancing root development, increasing the enzymatic activity of the plant or "helping" other beneficial microorganisms to enhance their action on the plants; (ii) or may promote the plant growth by suppressing plant pathogens. These abilities are of great agriculture importance in terms of improving soil fertility and crop yield, thus reducing the negative impact of chemical fertilizers on the environment. The progress in the last decade in using PGPR in a variety of plants (maize, rice, wheat, soybean and bean) along with their mechanism of action are summarized and discussed here.
Biotechnology is the rapidly growing segment in biological sciences. It has diversified applications in sustainable agriculture. The review deals with microbes in biotechnology and their diversified applications in agriculture as biofertilizers, bio-pesticides, bio-herbicides, bioinsecticides, fungal based bioinsecticides and viral based bioinsecticides. Further, precise descriptions have been made on Microbiology Ecology Biotechnology and Sustainable agriculture in the later part of the review. Finally, a brief highlight has been given on the role of Microbial Biotechnology on Environmental Health
To feed all of the world's people, it is necessary to sustainably increase agricultural productivity. One way to do this is through the increased use of plant growth-promoting bacteria; recently, scientists have developed a more profound understanding of the mechanisms employed by these bacteria to facilitate plant growth. Here, it is argued that the ability of plant growth-promoting bacteria that produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase to lower plant ethylene levels, often a result of various stresses, is a key component in the efficacious functioning of these bacteria. The optimal functioning of these bacteria includes the synergistic interaction between ACC deaminase and both plant and bacterial auxin, indole-3-acetic acid (IAA). These bacteria not only directly promote plant growth, they also protect plants against flooding, drought, salt, flower wilting, metals, organic contaminants, and both bacterial and fungal pathogens. While a considerable amount of both basic and applied work remains to be done before ACC deaminase-producing plant growth-promoting bacteria become a mainstay of plant agriculture, the evidence indicates that with the expected shift from chemicals to soil bacteria, the world is on the verge of a major paradigm shift in plant agriculture.
The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.
Research studies were conducted to elucidate the chemical, physical and microbiological properties of an organic fertilizer that was inoculated and fermented with a microbial inoculant (Effective Microorganisms or EM). The quality estimation methods employed addressed the mechanistic basis for beneficial effects of soil improvement and crop yield. Effective Microorganisms or EM was utilized as the microbial inoculant that is a mixed culture of beneficial microorganisms. Tests showed that the fermented organic fertilizer contained large populations of propagated Lactobacillus spp. Actinomycetes, photo-synthetic bacteria and yeasts; high concentrations of intermediate compounds such as organic acids and amino acids; 0.1% of mineral nitrogen mainly in the ammonium (NH4 ) form, and 1.0% of available phosphorus; and a C:N ratio of 10. The quality of the fermented organic fertilizer depends on the initial water content; addition of molasses as a carbon and energy source; and the microbial inoculant. The medium pH appears to be reliable fermentation quality criterion for producing this organic fertilizer. Beneficial effects of the fermented organic fertilizer on soil fertility and crop growth will likely depend upon the organic fraction, direct effects of the introduced microorganisms, and indirect effects of microbially-synthesized metabolites (e.g., phytohormones and growth regulators).
Microorganisms, their cells or replicable parts (e.g. genomes, plasmids, viruses, cDNAs) are the tools for biotechnology and underpin the life sciences. The vast majority of microorganisms around the globe still remain hidden and need to be explored, identified, conserved and utilized for the benefit of humankind in particular, and the biota and environment, in general. Microbial culture collections are established in many countries around the world having a variety of purposes. These range from small, specialized collections that support small groups of researchers to the large international public service collections that provide reference materials and services to the scientific community and bio-industries. The huge gap between the discovery of new microorganisms and their potential numbers in nature has stimulated an interest in microbial diversity and the harnessing of their genes, properties and products. The operations of microbial collections have changed over the last twenty years as a result of the advancement of bioinformatics and the facility to present electronic data over the internet This makes even the smaller collection resources more accessible.
By 2050 the world’s population will have increased by a third and demand for agricultural products will rise by 70% with meat
consumption doubling. Lateral expansion of the agricultural sector through the clearing of land is untenable without significant
negative implications on already stressed natural ecosystems and the range of drivers, including climate variability, that
farmers will have to cope with, will require changes in the way we undertake agriculture. In meeting future food production
demands without consuming more land and water will require technological innovation and changes in the way agriculture is
undertaken. The chapter discusses the future global demands for food and highlights the importance of addressing soil chemical
and physical constraints in increasing the productivity of degraded production systems. The role of clays in permanently changing
the surface charge characteristics of soils and the potential for selected grass species to remediate compacted soil layers
are presented as possible options in addressing the sustainability of degraded production systems.
Progress towards the commercial-scale use of plant cell cultures over the past three years has been significant. Elicitation, particularly with methyl jasmonate, has been effective at increasing the product yields of a wide variety of secondary metabolites, particularly when it is applied synergistically with enhancement strategies such as immobilization and in situ extraction. Rapid advances in understanding the regulation of the biosynthetic pathways of secondary metabolites are allowing the application of enhancement strategies to move from empirical to semirational. Much of this progress is exemplified by work on paclitaxel (Taxol), where yields have improved more than 100-fold in the past two years.
Fungal symbionts have been found associated with every plant studied in natural ecosystem, where they colonize and reside entirely in the internal tissues of their host plant or partially. Fungal endophytes can express/form a range of different lifestyle/relationships with different host including symbiotic, mutualistic, commensalistic and parasitic in response to host genotype and environmental factors. In mutualistic association fungal endophyte can enhance growth, increase reproductive success and confer biotic and abiotic stress tolerance to its host plant. Since abiotic stress such as, drought, high soil salinity, heat, cold, oxidative stress, heavy metal toxicity is the common adverse environmental conditions that affect and limit crop productivity worldwide. It may be a promising alternative strategy to exploit fungal endophytes to overcome the limitations to crop production brought by abiotic stress. There is increasing interest in developing the potential biotechnological applications of fungal endophytes for improving plant stress tolerance and sustainable production of food crops. Here we have described the fungal symbioses, fungal symbionts and their role in abiotic stress tolerance. A putative mechanism of stress tolerance by symbionts has also been covered.
This paper reviews recent literature concerning a wide range of processes through which climate change could potentially impact global-scale agricultural productivity, and presents projections of changes in relevant meteorological, hydrological and plant physiological quantities from a climate model ensemble to illustrate key areas of uncertainty. Few global-scale assessments have been carried out, and these are limited in their ability to capture the uncertainty in climate projections, and omit potentially important aspects such as extreme events and changes in pests and diseases. There is a lack of clarity on how climate change impacts on drought are best quantified from an agricultural perspective, with different metrics giving very different impressions of future risk. The dependence of some regional agriculture on remote rainfall, snowmelt and glaciers adds to the complexity. Indirect impacts via sea-level rise, storms and diseases have not been quantified. Perhaps most seriously, there is high uncertainty in the extent to which the direct effects of CO(2) rise on plant physiology will interact with climate change in affecting productivity. At present, the aggregate impacts of climate change on global-scale agricultural productivity cannot be reliably quantified.
To construct a versatile model host for heterologous expression of genes encoding secondary metabolite biosynthesis, the genome of the industrial microorganism Streptomyces avermitilis was systematically deleted to remove nonessential genes. A region of more than 1.4 Mb was deleted stepwise from the 9.02-Mb S. avermitilis linear chromosome to generate a series of defined deletion mutants, corresponding to 83.12-81.46% of the wild-type chromosome, that did not produce any of the major endogenous secondary metabolites found in the parent strain. The suitability of the mutants as hosts for efficient production of foreign metabolites was shown by heterologous expression of three different exogenous biosynthetic gene clusters encoding the biosynthesis of streptomycin (from S. griseus Institute for Fermentation, Osaka [IFO] 13350), cephamycin C (from S. clavuligerus American type culture collection (ATCC) 27064), and pladienolide (from S. platensis Mer-11107). Both streptomycin and cephamycin C were efficiently produced by individual transformants at levels higher than those of the native-producing species. Although pladienolide was not produced by a deletion mutant transformed with the corresponding intact biosynthetic gene cluster, production of the macrolide was enabled by introduction of an extra copy of the regulatory gene pldR expressed under control of an alternative promoter. Another mutant optimized for terpenoid production efficiently produced the plant terpenoid intermediate, amorpha-4,11-diene, by introduction of a synthetic gene optimized for Streptomyces codon usage. These findings highlight the strength and flexibility of engineered S. avermitilis as a model host for heterologous gene expression, resulting in the production of exogenous natural and unnatural metabolites.
Biochar is a promising soil additive for use in support of sustainable crop production. However, the high level of heterogeneity in biochar properties and the variations in soil composition present significant challenges to the successful uptake of biochar technologies in diverse agricultural soils. An improved understanding of the mechanisms that contribute to biochar-soil interactions is required to address issues related to climate change and cultivation practices. This review summarizes biochar modification approaches (physical, chemical and biochar-based organic composites) and discusses the potential role of biochar in sustainable crop production and soil resiliency, including the degradation of soil organic matter, the improvement of soil quality and reductions in greenhouse gas emissions. Biochar design is crucial to successful soil remediation, particularly with regard to issues arising from soil structure and composition related to crop production. Given the wide variety of feedstocks for biochar production and the resultant high surface heterogeneity, greater efforts are required to optimize biochar surface functionality and porosity through appropriate modifications. The design and establishment of these approaches and methods are essential for the future utilization of biochar as an effective soil additive to promote sustainable crop production.
The objectives of this study were to investigate how rumen fermentation, microbial community and Microbial Protein (MCP) yields changed with dietary protein. Experiments were conducted using four goats fitted with rumen cannula in a 4×4 Latin square design. Experimental diets were divided into 4 groups according to their nitrogen source, which was feather meal (A), corn gluten meal (B), soybean meal (C) and fish meal (D), respectively. The results showed that the mean pH value of group A and C were high, the reverse was true for group B and D (p<0.05); the change patterns of pH with time differed from each other although, the mean pH value of group A and C (B and D) seemed to be similar. Concentration of NH 3-N ranged between 6.77-21.67 mg/lOOmL, the lowest average NH 3-N concentration (11.08 mg/lOOmL) was observed in feather meal supplemental diet (A), while, the highest peak occurred in soybean meal supplemental diet (C) (15.04 mg/100 mL). No significant difference was detected in VFA concentrations among groups, except for valeric acid. Yields of microbial protein also varied with diets; microbial protein of the group C and D were comparatively higher than that of the group A and B (p<0.05); while, bacterial protein yields of group C was significantly higher than that of other 3 groups, protozoa to bacteria ratio was also lowest in group C. Further genetic fingerprint analysis revealed that microbial profile was modified by dietary protein within bacteria or protozoa community. It was concluded that rumen fermentation, microbial profile and rumen microbial protein could be modified properly by dietary protein.
Two species [Penicillium aurantiogriseum and Pseudomonas sp. (PI1889)] having high abilities in solubilizing inorganic phosphates (hydroxylapatite and brushite) were used to examine solubilization mechanisms. No direct contact between microorganisms and calcium phosphates (Ca-Ps) were necessary for effective solubilization. The P-concentration in solution did not increase according to a sigmoid curve type. Therefore, sampling time is of particular importance for estimating P mobilization. The widespread theory that solubilization is always caused by the release of organic acids may prove wrong for our two organisms. In our opinion the most probable reason for solubilization without acid production is the release of protons accompanying respiration or NH4+ assimilation. It was shown that solubilization of Ca-Ps with two different solubility products may lead to a short-term increase of the amount of at least one CaP. Precipitation and subsequent resolubilization of different organic or inorganic phosphates result in hardly predictable P-concentrations in culture solution.
Soil structure is defined as the arrangement of particles and associated pores in soils across the size range from nanometres to centimetres. Biologic influences can be demonstrated in the formation and stabilization of aggregates but it is necessary to distinguish clearly between those forces or agencies which create aggregations of particles and those which stabilize or degrade such aggregations.The formation of soil structure involves the physical forces of shrinking and swelling created by changes in water status of soils, freezing and thawing, tillage, or by movement of the larger biota in soils. Expansive properties of soils are controlled by the clay content. Thus changes of structural organisation are minimal in sands and maximal in clays. Plant roots, earthworms and other macrofauna large enough to move soil particles create pores recognisable by cylindrical shapes and smooth curved surfaces. Various visual and microscopic techniques aided by dyes are available to demonstrate the extent of biovoids in soils.Biology plays a major role in stabilization of soil structure. The major factors vary depending on the scale of soil structure. At larger scales plant roots and associated hyphae can be seen to enmesh soil particles by acting as a “sticky string bag”. At the microscale the influence of mucilages from roots, hyphae, bacteria and fauna such as earthworms can be shown by a range of microscopic techniques to be involved in stabilizing smaller aggregates and the linings of biopores. Techniques include optical and fluorescence microscopy, scanning electron microscopy including EDAX, transmission electron microscopy using heavy metals or other electron dense staining techniques for specific chemical compounds, and computer aided tomography. The microscopic techniques can be used on individual aggregates, stabilized soils, sections or separates of soils.Both microflora and fauna are involved in the degradation of stabilizing agents. Fauna may comminute roots and hyphae which stabilized larger aggregates and microorganisms utilize mucilaginous stabilizing agents as an energy source resulting in a slow breakdown of structural stability. Such effects can be established by combinations of studies of aggregation including microscopy. Further destruction of structure is caused by tillage and compaction by vehicles and animals.
Experiments were conducted to test the relative ability of mycorrhizal and non-mycorrhizal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] seedlings to tolerate and recover from drought conditions, using reduction in CO2 fixation as an overall indicator of plant moisture stress. Seedlings were watered daily or conditioned to cyclic drying and re-wetting of the soil. Net photosynthetic rates of mycorrhizal and non-mycorrhizal seedlings watered daily did not differ significantly; however, drought-stressed mycorrhizal seedlings fixed CO20 at a rate ten times that of non-mycorrhizal seedlings. Total leaf water potentials of mycorrhizal plants were lower (more negative) than those of non-mycorrhizal plants but they recovered more rapidly.
Non-mycorrhizal seedlings and seedlings inoculated with four ectomycorrhizal fungus species were allowed to become desiccated, then were rewatered and compared for their ability to tolerate and recover from drought. Seedlings inoculated with Rhizapogon vintcolor were less affected by drought than any of the other mycorrhizal or non-mycorrhizal treatments. Net photosynthetic rate of Rhizopogon-inoculated seedlings 24 h following re-watering was seven times that of non-mycorrhizal seedlings. The transpiration rate of Rhizopogon-inoculated seedlings was low before desiccation, declined rapidly during the drought period and, after re-watering, quickly resumed a rate higher than that for other treatments.
Cylindrocladium floridanum Sobers and Seymour, principal causal agent of root rot of conifers in forest nurseries, was grown in vitro with four species of ectomycorrhizal fungi, Paxillus involutus, Hebeloma cylindrosporum, Laccaria bicolor, and Tricholoma sp. The effect of inoculating black spruce seedlings (Picea mariana (Mill.) B.S.P.) with P. involutus was also investigated. Tricholoma sp. and especially P. involutus and H. cylindrosporum inhibited growth of C. floridanum in Petri dishes, while L. bicolor was inhibited and completely covered by C. floridanum. Hyphae of the pathogen in the contact zone were deteriorated in the presence of P. involutus and H. cylindrosporum. The inoculation of P. involutus reduced the number of infected black spruce seedlings by approximately 50%. However, the simultaneous inoculation of two different strains of P. involutus did not significantly reduce disease development. Linear regression demonstrated that the percentage of infected plants was negatively correlated with mycorrhiza formation. The relation between these two variables also showed that even if colonization by P. involutus is poor or null, it has some inhibitory effect against Cylindrocladium root rot.Key words: Paxillus involutus, Cylindrocladium floridanum, root rot, ectomycorrhizal fungi, biological control, Picea mariana.
The suppressiveness of Sahel soil against the root-knot nematode Meloidogyne javanica was studied. This soil was compared to another of the same type, collected from an adjacent vegetable plot. However, only one soil was infested by Pasteuria penetrans. Tomato plant and nematode development were greater in the soil with the P. penetrans. The multiplication of P. penetrans added to both sterilized soils was effective. Moreover, the presence of P. penetrans was associated with a larger microbial population (bacteria (fluorescent Pseudomonas), nematophagous and mycorrhizal fungi) which stimulated the attachment of Pasteuria spores to root-knot nematode juveniles. The incidence of the interactions between these microorganisms on the multiplication of the root-knot nematodes is discussed.
Interactions between Pseudomonas fluorescens biocontrol agents and Glomus mosseae, an arbuscular mycorrhizal fungus, were studied. The biocontrol agents included the genetically modified strains CHA96 and CHA0 pME3424 which produced enhanced levels of antifungal compounds. Tomato (Lycopersicum esculentum) and leek (Allium porrum) host plants were grown in sterile Terra-Green (calcined attapulgite clay) with limited nutrients. Mycorrhizal activity was indicated by shoot dry weight and phosphorus content. In all experiments, plants grown in the presence of G. mosseae had a significantly higher shoot dry weight than those grown in the absence of G. mosseae. Colonisation and activity of G. mosseae was unaltered in the presence of P. fluorescens isolates and presence of G. mosseae increased the population of P. fluorescens in the rhizosphere.
Guayule seedlings were inoculated with two Glomus species in pasteurised soil and grown in the glasshouse without added fertiliser for 8 wk prior to transplanting to the field. The survival rate of transplanted guayule seedlings was increased by inoculation with vesicular arbuscular mycorrhizal fungi compared with uninoculated controls. Inoculated guayule had greater concentrations of Ca, Fe, Mg and Mn at six months of age, and greater concentrations of Ca, Mg, and Zn at 12 months of age than did uninoculated plants. The latex content of both roots and shoots of guayule was greater in inoculated than in uninoculated guayule plants at 12 and 18 months of age. The resin content remained unchanged between treatments irrespective of sampling date.
The interactive effects of vesicular-arbuscular mycorrhizal (VAM) fungi and root-knot nematode (Meloidogyne hapla) were studied on nematode-susceptible cultivars of tomato (cv. Scoresby) and white clover (cv. Huia) at four levels of applied phosphate. The relative merits of simultaneous inoculation with mycorrhizal fungi and nematodes and of inoculation with mycorrhizal fungi prior to nematode inoculation were evaluated. Mycorrhizal plants were more resistant than non-mycorrhizal plants to root-knot nematode at all phosphate levels and growth benefits were generally greater in plants preinfected with mycorrhizal fungi. Nematode numbers increased with increasing levels of applied phosphate. In mycorrhizal root systems, nematode numbers increased in the lower phosphate soils; at higher phosphate levels nematode numbers were either unaffected or reduced. The numbers of juveniles and adults per gram of root were always lower in mycorrhizal treatments. Mycorrhizal root length remained unaffected by nematode inoculation.
Mycorrhizal inoculation thus increased the plants' resistance to infection by M. hapla. This was probably due to some alteration in the physiology of the root system but was not entirely a result of better host nutrition and improved phosphorus uptake by mycorrhizal plants.
Micropropagated plantlets of Eucalyptus tereticornis at the root initiation stage were inoculated in vitro with Amanita murina, Hysterangium incarceratum, Laccaria laccata, Pisolithus tinctorius (3 isolates), Scleroderma cepa and S. flavidum in order to select the most compatible ectomycorrhizal partner. H. incarceratum and the two Scleroderma species did not form mycorrhizas with E. tereticornis. Two local isolates of P. tinctorius formed significantly more mycorrhizas than the other isolates tested. Plantlets with mycorrhizas formed by one of the local isolates of P. tinctorius were transplanted to the nursery where their growth significantly exceeded that of non-mycorrhizal plants.
High concentrations of heavy metals in soil have an adverse effect on micro-organisms and microbial processes. Among soil
microorganisms, mycorrhizal fungi are the only ones providing a direct link between soil and roots, and can therefore be of
great importance in heavy metal availability and toxicity to plants. This review discusses various aspects of the interactions
between heavy metals and mycorrhizal fungi, including the effects of heavy metals on the occurrence of mycorrhizal fungi,
heavy metal tolerance in these micro-organisms, and their effect on metal uptake and transfer to plants. Mechanisms involved
in metal tolerance, uptake and accumulation by mycorrhizal hyphae and by endo- or ectomycorrhizae are covered. The possible
use of mycorrhizal fungi as bioremediation agents in polluted soils or as bioindicators of pollution is also discussed.
Soil remediation that revitalizes degraded or contaminated land while simultaneously contributing to biomass biofuel production and carbon sequestration is an attractive strategy to meet the food and energy requirements of the burgeoning world population. As a result, plant-based remediation approaches have been gaining in popularity. The drawbacks of phytoremediation, particularly those associated with low productivity and limitations to the use of contaminant-containing biomass, could be addressed through novel biotechnological approaches that harness recent advances in our understanding of chemical interactions between plants and microorganisms in the rhizosphere and within plant tissues. This opinion article highlights three promising approaches that provide environmental and economic benefits of bioremediation: transgenics, low-input 'designer' plants and nanotechnology.
A pot experiment in Kenya examined the effects of mycorrhizal and rhizobial inoculation on the growth and symbiont infection of Acacia tortilis seedlings in unsterile soil, in comparison with sterile and unsterile soil controls. Three mixed, arbuscular mycorrhizal inocula, originating from A. tortilis, Terminalia brownii, T. spinosa and Prosopis juliflora (produced under nursery conditions), were used to inoculate the seedlings, which also received a standard, mixed, rhizobial inoculum. Mycorrhizal infection and plant growth were significantly affected by experimental treatment (p<0.001). Some mycorrhizal infection (presumably with indigenous soil-borne inoculum) occurred in the unsterile soil control, but not in the sterile soil control, indicating that transfer of inoculum between pots in the experiment did not occur. Mycorrhizal formation was significantly more extensive in inoculated plants, which also had better shoot and root growth. 24 weeks after inoculation, plants which had received inoculum of A. tortilis origin were 105 mm tall and their roots were 56% mycorrhizal, whereas the controls most representative of normal nursery treatment were only 77 mm tall and 29% mycorrhizal. Nodulation was erratic and poor in all treatments. The results suggest that mycorrhizal inoculation can improve both mycorrhizal infection and growth of tree seedlings in unsterile nursery soil. The methods of culture and inoculation described here could easily be adopted by nurseries at little cost.
The aim of the present study was to compare the bioleaching efficiency of Cu, Zn and Cr from anaerobically digested sewage sludge using iron- and sulfur-oxidizing bacteria. Bioleaching was performed on sewage sludge collected from the Yuen Long wastewater treatment plant. A 15% (v/v) inoculation of either iron- or sulfur-oxidizing bacteria with 4 g FeSO4 l−1 and 0.75% elemental sulfur, respectively, was added to sewage sludge with or without autoclaving in the bioleaching experiment. The mixtures were shaken continuously in an incubator at 30 °C for 16 days and samples were tested at 2-day intervals for pH, ORP and metal determination. The results showed that the iron-oxidizing system required only 2 days as compared to 4 days for the sulfur-oxidizing system to reduce the sludge pH from 7 to 2. Both systems achieved a maximum Cr removal of 52–58% after 12 days of bioleaching, but for iron-oxidizing bacteria with iron-sulfate as an energy source it was 20% higher at the beginning of leaching process. Although it took only 2 days to solubilize Cu by iron-oxidizing bacteria as compared to 8 days for sulfur oxidizing bacteria, the iron-oxidizing system removed only 80% of the total Cu, which was 20% lower than that of the sulfur-oxidizing system. Both iron- and sulfur-oxidizing bacteria achieved 95% Zn removals after 4 days of bioleaching. The results demonstrated that the iron-oxidizing system had a faster removal rate than the sulfur-oxidizing bacteria. Nevertheless, further work should be done to improve the bioleaching efficiency of iron-oxidizing bacteria, especially for Cu and Cr.
Although viruses are most often studied as pathogens, many are beneficial to their hosts, providing essential functions in some cases and conditionally beneficial functions in others. Beneficial viruses have been discovered in many different hosts, including bacteria, insects, plants, fungi and animals. How these beneficial interactions evolve is still a mystery in many cases but, as discussed in this Review, the mechanisms of these interactions are beginning to be understood in more detail.