Relationship Between Microbes and Environment for Sustainable Ecosystem Services, Volume 1
Abstract
Relationship Between Microbes and Environment for Sustainable Ecosystem Services, Volume One: Microbial Products for Sustainable Ecosystem Services promotes advances in sustainable solutions, value-added products, and fundamental research in microbes and the environment. Topics include advanced and recent discoveries in the use of microbes for sustainable development. Users will find reference information ranging from the description of various microbial applications for sustainability in different aspects of food, energy, the environment and social development. Volume One includes the direct and indirect role of bacteria, fungi, actinomycetes, viruses, mycoplasma and protozoans in the development of products contributing towards sustainable. The book provides a holistic approach to the most recent advances in the application of various microbes as a biotechnological tool for a vast range of sustainable applications, modern practices, exploring futuristic strategies to harness its full potential.
Postharvest disease management is vital to increase the quality and productivity of crops. As part of crop disease protection, people used different agrochemicals and agricultural practices to manage postharvest diseases. However, the widespread use of agrochemicals in pest and disease control has detrimental effects on consumer health, the environment, and fruit quality. To date, different approaches are being used to manage postharvest diseases. The use of microorganisms to control postharvest disease is becoming an eco-friendly and environmentally sounds approach. There are many known and reported biocontrol agents, including bacteria, fungi, and actinomycetes. Nevertheless, despite the abundance of publications on biocontrol agents, the use of biocontrol in sustainable agriculture requires substantial research, effective adoption, and comprehension of the interactions between plants, pathogens, and the environment. To accomplish this, this review made an effort to locate and summarize earlier publications on the function of microbial biocontrol agents against postharvest crop diseases. Additionally, this review aims to investigate biocontrol mechanisms, their modes of operation, potential future applications for bioagents, as well as difficulties encountered during the commercialization process.
Plant pathogenic microorganisms cause great damage to the yield of agricultural crops and also reduce their commercial quality. This article highlights information on the level of damage caused to agricultural crops by pests, as well as the development of organic agriculture, which in recent years has received great attention in many developed countries. In addition, the data from literature were analyzed on the current state and problems of production of pesticides in the world and their use in agriculture, the use of biofungicides against plant diseases. The importance of synthetic pesticides, as well as, controlling the use of synthetic fungicides, and the use of alternative biofungicides in their replacement were also revealed. The article concludes on the need for public reforms and the role of systematic scientific research in creating a local biopesticides market.
Drought stress is a major environmental concern that limits crop growth on a large scale around the world. Significant efforts are required to overcome this issue in order to improve crop production. Therefore, the exciting role of beneficial microorganisms under stress conditions needs to be deeply explored. In this study, the role of two biotic entities, i.e., Arbuscular mycorrhizal fungi (AMF, Glomus versiforme) and plant growth-promoting rhizobacteria (PGPR, Bacillus methylotrophicus) inoculation in drought tolerance of tobacco (Nicotiana tabacum L.), was investigated. The present results showed that drought stress considerably reduced tobacco plant’s growth and their physiological attributes. However, the plants co-inoculated with AMF and PGPR showed higher drought tolerance by bringing up significant improvement in the growth and biomass of tobacco plants. Moreover, the co-inoculation of AMF and PGPR considerably increased chlorophyll a, b, total chlorophylls, carotenoids, photosynthesis, and PSII efficiency by 96.99%, 76.90%, and 67.96% and 56.88%, 53.22%, and 33.43% under drought stress conditions, respectively. Furthermore, it was observed that drought stress enhanced lipid peroxidation and electrolyte leakage. However, the co-inoculation of AMF and PGPR reduced the electrolyte leakage and lipid peroxidation and significantly enhanced the accumulation of phenols and flavonoids by 57.85% and 71.74%. Similarly, the antioxidant enzymatic activity and the plant nutrition status were also considerably improved in co-inoculated plants under drought stress. Additionally, the AMF and PGPR inoculation also enhanced abscisic acid (ABA) and indole-3-acetic acid (IAA) concentrations by 67.71% and 54.41% in the shoots of tobacco plants. The current findings depicted that inoculation of AMF and PGPR (alone or in combination) enhanced the growth and mitigated the photosynthetic alteration with the consequent up-regulation of secondary metabolism, osmolyte accumulation, and antioxidant system.
Plant beneficial microorganisms are now accepted as potential alternatives to chemical fertilizers and pesticides in agriculture. However, despite the enormous research efforts, there is still much to be learnt about the underlying processes that affect the efficacy of biocontrol and biofertilizer products in crop systems. A deeper ecological understanding of complex interactions among introduced beneficial strains and resident microbiota under changing environment is essential. These complex interactions are greatly influenced by the formulation of beneficial microbial strains as well as the growing substrate characteristics and commercial agricultural practices. This Research Topic presents 33 articles that describe the recent research progresses on the exploitation of beneficial microbes in agriculture.
The major forces driving farm-level production for the ever-growing global population have relied upon mechanized farming techniques, synthetic inputs, and developing high-yielding crop varieties. Recently, however, there has been a gradual shift toward developing sustainable approaches addressing the potential use of beneficial traits of the soil-plant microbiome to establish a sustainable food supply as well as to maintain soil and plant health. The intricate relationship of the soil-plant microbiome complex often faces difficulty in the efficient translation for the broad spectrum of audiences across society. In recent years, there has been a growing need to formulate strategies and streamline the global sharing of the generated information on plant microbiome interactions. In this review, we discuss novel and emerging strategies to use indigenous microbial consortia and engineered exogenous microbial inoculants for rhizosphere engineering. In addition, this review also details the use of these microbial consortia to improve crop yields and environmental protection that are currently in practice.
The development of environmentally sustainable, economical, and reliable sources of energy is one of the great challenges of the 21st century. Large-scale cultivation of cellulosic feedstock crops (henceforth, bioenergy crops) is considered one of the most promising renewable sources for liquid transportation fuels. However, the mandate to develop a viable cellulosic bioenergy industry is accompanied by an equally urgent mandate to deliver not only cheap reliable biomass but also ecosystem benefits, including efficient use of water, nitrogen, and phosphorous; restored soil health; and net negative carbon emissions. Thus, sustainable bioenergy crop production may involve new agricultural practices or feedstocks and should be reliable, cost effective, and minimal input, without displacing crops currently grown for food production on fertile land. In this editorial perspective for the Phytobiomes Journal Focus Issue on Phytobiomes of Bioenergy Crops and Agroecosystems, we consider the microbiomes associated with bioenergy crops, the effects beneficial microbes have on their hosts, and potential ecosystem impacts of these interactions. We also address outstanding questions, major advances, and emerging biotechnological strategies to design and manipulate bioenergy crop microbiomes. This approach could simultaneously increase crop yields and provide important ecosystem services for a sustainable energy future.
Microbial diversity formed by ages of evolution in soils plays an important role in sustainability of crop production by enriching soil and alleviating biotic and abiotic stresses. This diversity is as an essential part of the agro-ecosystems, which is being pushed to edges by pumping agrochemicals and constant soil disturbances. Consequently, efficiency of cropping system has been decreasing, aggravated further by the increased incidence of abiotic stresses due to changes in climatic patterns. Thus, the sustainability of agriculture is at stake. Understanding the microbiota inhabiting phyllosphere, endosphere, spermosphere, rhizosphere, and non-rhizosphere, and its utilization could be a sustainable crop production strategy. This review explores the available information on diversity of beneficial microbes in agricultural ecosystem and synthesizes their commercial uses in agriculture. Microbiota in agro-ecosystem works by nutrient acquisition, enhancing nutrient availability, water uptake, and amelioration of abiotic and abiotic stresses. External application of such beneficial microbiota or microbial consortia helps in boosting plant growth and provides resistance to drought, salinity, heavy metal, high-temperature and radiation stress in various crop plants. These have been instrumental in enhancing tolerance to diseases, insect pest and nematodes in various cropping system. However, studies on the microbiome in revolutionary production systems like conservation agriculture and protected cultivation, which use lesser agrochemicals, are limited and if exploited can provide valuable input in sustainable agriculture production.
The agricultural sector is currently facing many global challenges, such as climate change, and environmental problems such as the release of pesticides and fertilizers, which will be exacerbated in the face of population growth and food shortages. Therefore, the need to change traditional farming methods and replace them with new technologies is essential, and the application of nanotechnology, especially green technology offers considerable promise in alleviating these problems. Nanotechnology has led to changes and advances in many technologies and has the potential to transform various fields of the agricultural sector, including biosensors, pesticides, fertilizers, food packaging and other areas of the agricultural industry. Due to their unique properties, nanomaterials are considered as suitable carriers for stabilizing fertilizers and pesticides, as well as facilitating controlled nutrient transfer and increasing crop protection. The production of nanoparticles by physical and chemical methods requires the use of hazardous materials, advanced equipment, and has a negative impact on the environment. Thus, over the last decade, research activities in the context of nanotechnology have shifted towards environmentally friendly and economically viable ‘green’ synthesis to support the increasing use of nanoparticles in various industries. Green synthesis, as part of bio-inspired protocols, provides reliable and sustainable methods for the biosynthesis of nanoparticles by a wide range of microorganisms rather than current synthetic processes. Therefore, this field is developing rapidly and new methods in this field are constantly being invented to improve the properties of nanoparticles. In this review, we consider the latest advances and innovations in the production of metal nanoparticles using green synthesis by different groups of microorganisms and the application of these nanoparticles in various agricultural sectors to achieve food security, improve crop production and reduce the use of pesticides. In addition, the mechanism of synthesis of metal nanoparticles by different microorganisms and their advantages and disadvantages compared to other common methods are presented.
Wheat is one of the world’s most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.
Wheat variety PBW343, released in India in 1995, became the most widely grown cultivar in the country by the year 2000 owing to its wide adaptability and yield potential. It initially succumbed to leaf rust, and resistance genes Lr24 and Lr28 were transferred to PBW343. After an unbroken reign of about 10 years, the virulence against gene Yr27 made PBW343 susceptible to stripe rust. Owing to its wide adaptability and yield potential, PBW343 became the prime target for marker-assisted introgression of stripe rust resistance genes. The leaf rust-resistant versions formed the base for pyramiding stripe rust resistance genes Yr5, Yr10, Yr15, Yr17, and Yr70, in different introgression programs. Advanced breeding lines with different gene combinations, PBW665, PBW683, PBW698, and PBW703 were tested in national trials but could not be released as varieties. The genes from alien segments, Aegilops ventricosa (Lr37/Yr17/Sr38) and Aegilops umbellulata (Lr76/Yr70), were later pyramided in PBW343. Modified marker-assisted backcross breeding was performed, and 81.57% of the genetic background was recovered in one of the selected derivative lines, PBW723. This line was evaluated in coordinated national trials and was released for cultivation under timely sown irrigated conditions in the North Western Plain Zone of India. PBW723 yields an average of 58.0 qtl/ha in Punjab with high potential yields. The genes incorporated are susceptible to stripe rust individually, but PBW723 with both genes showed enhanced resistance. Three years post-release, PBW723 occupies approximately 8–9% of the cultivated area in the Punjab state. A regular inflow of diverse resistant genes, their rapid mobilization to most productive backgrounds, and keeping a close eye on pathogen evolution is essential to protect the overall progress for productivity and resistance in wheat breeding, thus helping breeders to keep pace with pathogen evolution.
In the past, the potato plant microbiota and rhizosphere have been studied in detail to improve plant growth and fitness. However, less is known about the postharvest potato tuber microbiome and its role in storage stability. The storage stability of potatoes depends on genotype and storage conditions, but the soil in which tubers were grown could also play a role. To understand the ecology and functional role of the postharvest potato microbiota, we planted four potato varieties in five soil types and monitored them until the tubers started sprouting. During storage, the bacterial community of tubers was analysed by next-generation sequencing of the 16S rRNA gene amplicons. The potato tubers exhibited soil-dependent differences in sprouting behaviour. The statistical analysis revealed a strong shift of the tuber-associated bacterial community from harvest to dormancy break. By combining indicator species analysis and a correlation matrix, we predicted associations between members of the bacterial community and tuber sprouting behaviour. Based on this, we identified Flavobacterium sp. isolates, which were able to influence sprouting behaviour by inhibiting potato bud outgrowth.
Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.
The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically. Promoting plant growth by harnessing the soil microbiome holds tremendous potential for providing an environmentally friendly solution to the increasing food demands of the world’s rapidly growing population, while also helping to alleviate the associated environmental and societal issues of large-scale food production. There recently have been many studies on the disease suppression and plant growth promoting abilities of the rhizosphere microbiome; however, these findings largely have not been translated into the field. Therefore, additional research into the dynamic interactions between crop plants, the rhizosphere microbiome and the environment are necessary to better guide the harnessing of the microbiome to increase crop yield and quality. This review explores the biotic and abiotic interactions that occur within the plant’s rhizosphere as well as current agricultural practices, and how these biotic and abiotic factors, as well as human practices, impact the plant microbiome. Additionally, some limitations, safety considerations, and future directions to the study of the plant microbiome are discussed.
Excess atmospheric ammonia (NH3) leads to deleterious effects on biodiversity, ecosystems, air quality and health, and it is therefore essential to monitor its budget and temporal evolution. Hyperspectral infrared satellite sounders provide daily NH3 observations at global scale for over a decade. Here we use the version 3 of the Infrared Atmospheric Sounding Interferometer (IASI) NH3 dataset to derive global, regional and national trends from 2008 to 2018. We find a worldwide increase of 12.8 ± 1.3 % over this 11-year period, driven by large increases in east Asia (5.80 ± 0.61% increase per year), western and central Africa (2.58 ± 0.23 % yr-1), North America (2.40 ± 0.45 % yr-1) and western and southern Europe (1.90 ± 0.43 % yr-1). These are also seen in the Indo-Gangetic Plain, while the southwestern part of India exhibits decreasing trends. Reported national trends are analyzed in the light of changing anthropogenic and pyrogenic NH3 emissions, meteorological conditions and the impact of sulfur and nitrogen oxides emissions, which alter the atmospheric lifetime of NH3. We end with a short case study dedicated to the Netherlands and the 'Dutch Nitrogen crisis' of 2019.
Plant pathogens cause severe losses or damage to crops worldwide and thereby significantly reduce the quality and quantity of agricultural commodities. World tendencies are shifting towards reducing the usage of chemically synthesized pesticides, while various biocontrol methods, strategies and approaches are being used in plant disease management. Fungal antagonists play a significant role in controlling plant pathogens and diseases and they are used as Biocontrol Agents (BCAs) throughout the world. This review provides a comprehensive list of fungal BCAs used against fungal plant pathogens according to modern taxonomic concepts, and clarifies their phylogenetic relationships because thewrong names are frequently used in the literature of biocontrol. Details of approximately 300 fungal antagonists belonging to 13 classes and 113 genera are listed together with the target pathogens and corresponding plant diseases. Trichoderma is identified as the genus with greatest potential comprising 25 biocontrol agents that have been used against a number of plant fungal diseases. In addition to Trichoderma, nine genera are recognized as significant comprising five or more known antagonistic species, namely, Alternaria, Aspergillus, Candida, Fusarium, Penicillium, Pichia, Pythium, Talaromyces, and Verticillium. A phylogenetic analysis based on partial sequences of the 28S nrRNA gene (LSU) of fungal antagonists was performed to establish their phylogenetic relationships.
Modern transformation and genome editing techniques have shown great success across a broad variety of organisms. However, no study of successfully applied genome editing has been reported in a dinoflagellate despite the first genetic transformation of Symbiodinium being published about 20 years ago. Using an array of different available transformation techniques, we attempted to transform Symbiodinium microadriaticum (CCMP2467), a dinoflagellate symbiont of reef-building corals, with the view to performing subsequent CRISPR-Cas9 mediated genome editing. Plasmid vectors designed for nuclear transformation containing the chloramphenicol resistance gene under the control of the CaMV p35S promoter as well as several putative endogenous promoters were used to test a variety of transformation techniques including biolistics, electroporation and silicon carbide whiskers. Chloroplast-targeted transformation were attempted using an engineered Symbiodinium chloroplast minicircle encoding a modified PsbA protein that confers atrazine resistance. We report that we have been unable to confer chloramphenicol or atrazine resistance to Symbiodinium microadriaticum strain CCMP2467.
Healthy soil acts as a dynamic living system that delivers multiple ecosystem services, such as sustaining water quality and plant productivity, controlling soil nutrient recycling decomposition, and removing greenhouse gases from the atmosphere. Soil health is closely associated with sustainable agriculture because soil microorganism diversity and activity are the main components of soil health. Agricultural sustainability is defined as the ability of a crop production system to continuously produce food without environmental degradation. Arbuscular mycorrhizal fungi (AMF), cyanobacteria, and beneficial nematodes enhance water use efficiency and nutrient availability to plants, phytohormones production, soil nutrient cycling, and plant resistance to environmental stresses. Farming practices have shown that organic farming and tillage improve soil health by increasing the abundance, diversity, and activity of microorganisms. Conservation tillage can potentially increase grower's profitability by reducing inputs and labor costs as compared to conventional tillage while organic farming might add extra management costs due to high labor demands for weeding and pest control, and for fertilizer inputs (particularly N-based), which typically have less consistent uniformity and stability than synthetic fertilizers. This review will discuss the external factors controlling the abundance of rhizosphere microbiota and the impact of crop management practices on soil health and their role in sustainable crop production.
Plants are associated with the combination of microbiomes, which can improve plant growth, stress tolerance, and control plant pathogens. The incorporation of a beneficial microbiome represents a promising sustainable key to enhance agricultural production. Sugarcane is an essential crop with many agricultural and industrial uses including animal feed, biofuels and bagasse. There is a need to strengthen sugarcane crop production sustainably and to locate solutions to control pathogens, abiotic stress, and pests. The utilization of beneficial microbes as a biofertilizer has become essential in sugarcane agriculture for sustainable crop production. In this perspective, the sugarcane microbiome becomes a promising approach for sustainable production. The chapter describes the application of sugarcane-associated microbiome.
Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic (N 2-fixing) bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and composed three major diazotrophic groups based on nitrogen fixation gene content. In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization as alternative mechanisms of direct plant growth promotion (PGP). Genome mining showed that isolates of all diazotrophic groups possessed marker genes for multiple mechanisms of direct plant growth promotion (PGP). Implementing in vitro assays corroborated isolate genotypes by measuring each isolate's potential to confer the targeted PGP traits and revealed phenotypic variation among isolates based on diazotrophic group assignment. Investigating the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta led to the identification of 16 bio-stimulant candidates. Conducting nitrogen-stress greenhouse experiments demonstrated that potato inoculation with a synthetic community of bio-stimulant candidates, as well as with its individual components, resulted in PGP phenotypes. We further demonstrated that one dia-zotrophic isolate conferred PGP to a conventional maize variety under nitrogen-stress in the greenhouse. These results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize, potentially through the use of multiple promotion mechanisms. PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.
Plant growth‐promoting rhizobacteria (PGPR) are diverse groups of plant‐associated microorganisms, which can reduce the severity or incidence of disease during antagonism among bacteria and soil‐borne pathogens, as well as by influencing a systemic resistance to elicit defense response in host plants. An amalgamation of various strains of PGPR has improved the efficacy by enhancing the systemic resistance opposed to various pathogens affecting the crop. Many PGPR used with seed treatment causes structural improvement of the cell wall and physiological/biochemical changes leading to the synthesis of proteins, peptides, and chemicals occupied in plant defense mechanisms. The major determinants of PGPR‐mediated induced systemic resistance (ISR) are lipopolysaccharides, lipopeptides, siderophores, pyocyanin, antibiotics 2,4‐diacetylphoroglucinol, the volatile 2,3‐butanediol, N‐alkylated benzylamine, and iron‐regulated compounds. Many PGPR inoculants have been commercialized and these inoculants consequently aid in the improvement of crop growth yield and provide effective reinforcement to the crop from disease, whereas other inoculants are used as biofertilizers for native as well as crops growing at diverse extreme habitat and exhibit multifunctional plant growth‐promoting attributes. A number of applications of PGPR formulation are needed to maintain the resistance levels in crop plants. Several microarray‐based studies have been done to identify the genes, which are associated with PGPR‐induced systemic resistance. Identification of these genes associated with ISR‐mediating disease suppression and biochemical changes in the crop plant is one of the essential steps in understanding the disease resistance mechanisms in crops. Therefore, in this review, we discuss the PGPR‐mediated innovative methods, focusing on the mode of action of compounds authorized that may be significant in the development contributing to enhance plant growth, disease resistance, and serve as an efficient bioinoculants for sustainable agriculture. The review also highlights current research progress in this field with a special emphasis on challenges, limitations, and their environmental and economic advantages.
To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helping to solve these challenges. However, the results of their use in agriculture have been variable, probably because of poor colonization. Phytomicrobiome engineering is an emerging field of synthetic biology that may offer ways to alleviate this limitation. This review highlights recent advances in both bottom-up and top-down approaches to engineering non-model bacteria and microbiomes to promote beneficial plant–microbe interactions, as well as advances in strategies to evaluate these interactions. Biosafety, biosecurity, and biocontainment strategies to address the environmental concerns associated with field use of synthetic microbes are also discussed.
For all living organisms, nitrogen is an essential element, while being the most limiting in ecosystems and for crop production. Despite the significant contribution of synthetic fertilizers, nitrogen requirements for food production increase from year to year, while the overuse of agrochemicals compromise soil health and agricultural sustainability. One alternative to overcome this problem is biological nitrogen fixation (BNF). Indeed, more than 60% of the fixed N on Earth results from BNF. Therefore, optimizing BNF in agriculture is more and more urgent to help meet the demand of the food production needs for the growing world population. This optimization will require a good knowledge of the diversity of nitrogen-fixing microorganisms, the mechanisms of fixation, and the selection and formulation of efficient N-fixing microorganisms as biofertilizers. Good understanding of BNF process may allow the transfer of this ability to other non-fixing microorganisms or to non-leguminous plants with high added value. This minireview covers a brief history on BNF, cycle and mechanisms of nitrogen fixation, biofertilizers market value, and use of biofertilizers in agriculture. The minireview focuses particularly on some of the most effective microbial products marketed to date, their efficiency, and success-limiting in agriculture. It also highlights opportunities and difficulties of transferring nitrogen fixation capacity in cereals.
Soil salinity is one of the major abiotic stresses restricting the use of land for agriculture because it limits the growth and development of most crop plants. Improving productivity under these physiologically stressful conditions is a major scientific challenge because salinity has different effects at different developmental stages in different crops. When supplied exogenously, proline has improved salt stress tolerance in various plant species. Under high-salt conditions, proline application enhances plant growth with increases in seed germination, biomass, photosynthesis, gas exchange, and grain yield. These positive effects are mainly driven by better nutrient acquisition, water uptake, and biological nitrogen fixation. Exogenous proline also alleviates salt stress by improving antioxidant activities and reducing Na⁺ and Cl⁻ uptake and translocation while enhancing K⁺ assimilation by plants. However, which of these mechanisms operate at any one time varies according to the proline concentration, how it is applied, the plant species, and the specific stress conditions as well as the developmental stage. To position salt stress tolerance studies in the context of a crop plant growing in the field, here we discuss the beneficial effects of exogenous proline on plants exposed to salt stress through well-known and more recently described examples in more than twenty crop species in order to appreciate both the diversity and commonality of the responses. Proposed mechanisms by which exogenous proline mitigates the detrimental effects of salt stress during crop plant growth are thus highlighted and critically assessed.
Sustainable strategies for managing weeds are critical to meeting agriculture’s potential to feed the world’s population while conserving the ecosystems and biodiversity on which we depend. The dominant paradigm of weed management in developed countries is currently founded on the two principal tools of herbicides and tillage to remove weeds. However, evidence of negative environmental impacts from both tools is growing, and herbicide resistance is increasingly prevalent. These challenges emerge from a lack of attention to how weeds interact with and are regulated by the agroecosystem as a whole. Novel technological tools proposed for weed control, such as new herbicides, gene editing, and seed destructors, do not address these systemic challenges and thus are unlikely to provide truly sustainable solutions. Combining multiple tools and techniques in an Integrated Weed Management strategy is a step forward, but many integrated strategies still remain overly reliant on too few tools. In contrast, advances in weed ecology are revealing a wealth of options to manage weeds at the agroecosystem level that, rather than aiming to eradicate weeds, act to regulate populations to limit their negative impacts while conserving diversity. Here, we review the current state of knowledge in weed ecology and identify how this can be translated into practical weed management. The major points are the following: (1) the diversity and type of crops, management actions and limiting resources can be manipulated to limit weed competitiveness while promoting weed diversity; (2) in contrast to technological tools, ecological approaches to weed management tend to be synergistic with other agroecosystem functions; and (3) there are many existing practices compatible with this approach that could be integrated into current systems, alongside new options to explore. Overall, this review demonstrates that integrating systems-level ecological thinking into agronomic decision-making offers the best route to achieving sustainable weed management.
The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes.
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Is it possible to omit parasites when studying free-living organisms? The answer is clearly no! Parasites have evolved independently in numerous animal lineages, and now make up a considerable proportion of the biodiversity of life. Ecologists, epidemiologists, conservationists and evolutionary biologists are increasingly aware of the universal significance of parasites to the study of ecology and evolution where they have become a powerful model system. This book provides a summary of the issues involved as well as an overview of the possibilities offered by this research topic including the practical applications for disease prevention. It uses well-documented case-studies across a range of scales to illustrate the main trends and prospects in this area, outlining areas for future research. Ecology and Evolution of Parasitism is the first book to provide a broad synthesis of both the roles and consequences of pathogens on the ecology and evolution of free living systems. It focuses on hosts rather than the parasites themselves, integrating those aspects related to the ecology and the evolution of free-living species (sexual selection, behaviour, life history traits, regulation of populations etc.). The book includes examples across a range of scales from individuals to populations, communities and ecosystems.
Nanotechnology is working with the smallest possible particles which raise hopes for improving
agricultural productivity through encountering problems unsolved conventionally. Improvement of crops
in agriculture is a continuous process. Breeding varieties to suite the growing needs are done through
conventional breeding and biotechnical means. Recently scientists have started using nanotechnology
to deliver the genes to specific sites at cellular levels and rearrange the atoms in the DNA of the same
organism to get expression of desired character, thus skipping the time consuming process of
transferring the gene from the foreign organisms. In the management aspects, efforts are made to
increase the efficiency of applied fertilizer with the help of nano clays and zeolites and restoration of
soil fertility by releasing fixed nutrients. Research on smart seeds programmed to germinate under
favourable conditions with nanopolymer coating are encouraging. In the controlled environment
agriculture and precision farming input requirement of crops are diagnosed based on needs and
delivered the required quantities in right time at right place with the help of nanobiosensor and satellite
system. Nanoherbicides are being developed to address the problems in perennial weed management
and exhausting weed seed bank. Remediation of environmental contamination of the industrial waste
and agricultural chemicals like pesticides and herbicide residues are possible through metal
nanoparticles. Details of possibilities and concepts of application of nanotechnology in the crop
production and results obtained already in these areas are reviewed in this paper.
The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.
Endophytes are the microorganisms that mutually live inside healthy plant tissues, playing important roles in promoting plant growth and providing adaptation toward various environments. Bacteria and fungi are the two major groups that have been recognized as endophytes. Endophytes have been reported to promote plant growth by improving nutrient uptake and solubilization of phosphate, potassium, nitrogen, and iron. Endophytes also biologically fix nitrogen and make it available to host plants. Endophytes produce growth-promoting phytohormones, including auxins, cytokinins, and gibberellins, and modulate the level of the growth-inhibiting hormone, ethylene, by producing 1-aminocyclopropane-1-carboxylate deaminase activity. Many endophytes also share antifungal activity and have been reported to protect plants from pathogenic microorganisms. Endophytic species of Bacillus are known to produce antifungal lipopeptides; species of Pseudomonas and Burkholderia produce a variety of antifungal secondary metabolites and HCN and protect plants from fungal infection. Thus the endophytes are natural inhabitants of plants that can be exploited as biofertilizers and biocontrol agents for the sustainable cultivation of crop plants.
The intimate coupling of photocatalysis and biodegradation (ICPB) possesses an enhanced ability of recalcitrant contaminant removal and energy generation, owing to the compact communication between biotic components and photocatalysts during the system operation. The photocatalysts in the ICPB system could dispose of noxious contaminants to relieve the external pressure on microorganisms which could realize the mineralization of the photocatalytic degradation products. However, due to the complex components in the composite system, the mechanism of the ICPB system has not been completely understood. Moreover, the variable environmental conditions would play a significant role in the ICPB system performance. The further development of the ICPB scheme requires clarification on how to reach an accurate understanding of the system condition during the practical application. This review starts by offering detailed information on the system construction and recent progress in the system components' amelioration. We then describe the potential influences of relevant environmental factors on the system performance, and the analytical strategies applicable for comprehending the critical processes during the system operation are further summarized. Finally, we put forward the research gaps in the current system and envision the system's prospective application. This review provides a valuable reference for future researches that are devoted to assessing the environmental disturbance and exploring the reaction mechanisms during the practical application of the ICPB system.
Microbiome Stimulants for Crops
Mechanisms and Applications
2021, Pages 369-379
Chapter 22 - Microbiome establishment, adaptation, and contributions to anaerobic stress tolerance and nutrient acquisition in rice
Author links open overlay panelRamyaSugavanamBalasubramanianRamakrishnan
https://doi.org/10.1016/B978-0-12-822122-8.00019-4
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Abstract
Rice is the most popular food crop globally for human food security and economic growth. This semiaquatic plant is generally cultivated under flooded conditions in various environments. The microbiomes of different soil types are characteristically different and they determine the nutrient transformations and redox reactions. When rice seeds germinate in the predominantly anaerobic soils, the challenges for their early growth are not only limited by the genetic potential and physiological capabilities but also the establishment and interactions with the microbiomes in and around the seeds. The rice plants select and shape their microbiomes, especially in their rhizospheres, by the supply of root exudates. Concurrently, the signaling from the rice microbiomes influences the growth and development, and the nutrition of host plants. Future studies should focus on enhancing the activities of beneficial members of microbiomes or enriching them with the synthetic microbial communities
We developed and demonstrated a novel intimately coupled photocatalysis and biodegradation (ICPB) system. The ICPB system was comprised of photocatalytic optical hollow-fibers (POHFs) coated with Ag-loaded GeO2 and N-doped TiO2 photocatalyst, along with a biofilm that included phototrophic and heterotrophic microorganisms. The POHFs exhibit high UV-visible photocatalytic activity to degrade phenolic compounds rapidly and stably, decrease toxicity, generate readily biodegradable products, and emit visible light for biofilm growth and O2 production by phototrophs. O2 produced by the phototrophs was transferred to the POHFs, helping generate hydroxyl free radicals for photocatalysis. The biofilm, which became enriched in Rhodococcus and Pseudomonas, maintained rapid and stable biodegradation of photocatalytic products from the phenolics. Thus, the synergism among photocatalysis, biodegradation, and photosynthesis in the novel ICPB system provided an efficient means to rapidly and sustainably degraded and mineralized high concentrations of phenolic compounds.
The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative traits in experimental organisms. We describe here a set of analytical methods that modify and extend the classical theory for mapping such quantitative trait loci (QTLs). These include: (i) a method of identifying promising crosses for QTL mapping by exploiting a classical formula of SEWALL WRIGHT; (ii) a method (interval mapping) for exploiting the full power of RFLP linkage maps by adapting the approach of LOD score analysis used in human genetics, to obtain accurate estimates of the genetic location and phenotypic effect of QTLs; and (iii) a method (selective genotyping) that allows a substantial reduction in the number of progeny that need to be scored with the DNA markers. In addition to the exposition of the methods, explicit graphs are provided that allow experimental geneticists to estimate, in any particular case, the number of progeny required to map QTLs underlying a quantitative trait.
The efficiency of marker-assisted selection (MAS) depends on the power of quantitative trait locus (QTL) detection and unbiased estimation of QTL effects. Two independent samples (N = 344 and 107) of F2 plants were genotyped for 89 RFLP markers. For each sample, testcross (TC) progenies of the corresponding F3 lines with two testers were evaluated in four environments. QTL for grain yield and other agronomically important traits were mapped in both samples. QTL effects were estimated from the same data as used for detection and mapping of QTL (calibration) and, based on QTL positions from calibration, from the second, independent sample (validation). For all traits and both testers we detected a total of 107 QTL with N = 344, and 39 QTL with N = 107, of which only 20 were in common. Consistency of QTL effects across testers was in agreement with corresponding genotypic correlations between the two TC series. Most QTL displayed no significant QTL × environment nor epistatic interactions. Estimates of the proportion of the phenotypic and genetic variance explained by QTL were considerably reduced when derived from the independent validation sample as opposed to estimates from the calibration sample. We conclude that, unless QTL effects are estimated from an independent sample, they can be inflated, resulting in an overly optimistic assessment of the efficiency of MAS.
The use of genetically tractable plant–microbe pairs has driven research in plant immunity and mutualistic symbiosis. Clear functional readouts for the outcomes of symbiosis or immunity have facilitated forward genetic screening and identification of signals, molecules and mechanisms that determine the outcome of these interactions. Plants also associate with beneficial microbial communities that form the microbiome. However, the complexity of the microbiome, combined with relatively subtle effects on plant growth and immunity, has impeded forward genetic screening to identify plant and bacterial genes that shape the microbiome. As a result, microbiome research has relied largely on reverse genetics approaches, based on what is known about plant nutrient uptake and immunity, to identify mechanisms in plant–microbiome research. Here we revisit the features of reductionist model systems that have made them so powerful for studying plant–microbe interactions, and how modeling microbiome research after these systems can propel discovery of novel mechanisms.
Tetracycline (TC) is a commonly used human and veterinary antibiotic that is mostly discharged into wastewater in the form of the parent compounds. At present, wastewater treatment plants (WWTPs) use activated sludge processes that are not specifically designed to remove such pollutants. Considering the biological toxicity of TC in aquatic environment, the migration and fate of TC in the process of wastewater treatment deserve attention. This paper reviews the influence of TC on the functional bacteria in the sludge matrix and the development of tetracycline-resistant genes, and also discusses their adsorption removal rates, their adsorption kinetics and adsorption isotherm models, and infers their adsorption mechanism. In addition, the biodegradation of TC in the process of biological treatment is reviewed. Co-metabolism and the role of dominant bacteria in the degradation process are described, along with the formation of degradation byproducts and their toxicity. Furthermore, the current popular integrated coupling-system for TC degradation is also introduced. This paper systematically introduces the interaction between TC and activated sludge in WWTPs. The review concludes by providing directions to address research and knowledge gaps in TC removal from wastewater.
A screen of fungi for insecticidal activity revealed the ability of Aspergillus versicolor to make versimide, methyl-α-(methylsuccinimido)acrylate, a novel contact insecticide. The larvicidal activities of Alternaria tenuis and Fusarium lateritium were found to be due to tenuazonic acid and diacetoxyscirpenol, respectively. Thiolutin, cycloheximide, rubratoxin, patulin, trichothecin, an actinomycin, and scirpene-producing fungi also had insecticidal activity.
The overuse of agrochemicals for agricultural productivity to meet the global food demand of the rapidly growing human population is a great environmental threat, particularly for aquatic ecosystems. Being associated intimately with plant health, growth, and productivity, the plant microbiome is emerging as a promising environmentally friendly and sustainable resource for agricultural productivity. For the past decades, our understanding of the interactions between plants and microorganisms and our knowledge of how to improve the plant microbiome by using microbial inoculants has increased significantly. A better understanding of the impact of the plant microbiome on mineral resources will benefit plant and soil health. In this review, we highlight the importance of microbial inoculants and their interactions with mineral fertilizers in enhancing crop productivity, as well as current challenges.
Phytoremediation of cadmium (Cd) contaminated soils by accumulators or hyperaccumulators has received considerable attention. However, there is still limited information about its migration, dynamic characteristics, and interaction with microbial communities in rhizosphere. In this study, the behaviors of Cd in rhizosphere soils in phytoremediation were carefully studied and illustrated. We find that the migration rate of Cd in rhizosphere is higher than the absorption rate of Cd by roots of plants, and Cd in near-rhizosphere moves sluggishly, and near-rhizosphere soils forms a mass pool of Cd for absorption by plants. Additionally, in tall fescue and Indian mustard treatments, shoot biomasses, total extracted Cd and migration rate of Cd in near-rhizosphere soils were comparable. It suggests that shoot biomasses of plants significantly affect their extraction of heavy metals from rhizosphere soils. Biomasses of bacteria significantly increased after phytoremediation, and structures of microbiome communities of soils after phytoremediation reassembled significantly. Furthermore, Indian mustard, even with relative lower root biomasses, could better reassembled the microbiome communities in rhizosphere than tall fescue which possesses a higher developed root system. In the end, analyses of functional microorganisms in rhizosphere soils provide new insights into biological and physiochemical roles of these populations in phytoremediation.
One of negative side-effects of usage of bio-renewables might be generation of mineral (ash) material, potential source of environmental pollution. A hypothesis was that bottom ash (BA; from biomass cogeneration facility) could be efficiently (re) used in soil chemical conditioning similarly to widely-used dolomite-based soil conditioner (DO; from Croatian Dinaric-coastal region) which we tested by: i) physicochemical characterisation of BA and DO, and ii) bioassay with Raphanus sativus cultivated in acidic soil amended with BA or DO. Scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) confirmed complex chemical/physical structures and morphology between amendments, X-ray diffraction (XRD) showed their distinctive mineralogy with predominantly dolomite (in DO) vs. quartz and calcite (in BA), while secondary ion mass spectrometry (SIMS) revealed their diverse elemental/isotopic composition. The BA or DO amendments ameliorated soil acidity, increased available P, K and most other nutrients, but not Cd. The BA or DO amendments improved vegetative growth and edible hypocotyl yield. However, both amendments also increased Cd accumulation in all radish tissues, which was unexpected given the alkaline matrix of bio-ash and dolomite that would be likely to facilitate retention and immobilisation of toxic Cd. Thus, thorough characterisation and evaluation of BA- and/or DO-based materials and relevant soils (with an emphasis on metal sorption/immobilisation) prior to application in (agro) ecosystems is crucial for producing food clean of toxic metals.
The lichen Cladonia portentosa is generally considered to be sensitive to increased environmental nitrogen (N) deposition. However, the presence of this lichen in impacted environments suggests that it can cope with prolonged exposure to high N availability. To test the tolerance of this species to N, photosynthetic parameters, carbon and N concentrations and isotopic signature, chitin concentration, surface pH and extracellular enzymatic activity were measured in samples exposed for 11 years to different N doses and forms at the Whim bog N manipulation experimental site (United Kingdom). The results showed that C. portentosa is tolerant to long-term exposure to wet N deposition, maintaining its functionality with almost unaltered physiological parameters. The comparison of the proteome of short- and long-term exposed samples showed similar changes in protein expression suggesting that mechanisms to cope with N are not dependent on the exposure time even after more than a decade. Since empirical N Critical Loads are based on the response of sensitive components of the ecosystem, like C. portentosa, its capacity to cope with short- and long-term exposure to N needs to be recognized and taken into account when setting them, likewise, the significance of the form of N.
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Updated knowledge on tolerance of sensitive species to nitrogen must be taken into account to establish environmental policy.
Nanomaterials (NMs) are gaining significance in technological applications due to their tunable chemical, physical, and mechanical properties and enhanced performance when compared with their bulkier counterparts. This review presents a summary of the general types of NMs and provides an overview of the various synthesis methods of nanoparticles (NPs) and their functionalization via covalent or noncovalent interactions using different methods. It highlights the techniques used for the characterization of NPs and discusses their physical and chemical properties. Due to their unique properties, NMs have several applications and have become part of our daily lives. As a result, nanotoxicity research is gaining attention since some NPs are not easily degraded by the environment. Thus, this review also highlights research efforts into the fate, behavior, and toxicity of different classes of NMs in the environment.
Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications.