Effects of Abiotic Stress on Soil Microbiome

A meta-analysis on crop growth and heavy metals accumulation with PGPB inoculation in contaminated soils

Plant growth-promoting bacteria (PGPB) offer a promising solution for mitigating heavy metals (HMs) stress in crops, yet the mechanisms underlying the way they operate in the soil-plant system are not fully understood. We therefore conducted a meta-analysis with 2037 observations to quantitatively evaluate the effects and determinants of PGPB inoculation on crop growth and HMs accumulation in contaminated soils. We found that inoculation increased shoot and root biomass of all five crops (rice, maize, wheat, soybean, and sorghum) and decreased metal accumulation in rice and wheat shoots together with wheat roots. Key factors driving inoculation efficiency included soil organic matter (SOM) and the addition of exogenous fertilizers (N, P, and K). The phylum Proteobacteria was identified as the keystone taxa in effectively alleviating HMs stress in crops. More antioxidant enzyme activity, photosynthetic pigment, and nutrient absorption were induced by it. Overall, using PGPB inoculation improved the growth performance of all five crops, significantly increasing crop biomass in shoots, roots, and grains by 33 %, 35 %, and 20 %, respectively, while concurrently significantly decreasing heavy metal accumulation by 16 %, 9 %, and 37 %, respectively. These results are vital to grasping the benefits of PGPB and its future application in enhancing crop resistance to HMs.

Connections between soil microbes, land use and European climate: Insights for management practices

Soil microbial biomass and activity strongly depend on land use, vegetation cover, climate, and soil physicochemical properties. In most cases, this dependence was assessed by one-to-one correlations while by employing network analysis, information about network robustness and the balance between stochasticity and determinism controlling connectivity, was revealed. In this study, we further elaborated on the hypothesis of Smith et al. (2021) that cropland soils depended more on climate variables and therefore are more vulnerable to climate change. We used the same dataset with that of Smith et al. (2021) that contains seasonal microbial, climate and soil variables collected from 881 soil points representing the main land uses in Europe: forests, grassland, cropland. We examined complete (both direct and indirect relationships) and incomplete networks (only direct relationships) and recorded higher robustness in the former. Partial Least Square results showed that on average more than 45% of microbial attributes' variability was predicted by climate and habitat drivers denoting medium to strong effect of habitat filtering. Network architecture slightly affected by season or land use type; it followed the core/periphery structure with positive and negative interactions and no hub nodes. Microbial attributes (biomass, activity and their ratio) mostly belong to core block together with Soil Organic Carbon (SOC), while climate and soil variables to periphery block with the exception of cropland networks, denoting the higher dependence between microbial and climate variables in these latter. All complete networks appeared robust except for cropland and forest in summer, a finding that disagrees with our initial hypothesis about cropland. Networks' connectivity was controlled stronger by stochasticity in forest than in croplands. The lack of human interventions in forest soils increase habitat homogeneity enhancing the influence of stochastic agents such as microbial unlimited dispersal and/or stochastic extinction. The increased stochasticity implies the necessity for proactive management actions.

A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea

BACKGROUND

Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.

RESULTS

The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.

CONCLUSION

Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.

Improving crop salt tolerance through soil legacy effects

Soil salinization poses a critical problem, adversely affecting plant development and sustainable agriculture. Plants can produce soil legacy effects through interactions with the soil environments. Salt tolerance of plants in saline soils is not only determined by their own stress tolerance but is also closely related to soil legacy effects. Creating positive soil legacy effects for crops, thereby alleviating crop salt stress, presents a new perspective for improving soil conditions and increasing productivity in saline farmlands. Firstly, the formation and role of soil legacy effects in natural ecosystems are summarized. Then, the processes by which plants and soil microbial assistance respond to salt stress are outlined, as well as the potential soil legacy effects they may produce. Using this as a foundation, proposed the application of salt tolerance mechanisms related to soil legacy effects in natural ecosystems to saline farmlands production. One aspect involves leveraging the soil legacy effects created by plants to cope with salt stress, including the direct use of halophytes and salt-tolerant crops and the design of cropping patterns with the specific crop functional groups. Another aspect focuses on the utilization of soil legacy effects created synergistically by soil microorganisms. This includes the inoculation of specific strains, functional microbiota, entire soil which legacy with beneficial microorganisms and tolerant substances, as well as the application of novel technologies such as direct use of rhizosphere secretions or microbial transmission mechanisms. These approaches capitalize on the characteristics of beneficial microorganisms to help crops against salinity. Consequently, we concluded that by the screening suitable salt-tolerant crops, the development rational cropping patterns, and the inoculation of safe functional soils, positive soil legacy effects could be created to enhance crop salt tolerance. It could also improve the practical significance of soil legacy effects in the application of saline farmlands.

Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors

Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.

Impact of Heavy Metal Pollution in the Environment on the Metabolic Profile of Medicinal Plants and Their Therapeutic Potential

The paper provides a comprehensive examination of heavy metal stress on medicinal plants, focusing on its impact on antioxidant capacity and biosynthetic pathways critical to their therapeutic potential. It explores the complex relationship between heavy metals and the physiological and biochemical responses of medicinal plants, highlighting how metal stress disrupts biosynthetic pathways, altering concentrations of secondary metabolites. This disruption may compromise the overall quality and efficacy of medicinal plants, requiring a holistic understanding of its cumulative impacts. Furthermore, the study discusses the potential of targeted genetic editing to enhance plant resilience against heavy metal stress by manipulating genes associated with antioxidant defenses. This approach represents a promising frontier in safeguarding medicinal plants in metal-contaminated environments. Additionally, the research investigates the role of phytohormone signaling in plant adaptive mechanisms to heavy metal stress, revealing its influence on biochemical and physiological responses, thereby adding complexity to plant adaptation. The study underscores the importance of innovative technologies and global cooperation in protecting medicinal plants' therapeutic potential and highlights the need for mitigation strategies to address heavy metal contamination effectively.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Distillers' grains organic fertilizer alters soil bacterial composition and co-occurrence patterns in a tobacco-growing field

In recent years, numerous studies have indicated that the combination of organic and inorganic fertilizers can effectively improve soil fertility and soil productivity. Distillers' grain (DG), the primary by-product of Chinese spirits production, has a high utilization value for producing organic fertilizer. We investigated the effects of distillers' grain organic fertilizer (DGOF) on soil chemical properties and microbial community composition, as well as the effects of chemical properties on the abundance of keystone species. The results indicated that the application of DGOF significantly increased tobacco yield by 14.8% and mainly affected the composition rather than the alpha diversity of the bacterial community. Ten amplicon sequence variants (ASVs) were identified as keystone species in the bacterial communities, and most of their relative abundance was influenced by the DGOF addition through affecting soil chemical properties. Our results elucidated the alterations in soil chemical properties and microbial community composition resulting from DGOF application, which is of great importance to better understand the relationship between DGOF and soil microorganisms in the flue-cured tobacco cultivation field.

Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change

Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.

Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco

Research on microorganisms in various biotopes is required to identify new, natural potent molecules. These molecules are essential to control the development of multi-drug resistance (MDR). In the present study, a Streptomyces sp., namely SCJ, was isolated from a soil sample collected from a Moroccan garden. SCJ isolate was identified on the basis of a polyphasic approach, which included cultural, micro-morphological, biochemical, and physiological characteristics. The sequence of the 16S rRNA gene of the SCJ strain showed 99.78% similarity to strains of Streptomyces coeruleofuscus YR-T (KY753282.1). The preliminary screening indicated that the SCJ isolate exhibited activity against Candida albicans ATCC 60,193, Escherichia coli ATCC 25,922, Staphylococcus aureus CECT 976, Staphylococcus aureus ATCC 25,923, Bacillus cereus ATCC 14,579, Pseudomonas aeruginosa ATCC 27,853, as well as various other clinical MDR bacteria and five phytopathogenic fungi. The ethyl acetate extract of the isolated strain demonstrated highly significant (p < 0.05) antimicrobial activity against multi-resistant bacteria and phytopathogenic fungi. The absorption spectral analysis of the ethyl acetate extract of the SCJ isolate obtained showed no absorption peaks characteristic of polyene molecules. Moreover, no hemolytic activity against erythrocytes was observed in this extract. GC-MS analysis of the ethyl acetate extract of the SCJ isolate revealed the presence of 9 volatile compounds including 3,5-Dimethylpyrazole, and pyrrolizidine derivatives (Pyrrolo[1,2-a]pyrazine 1,4-dione, hexahydro-3-(2-methylpropyl)), which could potentially explain the antimicrobial activity demonstrated in this study.

Prospecting the Potential of Plant Growth-Promoting Microorganisms for Mitigating Drought Stress in Crop Plants

Drought is a global phenomenon affecting plant growth and productivity, the severity of which has impacts around the whole world. A number of approaches, such as agronomic, conventional breeding, and genetic engineering, are followed to increase drought resilience; however, they are often time consuming and non-sustainable. Plant growth-promoting microorganisms are used worldwide to mitigate drought stress in crop plants. These microorganisms exhibit multifarious traits, which not only help in improving plant and soil health, but also demonstrate capabilities in ameliorating drought stress. The present review highlights various adaptive strategies shown by these microbes in improving drought resilience, such as modulation of various growth hormones and osmoprotectant levels, modification of root morphology, exopolysaccharide production, and prevention of oxidative damage. Gene expression patterns providing an adaptive edge for further amelioration of drought stress have also been studied in detail. Furthermore, the practical applications of these microorganisms in soil are highlighted, emphasizing their potential to increase crop productivity without compromising long-term soil health. This review provides a comprehensive coverage of plant growth-promoting microorganisms-mediated drought mitigation strategies, insights into gene expression patterns, and practical applications, while also guiding future research directions.

Antifungal efficacy of biogenic waste derived colloidal/nanobiochar against Colletotrichum gloeosporioides species complex

Anthracnose caused by Colletotrichum spp. usually resulting in significant postharvest losses in the banana production chain. This study investigated the inhibitory effect of corn cob colloidal/nanobiochar (CCN) and Gliricidia sepium wood colloidal/nanobiochar (GCN) on the Colletotrichum gloeosporioides species complex. The CCN and GCN materials were synthesized and thoroughly characterized using various techniques, including UV-Vis and Fluorescence spectroscopy. Then after the fungal growth was examined on Potato Dextrose Agar (PDA) media supplemented with different CCN and GCN concentrations of 0.4 - 20 g/L and CCN and GCN with zeolite at various weight percentages of 10% to 50% w/w. Results from the characterization revealed that CCN exhibited a strong UV absorbance peak value of 0.630 at 203 nm, while GCN had a value of 0.305 at 204 nm. In terms of fluorescence emission, CCN displayed a strong peak intensity of 16,371 at 412 nm, whereas GCN exhibited a strong peak intensity of 32,691 at 411 nm. Both CCN and GCN, at concentrations ranging from 1 to 8 and 0.4 - 20 g/L, respectively, displayed notable reductions in mycelial densities and inhibited fungal growth compared to the control. Zeolite incorporation further enhanced the antifungal effect. To the best of our knowledge, this is the first study to demonstrate the promising potential of colloidal/nanobiochar in effectively controlling anthracnose disease. The synthesized CCN and GCN demonstrate promising antifungal potential against Colletotrichum gloeosporioides species complex, offering the potential for the development of novel and effective antifungal strategies for controlling anthracnose disease in Musa spp.

Effects of coffee pericarp and litter mulsching on soil microbiomes diversity and functions in a tropical coffee plantation, South China

In recent decades, ecological cyclic cultivation models have attracted increasing attention, primarily because the decomposition of crop residues and litter enhances soil organic matter content, thereby altering the soil microenvironment and regulating the diversity and functions of soil microbial communities. However, the effects of different coffee waste mulching on the diversity of soil microbial communities and their functions are still unclear. Therefore, this study set up four kinds of covering treatments: uncovered coffee waste (C), covered coffee litter (L), covered coffee pericarp (P), and both covered coffee litter and pericarp (PL). The results showed that compared to the control, coffee pericarp mulching significantly increased the soil available potassium (SAK) content by 18.45% and alkali hydrolyzed N (SAN) content by 17.29%. Furthermore, coffee pericarp mulching significantly increased bacterial richness and diversity by 7.75 and 2.79%, respectively, while litter mulching had little effect on bacterial abundance and diversity was smaller. The pericarp mulching significantly increased the abundance of Proteus by 22.35% and the abundance of Chlamydomonas by 80.04%, but significantly decreased the abundance of Cyanobacteria by 68.38%, while the coffee litter mulching significantly increased the abundance of Chlamydomonas by 48.28%, but significantly decreased the abundance of Cyanobacteria by 73.98%. The increase in soil SAK promoted bacterial Anoxygenic_photoautotrophy, Nitrogen_respiration, Nitrate_respiration, Nitrite_respiration, and Denitrification functions. The above results indicate that the increase in available soil potassium and alkali hydrolyzed N content under coffee pericarp cover is the main reason for promoting the diversity and richness of bacterial community and promoting the changes in bacterial community structure and function. The use of coffee pericarps in coffee plantations for ecological recycling helps to improve the diversity of the soil microbial community and maintain the relative stability of the microbial community structure and function, promoting soil health conservation and the sustainable development of related industries.

Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture

In the rhizosphere, the activities within all processes and functions are primarily influenced by plant roots, microorganisms present in the rhizosphere, and the interactions between roots and microorganisms. The rhizosphere, a dynamic zone surrounding the roots, provides an ideal environment for a diverse microbial community, which significantly shapes plant growth and development. Microbial activity in the rhizosphere can promote plant growth by increasing nutrient availability, influencing plant hormonal signaling, and repelling or outcompeting pathogenic microbial strains. Understanding the associations between plant roots and soil microorganisms has the potential to revolutionize crop yields, improve productivity, minimize reliance on chemical fertilizers, and promote sustainable plant growth technologies. The rhizosphere microbiome could play a vital role in the next green revolution and contribute to sustainable and eco-friendly agriculture. However, there are still knowledge gaps concerning plant root-environment interactions, particularly regarding roots and microorganisms. Advances in metabolomics have helped to understand the chemical communication between plants and soil biota, yet challenges persist. This article provides an overview of the latest advancements in comprehending the communication and interplay between plant roots and microbes, which have been shown to impact crucial factors such as plant growth, gene expression, nutrient absorption, pest and disease resistance, and the alleviation of abiotic stress. By improving these aspects, sustainable agriculture practices can be implemented to increase the overall productivity of plant ecosystems.

Slow-release microencapsulates containing nanoliposomes for bioremediation of soil hydrocarbons contaminated

Encapsulation and nutrient addition in bacterial formulations have disadvantages concerning cell viability during release, storage, and under field conditions. Then, the objective of this work was to encapsulate a bacterial consortium with hydrocarbon-degrading capacities in different matrices composed of cross-linked alginate/ polyvinyl alcohol /halloysite beads (M1, M2, and M3) containing nanoliposomes loaded with or without nutrients and evaluate their viability and release in a liquid medium, and soil (microcosmos). Also, evaluate their capacity to remove total petroleum hydrocarbons (TPH) for 165 days and matrices characterization. The encapsulate consortium showed a quick adaptation to contaminated soil and a percentage of removal (PR) of TPH up to 30% after seven days. All the matrices displayed a PR of up to 90% after 165 days. The matrix M2 displayed significant resistance to degradation and higher cell viability with a PR of 94%. This result supports the encapsulation of bacteria in a sustainable matrix supplemented with nutrients as a well-looked strategy for improving viability and survival and, therefore, enhancing their effectiveness in the remediation of hydrocarbon-contaminated soils.

Gene expression changes throughout the life cycle allow a bacterial plant pathogen to persist in diverse environmental habitats

Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between habitats is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate pathogen adaptation to water and soil, two environments that act as bacterial reservoirs, and compare this information with gene expression in planta. Gene expression in water resembled that observed during late xylem colonization, with an intriguing induction of the type 3 secretion system (T3SS). Alkaline pH and nutrient scarcity-conditions also encountered during late infection stages-were identified as the triggers for this T3SS induction. In the soil environment, R. solanacearum upregulated stress-responses and genes for the use of alternate carbon sources, such as phenylacetate catabolism and the glyoxylate cycle, and downregulated virulence-associated genes. We proved through gain- and loss-of-function experiments that genes associated with the oxidative stress response, such as the regulator OxyR and the catalase KatG, are key for bacterial survival in soil, as their deletion cause a decrease in culturability associated with a premature induction of the viable but non culturable state (VBNC). This work identifies essential factors necessary for R. solanacearum to complete its life cycle and is the first comprehensive gene expression analysis in all environments occupied by a bacterial plant pathogen, providing valuable insights into its biology and adaptation to unexplored habitats.

Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities

The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.

Fine root decomposition in forest ecosystems: an ecological perspective

Fine root decomposition is a physio-biochemical activity that is critical to the global carbon cycle (C) in forest ecosystems. It is crucial to investigate the mechanisms and factors that control fine root decomposition in forest ecosystems to understand their system-level carbon balance. This process can be influenced by several abiotic (e.g., mean annual temperature, mean annual precipitation, site elevation, stand age, salinity, soil pH) and biotic (e.g., microorganism, substrate quality) variables. Comparing decomposition rates within sites reveals positive impacts of nitrogen and phosphorus concentrations and negative effects of lignin concentration. Nevertheless, estimating the actual fine root breakdown is difficult due to inadequate methods, anthropogenic activities, and the impact of climate change. Herein, we propose that how fine root substrate and soil physiochemical characteristics interact with soil microorganisms to influence fine root decomposition. This review summarized the elements that influence this process, as well as the research methods used to investigate it. There is also need to study the influence of annual and seasonal changes affecting fine root decomposition. This cumulative evidence will provide information on temporal and spatial dynamics of forest ecosystems, and will determine how logging and reforestation affect fine root decomposition.

Plant breeding for harmony between sustainable agriculture, the environment, and global food security: an era of genomics-assisted breeding

MAIN CONCLUSION

Genomics-assisted breeding represents a crucial frontier in enhancing the balance between sustainable agriculture, environmental preservation, and global food security. Its precision and efficiency hold the promise of developing resilient crops, reducing resource utilization, and safeguarding biodiversity, ultimately fostering a more sustainable and secure food production system. Agriculture has been seriously threatened over the last 40 years by climate changes that menace global nutrition and food security. Changes in environmental factors like drought, salt concentration, heavy rainfalls, and extremely low or high temperatures can have a detrimental effects on plant development, growth, and yield. Extreme poverty and increasing food demand necessitate the need to break the existing production barriers in several crops. The first decade of twenty-first century marks the rapid development in the discovery of new plant breeding technologies. In contrast, in the second decade, the focus turned to extracting information from massive genomic frameworks, speculating gene-to-phenotype associations, and producing resilient crops. In this review, we will encompass the causes, effects of abiotic stresses and how they can be addressed using plant breeding technologies. Both conventional and modern breeding technologies will be highlighted. Moreover, the challenges like the commercialization of biotechnological products faced by proponents and developers will also be accentuated. The crux of this review is to mention the available breeding technologies that can deliver crops with high nutrition and climate resilience for sustainable agriculture.

Unveiling novel insights into haloarchaea (Halolamina pelagica CDK2) for alleviation of drought stress in wheat

Plant growth promoting microorganisms have various implications for plant growth and drought stress alleviation; however, the roles of archaea have not been explored in detail. Herein, present study was aimed for elucidating potential of haloarchaea (Halolamina pelagica CDK2) on plant growth under drought stress. Results showed that haloarchaea inoculated wheat plants exhibited significant improvement in total chlorophyll (100%) and relative water content (30.66%) compared to the uninoculated water-stressed control (30% FC). The total root length (2.20-fold), projected area (1.60-fold), surface area (1.52-fold), number of root tips (3.03-fold), number of forks (2.76-fold) and number of links (1.45-fold) were significantly higher in the inoculated plants than in the uninoculated water stressed control. Additionally, the haloarchaea inoculation resulted in increased sugar (1.50-fold), protein (2.40-fold) and activity of antioxidant enzymes such as superoxide dismutase (1.93- fold), ascorbate peroxidase (1.58-fold), catalase (2.30-fold), peroxidase (1.77-fold) and glutathione reductase (4.70-fold), while reducing the accumulation of proline (46.45%), glycine betaine (35.36%), lipid peroxidation (50%), peroxide and superoxide radicals in wheat leaves under water stress. Furthermore, the inoculation of haloarchaea significantly enhanced the expression of stress-responsive genes (DHN, DREB, L15, and TaABA-8OH) and wheat vegetative growth under drought stress over the uninoculated water stressed control. These results provide novel insights into the plant-archaea interaction for plant growth and stress tolerance in wheat and pave the way for future research in this area.

Biochemical and metabolic signatures are fundamental to drought adaptation in PGPR Enterobacter bugandensis WRS7

Drought alone causes more annual loss in crop yield than the sum of all other environmental stresses. There is growing interest in harnessing the potential of stress-resilient PGPR in conferring plant resistance and enhancing crop productivity in drought-affected agroecosystems. A detailed understanding of the complex physiological and biochemical responses will open up the avenues to stress adaptation mechanisms of PGPR communities under drought. It will pave the way for rhizosphere engineering through metabolically engineered PGPR. Therefore, to reveal the physiological and metabolic networks in response to drought-mediated osmotic stress, we performed biochemical analyses and applied untargeted metabolomics to investigate the stress adaptation mechanisms of a PGPR Enterobacter bugendensis WRS7 (Eb WRS7). Drought caused oxidative stress and resulted in slower growth rates in Eb WRS7. However, Eb WRS7 could tolerate drought stress and did not show changes in cell morphology under stress conditions. Overproduction of ROS caused lipid peroxidation (increment in MDA) and eventually activated antioxidant systems and cell signalling cascades, which led to the accumulation of ions (Na+, K+, and Ca2+), osmolytes (proline, exopolysaccharides, betaine, and trehalose), and modulated lipid dynamics of the plasma membranes for osmosensing and osmoregulation, suggesting an osmotic stress adaption mechanism in PGPR Eb WRS7. Finally, GC-MS-based metabolite profiling and deregulated metabolic responses highlighted the role of osmolytes, ions, and intracellular metabolites in regulating Eb WRS7 metabolism. Our results suggest that understanding the role of metabolites and metabolic pathways can be exploited for future metabolic engineering of PGPR and developing bio inoculants for plant growth promotion under drought-affected agroecosystems.

Characterization of plant growth-promoting, antifungal, and enzymatic properties of beneficial bacterial strains associated with pulses rhizosphere from Bundelkhand region of India

The present study was conducted to characterize the native plant growth-promoting rhizobacteria (PGPRs) from the pulse rhizosphere of the Bundelkhand region of India. Twenty-four bacterial isolates belonging to nineteen species (B. amyloliquefaciens, B. subtilis, B. tequilensis, B. safensis, B. haynesii, E. soli, E. cloacae, A. calcoaceticus, B. valezensis, S. macrescens, P. aeruginosa, P. fluorescens, P. guariconensis, B. megaterium, C. lapagei, P. putida, K. aerogenes, B. cereus, and B. altitudinis) were categorized and evaluated for their plant growth-promoting potential, antifungal properties, and enzymatic activities to identify the most potential strain for commercialization and wider application in pulse crops. Phylogenetic identification was done on the basis of 16 s rRNA analysis. Among the 24 isolates, 12 bacterial strains were gram positive, and 12 were gram negative. Among the tested 24 isolates, IIPRAJCP-6 (Bacillus amyloliquefaciens), IIPRDSCP-1 (Bacillus subtilis), IIPRDSCP-10 (Bacillus tequilensis), IIPRRLUCP-5 (Bacillus safensis), IIPRCDCP-2 (Bacillus subtilis), IIPRAMCP-1 (Bacillus safensis), IIPRMKCP-10 (Bacillus haynesii), IIPRANPP-3 (Bacillus amyloliquefaciens), IIPRKAPP-5 (Enterobacter soli), IIPRAJCP-2 (Enterobacter cloacae), IIPRDSCP-11 (Acinetobacter calcoaceticus), IIPRDSCP-9 (Bacillus valezensis), IIPRMKCP-3 (Seratia macrescens), IIPRMKCP-1 (Pseudomonas aeruginosa), IIPRCKPP-3 (Pseudomonas fluorescens), IIPRMKCP-9 (Pseudomonas guariconensis), IIPRMKCP-8 (Bacillus megatirium), IIPRMWCP-9 (Cedecea lapagei), IIPRKUCP-10 (Pseudomonas putida), IIPRAMCP-4 (Klebsiella aerogenes), IIPRCKPP-7 (Enterobacter cloacae), IIPRAMCP-5 (Bacillus cereus), IIPRSHEP-6 (Bacillus subtilis), IIPRRSBa89 (Bacillus altitudinis) bacterial isolates, IIPRMKCP-9, IIPRAJCP-6, IIPRMKCP-10, IIPRAMCP-5, IIPRSHEP-6, and IIPRMKCP-3 showed the maximum antagonistic activity against Fusarium oxysporum f. sp. ciceris (FOC), Fusarium oxysporum f. sp. lentis (FOL), and Fusarium udum (FU) causing wilt disease of chickpea, lentil, and pigeonpea, respectively, and maximum plant growth-promoting enzyme (phosphatase), plant growth hormone (IAA), and siderophore production show promising results under greenhouse conditions. This study is the first report of bacterial diversity in the pulse-growing region of India.

Variability of blue carbon storage in arid evaporitic environment of two coastal Sabkhas or mudflats

Coastal Sabkhas are mudflats found in arid coastal regions that are located within the supratidal zone when high rates of evaporation lead to high salinity. While evaporitic minerals often accumulate underneath the surface, the microbial mats are present on the surface of Sabkhas. Coastal Sabkha, an under-studied ecosystem in Qatar, has the potential to store blue carbon. In the present study, we investigated the carbon storage capacity of two Sabkhas from contrasting geological backgrounds. The spatial and temporal variabilities of the carbon stocks were examined. The results showed that both studied Sabkhas exhibit a considerable potential for soil carbon storage with carbon stocks of 109.11 ± 7.07 Mg C ha-1 and 67.77 ± 18.10 Mg C ha-1 in Dohat Faishakh and Khor al Adaid Sabkha respectively. These values fall within the reported range for carbon stocks in coastal Sabkhas in the region (51-194 Mg C ha-1). Interestingly, the carbon stocks in the sediments of the Sabkhas were higher than those in the sediments of Qatari mangroves (50.17 ± 6.27 Mg C ha-1). These finding suggest that coastal Sabkhas can serve as blue carbon ecosystems in arid environments.

Effect of salinity on the fate of pesticides in irrigated systems: a first overview

This review investigates the impact of salinity on the fate of the active compounds of pesticides in a cultivated environment. Due to the over-exploitation of water resources and intensification of agriculture, salinity outbreaks are being observed more often in cultivated fields under pesticide treatments. Nevertheless, there is a poor understanding of the incidence of varying water salt loads on the behavior of pesticides' active ingredients in soil and water bodies. The present review established that water salinity can affect the diffusion of pesticides' active ingredients through numerous processes. Firstly, by increasing the vapor pressure and decreasing the solubility of the compounds, which is known as the salting-out effect, salinity can change the colligative properties of water towards molecules and the modification of exchange capacity and sorption onto the chemicals. It has also been established that the osmotic stress induced by salinity could inhibit the biodegradation process by reducing the activity of sensitive microorganisms. Moreover, soil properties like dissolved organic matter, organic carbon, clay content, and soil texture control the fate and availability of chemicals in different processes of persistence in water and soil matrix. In the same line, salinity promotes the formation of different complexes, such as between humic acid and the studied active compounds. Furthermore, salinity can modify the water flux due to soil clogging because of the coagulation and dispersion of clay particle cycles, especially when the change in salinity ranges is severe.

Red imported fire ant nesting affects the structure of soil microbial community

The red imported fire ants (RIFA, Solenopsis invicta) have become a well-known invasive species that poses significant ecological and economic threats globally. As of recent times, the geographic scope of its invasion in China is rapidly expanding, thereby aggravating the extent and severity of its detrimental effects. The importance of soil microorganisms for maintaining soil health and ecosystem function has been widely acknowledged. However, the negative impact of RIFAs on soil microbial communities and their functions has not yet been fully understood. In this study, we sequenced the V3-V4 variable region of the bacterial 16S rRNA gene in soil samples collected from three types of RIFA nests to investigate the impact of RIFA invasion on soil microbial diversity and composition. The results of alpha diversity analysis showed that the normal soil without nests of RIFAs exhibited the highest level of diversity, followed by the soil samples from RIFA-invaded nests and abandoned nests. Taxonomy and biological function annotation analyses revealed significant differences in microbial community structure and function among the different samples. Our findings demonstrate that RIFA invasion can significantly alter soil microbial community composition, which could ultimately affect ecosystem function. Therefore, effective management strategies are urgently needed to mitigate the negative impact of invasive species on native ecosystems.

Residue and soil dissipation kinetics of chloroacetanilide herbicides on rice (Oryzae sativa L.) and assessing the impact on soil microbial parameters and enzyme activity

The present investigation determines the persistence of herbicides like butachlor and pretilachlor in Indian soil, and their impact on soil biological properties including microbial biomass carbon (MBC), total microbial population numbers, and enzyme activities. Butachlor was degraded faster in autumn rice soil (t1/2 of 10-13 days) than in winter rice soil (half-life of 16-18 days). The t1/2 of pretilachlor in winter rice was 12-16 days. Regardless of the seasons under cultivation, no pesticide residue was detected in rice at harvest. Herbicides induced an initial decline (0-14th days after application) in MBC (averages of 332.7-478.4 g g-1 dry soil in autumn rice and 299.6-444.3 g g-1 dry soil in winter rice), microbial populations (averages of 6.4 cfu g-1 in autumn rice and 4.6 cfu g-1 in winter rice), and phosphatase (averages of 242.6-269.3 μg p-nitrophenol g-1 dry soil h-1 in autumn rice and 188.2-212.2 μg p-nitrophenol g-1 dry soil h-1 in winter rice). The application of herbicides favored dehydrogenase (averages of 123.1-156.7 g TPF g-1 dry soil in autumn and 126.7-151.1 g TPF g-1 dry soil in winter) and urease activities (averages of 279.0-340.4 g NH4 g-1 soil 2 h-1 in autumn and 226.7-296.5 g NH4 g-1 soil 2 h-1 in winter) in rice soil at 0-14th DAA. The study suggests that applications of butachlor and pretilachlor at the rates of 1000 g ha-1 and 750 g ha-1, respectively, to control the weeds in the transplanted rice fields do not have any negative impact on the harvested rice and associated soil environment.

Temperature and phosphorus: the main environmental factors affecting the seasonal variation of soil bacterial diversity in Nansi Lake Wetland

Introduction

The soil bacteria promote the circulation conversion of lake nutrients and play an important role in maintaining the balance of the lake ecosystem. Few studies have investigated the association of seasonal variation in bacteria and environmental factors in inland freshwater lake wetlands. Nansi Lake is a large shallow freshwater lake in northern China. It is an important hub of the eastern route of the South-to-North Water Diversion Project.

Methods

In this study, bacterial 16S rRNA genes were used to analyze the variation of soil bacterial community diversity in Nansi Lake Wetland and its influencing factors in different seasons.

Results

It is showed that the phylum, family, and genus with the largest relative abundance in the soil of Nansi Lake Wetland are Proteobacteria, Nitrosomonadaceae, and MND1, respectively. There were significant seasonal differences in soil bacterial diversity in Nansi Lake Wetland, which was significantly higher in summer than in winter. Seasonal variation in environmental factors was significantly correlated with the variation in bacterial communities. Temperature and the content of available phosphorus may be the key factors influencing seasonal variation in bacterial diversity.

Discussion

The results of this study further enhance our understanding of the relationship between bacterial community diversity and environmental factors in the lake wetland ecosystem, which can provide scientific data for the conservation of Nansi Lake Wetland.

The Role of the Plant-Soil Relationship in Agricultural Production-With Particular Regard to PGPB Application and Phytoremediation

Plant growth-promoting bacteria (PGPB) and other living organisms can help with the challenges of modern agriculture. PGPB offer ever-expanding possibilities for science and commerce, and the scientific results have been very advanced in recent years. In our current work, we collected the scientific results of recent years and the opinions of experts on the subject. Opinions and results on soil-plant relations, as well as the importance of PGPB and the latest related experiences, are important topics of our review work, which highlights the scientific results of the last 3-4 years. Overall, it can be concluded from all these observations that the bacteria that promote plant development are becoming more and more important in agriculture almost all over the world, thus, promoting more sustainable and environmentally conscious agricultural production and avoiding the use of artificial fertilizers and chemicals. Since many mechanisms of action, namely biochemical and operational processes, are still under investigation, a new emerging scientific direction is expected in the coming years with regard to PGPB, microbial, and other plant growth-stimulating substances, in which omics and microbial modulation also play a leading role.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita

Introduction

The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops.

Methods

To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods.

Results

Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents.

Discussion

These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.

Soil variables driven by host plant and growth season affect soil microbial composition and metabolism in extremely arid desert ecosystems

Assessment changes of soil microbial community structure and function is important in understanding the response to desert ecosystem management. In present study, variations of soil microbial community and edaphic factors associated with five desert shrubs were determined in Anxi extremely arid desert in Northwest China in growing (summer), deciduous (autumn), and snowfall (winter) seasons. For that, the microbial composition and catabolic metabolism were examined using methods of phospholipid fatty acid (PLFA) and Biolog EcoPlate, respectively. Regardless of plant species and seasonal patterns, the microbial community was mostly dominated by gram-negative bacteria (GN); and the carbohydrates, amino acids and polymers were the main carbon sources for desert microbial metabolism. Microbial biomass and metabolic levels were significantly higher in both summer and winter than those of autumn. There was no correlation between soil microbial community and carbon utilization in winter; but GN was positively correlated with metabolism of amines carbon sources in summer, while fungal community presented the strongest correlation with suites of carbon sources' metabolic levels in autumn, indicating the uncoupled relationship between microbial community and function in desert ecosystems. Desert shrubs significantly influenced the composition of soil microbial community, whereas the variation of microbial catabolic metabolism was most attributed to seasonality. Nevertheless, the effects of both plant species (21.3 %) and climate variation (84.9 %) interacted with soil properties, indicating the seasonality of soil nutrients predominately determined the changes in composition and metabolism of desert microbes. Both the comprehensive seasonal level and the intra-seasonal paired correlation analysis proved that phosphorus was the key factor in determining microbial community composition, while ammonia and nitrate nitrogen were more correlated to microbial functional metabolism. Additionally, soil moisture and organic carbon in desert environment also induced the shifts in ratio of fungi and bacterial communities. We conclude that the seasonal patterns of soil microbial community and metabolic function in extremely arid desert are predictable, and mainly influenced by specific soil factors driven by desert shrubs and climate factors. These findings will provide a basis for evaluating the management of soil resources and microbial function in desert environments.

Silicon Application for the Modulation of Rhizosphere Soil Bacterial Community Structures and Metabolite Profiles in Peanut under Ralstonia solanacearum Inoculation

Silicon (Si) has been shown to promote peanut growth and yield, but whether Si can enhance the resistance against peanut bacterial wilt (PBW) caused by Ralstonia solanacearum, identified as a soil-borne pathogen, is still unclear. A question regarding whether Si enhances the resistance of PBW is still unclear. Here, an in vitro R. solanacearum inoculation experiment was conducted to study the effects of Si application on the disease severity and phenotype of peanuts, as well as the microbial ecology of the rhizosphere. Results revealed that Si treatment significantly reduced the disease rate, with a decrement PBW severity of 37.50% as compared to non-Si treatment. The soil available Si (ASi) significantly increased by 13.62-44.87%, and catalase activity improved by 3.01-3.10%, which displayed obvious discrimination between non-Si and Si treatments. Furthermore, the rhizosphere soil bacterial community structures and metabolite profiles dramatically changed under Si treatment. Three significantly changed bacterial taxa were observed, which showed significant abundance under Si treatment, whereas the genus Ralstonia genus was significantly suppressed by Si. Similarly, nine differential metabolites were identified to involve into unsaturated fatty acids via a biosynthesis pathway. Significant correlations were also displayed between soil physiochemical properties and enzymes, the bacterial community, and the differential metabolites by pairwise comparisons. Overall, this study reports that Si application mediated the evolution of soil physicochemical properties, the bacterial community, and metabolite profiles in the soil rhizosphere, which significantly affects the colonization of the Ralstonia genus and provides a new theoretical basis for Si application in PBW prevention.

Effects of Salinity on Assembly Characteristics and Function of Microbial Communities in the Phyllosphere and Rhizosphere of Salt-Tolerant Avicennia marina Mangrove Species

It is of great significance to explore the structure and salinity response of microbial communities in salt-tolerant plants to understand the mechanisms of plant-microbe interactions. Herein, we investigated the phyllosphere and rhizosphere microbial communities of Avicennia marina, a pioneer salt-tolerant plant, at three sites with different salinities in the coastal intertidal zone. The results showed that salinity had different effects on phyllosphere and rhizosphere microbial communities and had a greater impact on bacterial communities and bacterial network interactions. The rhizosphere bacterial community alpha diversity significantly increased with increasing salinity. Moreover, the relative abundance of Proteobacteria decreased significantly, while that of Bacteroidota and Actinobacteriota, with stronger salt tolerance and nutrient utilization capacity, increased significantly. Functional prediction indicated that the microbial communities could produce catalase, peroxidase, 3-phytase, and tryptophan synthase, which may exert potential antistress and growth-promoting functions. Among them, catalase, 3-phytase, alkaline phosphatase, and acid phosphatase increased significantly in the phyllosphere and rhizosphere bacterial communities and the phyllosphere fungal community with increasing salinity. Importantly, the dominant taxa Kushneria and Bacillus, which are salt tolerant and growth promoting, were isolated from the phyllosphere and rhizosphere, respectively, and verified to have the ability to alleviate salt stress and promote the growth of rice. IMPORTANCE Avicennia marina is a pioneer salt-tolerant plant in coastal intertidal mangroves, an efficient blue carbon ecosystem. It is of great importance to explore how salinity affects the phyllosphere and rhizosphere microbial communities of A. marina. This study showed that the microbial communities in the phyllosphere and rhizosphere of A. marina had different constitutive properties, adaptive network interactions, and potential stress-promoting functions. Furthermore, the dominant bacteria Kushneria and Bacillus were obtained from the phyllosphere and rhizosphere, respectively, and their coculture with rice could effectively alleviate salt stress and promote rice growth. Additionally, the effects of salinity changes on microbial community structure, associations, and functional potential in the phyllosphere and rhizosphere of A. marina were observed. This study has enriched our understanding of the microbial community structure, function, and ecological stability of mangrove species in coastal intertidal zones and has practical significance for improving crop yield by using salt-tolerant plant microbiomes.

Mitigation of salinity stress effects on kochia (Bassia scoparia L.) biomass productivity using biochar application

Salinity continues to be a key factor limiting food security and agricultural sustainability in arid and semi-arid countries. Biochar has been promoted to reduce the risk of saline irrigation. In a controlled study, physiological and morphological growth factors of kochia plants that were irrigated with tap water (S1) and saline water (S2) were assessed to identify the ameliorative effects of biochar amendment to the soil at different levels (B1: 0%, B2: 2%, B3: 5%, and B4: 10%. According to our findings, salinity stress negatively affected morphological and physiological growth parameters of kochia plants by decreasing the fresh and dry weight (25% and 28%, respectively), plant height (30%), circumference (46%), total chlorophyll (51%), and relative water content (29%) when compared to the controls. Furthermore, electrolyte leakage increased considerably (19%) due to salt stress. Significant morphological and physiological growth enhancements were seen at all biochar levels in comparison to the control treatment, with the highest level increasing plant height by 55%, circumference by 76%, total chlorophyll concentrations by 121%, and relative water content by 28%. Furthermore, it resulted in a 36% reduction in the stressed plants' electrolyte leakage. The findings demonstrated biochar's benefits in reducing salinity's negative effects on kochia plants.

Symbiotic association of microalgae and plants in a deep water culture system

In this study, microalgae culture (Chlorella vulgaris) and mint seedlings (Mentha spp.) were combined in a hydroponic system to improve plant growth. Mint seedlings were grown both in microalgae-containing and in microalgae-free trial groups, and both groups were subjected to aerated and non-aerated conditions to show the effect of aeration and microalgae co-cultivation on the mint weight and height. The plant quality was also determined with color measurements of the mint leaves. The increase in the weight of the plants was the highest in microalgae-containing and aerated group (0.47 g) and the lowest in microalgae-free and non-aerated group (0.22 g). On the other hand, the variation in the plant height was not significant between the groups, the growth was lateral. The best quality mint leaves were also produced in microalgae-containing and aerated group. Our results have revealed the symbiotic life of the mint plant placed in the hydroponic system with microalgae and demonstrated improved mint growth and quality. This co-cultivation system is also potentially more environmentally friendly compared to growing microalgae and mint independently because of lower cost of aeration and mixing for microalgae cultivation, higher nutrient consumption efficiency, and reduced nutrient outflow.

Agricultural Land Use Influences Bacteriophage Community Diversity, Richness, and Heterogeneity

The last two decades have witnessed a large-scale conversion of crop cultivation areas into small and mid-sized tea plantations in Assam, India. Agricultural land-use pattern positively or negatively influences native hydrology and above- and belowground biodiversity. Very little is known about the effect of agricultural land-use patterns on the soil virus (especially, bacteriophage) community structure and function. This metagenomic-based study evaluated the rhizosphere viral community structure of three interlinked cultivation areas, viz., mixed cropping area (coded as CP1), tea-seed orchard (CP2), and monocropping tea cultivation (CP3). The bacteriophages belonged to four major classes with the dominance of Malgrandaviricetes (CP1: 79.37%; CP2: 64.62%; CP3: 4.85%) followed by Caudoviricetes (CP1: 20.49%; CP2: 35.22%; CP3: 90.29%), Faserviricetes (CP1: 0.03%; CP2: 0.08%; CP3: 3.88%), and Tectiliviricetes (CP1: 0.12%; CP2: 0.07%; CP3: 0.97%). Microviruses dominated the phage population in both CP1 and CP2, representing 79.35% and 64.59% of total bacteriophage abundance. Both CP1 and CP2 had higher bacteriophage richness (species richness, R in CP1: 65; R in CP2: 66) and lower evenness (Pielou's evenness index, J in CP1: 0.531; J in CP2: 0.579) compared to the CP3 (R: 30; J: 0.902). Principal component analysis of edaphic soil factors and bacteriophage community structure showed a reverse-proportional correlation between the levels of Al saturation, and exchangeable Al³⁺ ions with that of soil pH, and bacteriophage abundance. Our study indicates that monocropping tea cultivation soil bears less viral richness, abundance, and heterogeneity.

Evaluation of the Ecological Environment Affected by Cry1Ah1 in Poplar

Populus is a genus of globally significant plantation trees used widely in industrial and agricultural production. Poplars are easily damaged by Micromelalopha troglodyta and Hyphantria cunea, resulting in decreasing quality. Bt toxin-encoded by the Cry gene has been widely adopted in poplar breeding because of its strong insect resistance. There is still no comprehensive and sufficient information about the effects of Cry1Ah1-modified (CM) poplars on the ecological environment. Here, we sampled the rhizosphere soils of field-grown CM and non-transgenic (NT) poplars and applied 16S rRNA and internal transcribed spacer amplicon Illumina MiSeq sequencing to determine the bacterial community associated with the CM and NT poplars. Based on the high-throughput sequencing of samples, we found that the predominant taxa included Proteobacteria (about 40% of the total bacteria), Acidobacteria (about 20% of the total bacteria), and Actinobacteria (about 20% of the total bacteria) collected from the natural rhizosphere of NT and CM poplars. In addition, studies on the microbial diversity of poplar showed that Cry1Ah1 expression has no significant influence on rhizosphere soil alkaline nitrogen, but significantly affects soil phosphorus, soil microbial biomass nitrogen, and carbon. The results exhibited a similar bacterial community structure between CM varieties affected by the expression of Cry1Ah1 and non-transgenic poplars. In addition, Cry1Ah1 expression revealed no significant influence on the composition of rhizosphere microbiomes. These results broadly reflect the effect of the Bt toxin-encoded by Cry1Ah1 on the ecology and environment and provide a clear path for researchers to continue research in this field in the future.

Water Stress, Cadmium, and Plant Genotype Modulate the Rhizosphere Microbiome of Pisum sativum L

Drought and heavy metals seriously affect plant growth and the biodiversity of the associated rhizosphere microbiomes, which, in turn, could be involved in the adaptation of plants to these environmental stresses. Rhizosphere soil was collected from a three-factor pot experiment, where pea line SGE and its Cd-tolerant mutant SGECd^t were cultivated under both optimal and limited water conditions and treated with a toxic Cd concentration. The taxonomic structure of the prokaryotic rhizosphere microbiome was analyzed with the high-throughput sequencing of 16S rRNA amplicon libraries. A permutation test demonstrated statistically significant effects of Cd and water stress but not of pea genotype on the rhizosphere microbiome structure. Phylogenetic isometric log-ratio data transformation identified the taxonomic balances that were affected by abiotic factors and pea genotypes. A small number of significant (log ratio [-3.0:+3.0]) and phylogenetically deep balances characterized water stress, while a larger number of weak (log ratio [-0.8:+0.8]) phylogenetically lower balances described the influence of the plant genotype. Stress caused by cadmium took on an intermediate position. The main conclusion of the study is that the most powerful factor affecting the rhizosphere microbiome was water stress, and the weakest factor was plant genotype since it demonstrated a very weak transformation of the taxonomic structure of rhizosphere microbiomes in terms of alpha diversity indices, beta diversity, and the log ratio values of taxonomic balances.

Suaeda salsa Root-Associated Microorganisms Could Effectively Improve Maize Growth and Resistance under Salt Stress

Root-associated microorganisms are widely recognized as playing an important role in mitigating stress-induced damage to plants, but the responses of rhizosphere microbial communities after inoculation and their relationship with plant responses remain unclear. In this study, the bacterium Providencia vermicola BR68 and the fungus Sarocladium kiliense FS18 were selected from among 91 strains isolated from the halophyte Suaeda salsa to interact with maize seedlings under salt stress. The results showed that compared with NaCl-only treatment, inoculation with strains BR68 and FS18 significantly improved the growth, net photosynthetic rate, and antioxidant enzyme activities of maize; significantly reduced proline content and generation rate of reactive oxygen species (ROS); and alleviated oxidative stress and osmotic stress. Moreover, inoculation with these two strains increased the activities of soil microbiome enzymes such as sucrase, catalase, and fluorescein diacetate hydrolase, which improved maize physiologies and promoted maize growth under salt stress. In addition, these inoculated strains significantly affected the abundance of certain genera, and the correlation trends for these genera with soil properties and maize physiologies were similar to those of these inoculated strains. Strain BR68 was indirectly associated with bacterial communities through BR-specific biomarkers, and bacterial communities and soil properties explained most of the variation in maize physiologies and growth. Inoculation of strain FS18 was directly associated with variations in soil properties and maize physiologies. The two strains improved maize growth under salt stress and alleviated stress damage in maize in different ways. The links among salt-tolerant microorganisms, soil, and plants established in this study can inform strategies for improving crop cultivation in salinized lands.

IMPORTANCE This study demonstrates that halophyte root-associated microorganisms can promote crop tolerance to salt stress and clarify the mechanism by which the strains work in rhizosphere soil. The links among salt-tolerant microorganisms, soil, and plants established in this study can inform strategies for improving crop cultivation in salinized lands.

Microorganisms in Plant Growth and Development: Roles in Abiotic Stress Tolerance and Secondary Metabolites Secretion

Crops aimed at feeding an exponentially growing population are often exposed to a variety of harsh environmental factors. Although plants have evolved ways of adjusting their metabolism and some have also been engineered to tolerate stressful environments, there is still a shortage of food supply. An alternative approach is to explore the possibility of using rhizosphere microorganisms in the mitigation of abiotic stress and hopefully improve food production. Several studies have shown that rhizobacteria and mycorrhizae organisms can help improve stress tolerance by enhancing plant growth; stimulating the production of phytohormones, siderophores, and solubilizing phosphates; lowering ethylene levels; and upregulating the expression of dehydration response and antioxidant genes. This article shows the secretion of secondary metabolites as an additional mechanism employed by microorganisms against abiotic stress. The understanding of these mechanisms will help improve the efficacy of plant-growth-promoting microorganisms.

Actinomucor elegans and Podospora bulbillosa Positively Improves Endurance to Water Deficit and Salinity Stresses in Tomato Plants

Fungal strains isolated from the rhizosphere of healthy Solanum lycopersicum were examined to mitigate symptoms of drought and salinity stresses. The fungal strains were identified as Actinomucor elegans and Podospora bulbillosa based on their DNA sequencing and morphological analysis. Additionally, the fungal strains were assayed for a number of plant growth promoting traits and abiotic stresses on solid media. Moreover, a greenhouse experiment was conducted and tomato seedlings were treated with 25% PEG or 1.5% NaCl for 12 days, and the impact of plant growth promoting fungi (PGPF) on tomato seedling performance under these conditions was examined. PGPF application raised the survival of the stressed tomato plants, which was evidenced by higher physiological and biochemical processes. The PGPF-inoculated plants exhibited higher chlorophyll, carotenoid, protein, amino acid, antioxidant activities, salicylic acid, glucose, fructose, and sucrose contents, and showed lower hydrogen peroxide, and lipid metabolism relative to control plants under stress. Analysis using gene expression showed enhanced expression of SlF3H gene and reduced expression of SlNCED1, SlDEAD31, SlbZIP38, and SlGRAS10 genes following PGPFs application. Overall, the outcomes of this study elucidate the function of these fungal strains and present candidates with potential implementation as biofertilizers and in promoting plant stress endurance.

Management of abiotic stresses by microbiome-based engineering of the rhizosphere

Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stresses, efforts have accelerated in this direction. Though still in its infancy, microbiome-based engineering has gained popularity because of its advantages over microbe-based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by introduction to the conventional approach of microbe-based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focusses on the significance of rhizospheric microbiome, and harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host-mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of combinatorial scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.

Population Distribution of Phosphate-solubilizing Microorganisms in Agricultural Soil

Phosphorus (P) is an essential macronutrient for plant growth and is mainly present in agricultural soil in unavailable forms. Phosphate-solubilizing microorganisms (PSMs) increase soil P availability. The objective of the present study was to assess the population and type of PSMs and their relationships with soil characteristics in the agricultural soil of Manokwari. Twenty-one composite soil samples (0–20‍ ‍cm) were collected at the rhizospheres of plants in the Prafi and Masni Districts. A dilution technique and plate count method on Pikovskayas agar medium were used to examine the PSM population, phosphate-solubilizing index (PSI), and various soil properties. The results obtained showed that the total population of phosphate-solubilizing bacteria ranged between 25×10³ and 550×10³ CFU g^–1 of soil, while that of phosphate-solubilizing fungi was between 2.0×10³ and 5.0×10³ CFU g^–1 of soil at all locations. The PSI of the isolates ranged between 1.1 to 3.6‍ ‍mm, with the most efficient and highest PSI being obtained for Bacillus sp. (strain 8) and the lowest for Pseudomonas sp. (strain 15). Six isolates found at all locations were identified at the genus level: Chromobacterium sp., Pseudomonas sp., Bacillus sp., Micrococcus sp., Caulobacter sp., and Aspergillus sp. A correlation was observed between the number of PSMs and the level of soil P availability and moisture content, indicating an increase in soil P availability with a greater abundance of PSMs in soil.

Intercropping Walnut and Tea: Effects on Soil Nutrients, Enzyme Activity, and Microbial Communities

The practice of intercropping, which involves growing more than one crop simultaneously during the same growing season, is becoming more important for increasing soil quality, land-use efficiency, and subsequently crop productivity. The present study examined changes in soil physicochemical properties, enzymatic activity, and microbial community composition when walnut (Juglans spp.) was intercropped with tea (Camellia sinensis L.) plants in a forest and compared with a walnut and tea monocropping system. The results showed that walnut–tea intercropping improved the soil nutrient profile and enzymatic activity. The soil available nitrogen (AN), available phosphorus (AP), available potassium (AK), organic matter (OM) content, and sucrase activity were significantly boosted in intercropped walnut and tea than in monocropping forests. The interaction between crops further increased bacterial and fungal diversity when compared to monoculture tea forests. Proteobacteria, Bacteroidetes, Firmicutes, Chlamydiae, Rozellomycota, and Zoopagomycota were found in greater abundance in an intercropping pattern than in monoculture walnut and tea forest plantations. The walnut–tea intercropping system also markedly impacted the abundance of several bacterial and fungal operational taxonomic units (OTUs), which were previously shown to support nutrient cycling, prevent diseases, and ameliorate abiotic stress. The results of this study suggest that intercropping walnut with tea increased host fitness and growth by positively influencing soil microbial populations.

Microbial Community and Function-Based Synthetic Bioinoculants: A Perspective for Sustainable Agriculture

Interactions among the plant microbiome and its host are dynamic, both spatially and temporally, leading to beneficial or pathogenic relationships in the rhizosphere, phyllosphere, and endosphere. These interactions range from cellular to molecular and genomic levels, exemplified by many complementing and coevolutionary relationships. The host plants acquire many metabolic and developmental traits such as alteration in their exudation pattern, acquisition of systemic tolerance, and coordination of signaling metabolites to interact with the microbial partners including bacteria, fungi, archaea, protists, and viruses. The microbiome responds by gaining or losing its traits to various molecular signals from the host plants and the environment. Such adaptive traits in the host and microbial partners make way for their coexistence, living together on, around, or inside the plants. The beneficial plant microbiome interactions have been exploited using traditional culturable approaches by isolating microbes with target functions, clearly contributing toward the host plants' growth, fitness, and stress resilience. The new knowledge gained on the unculturable members of the plant microbiome using metagenome research has clearly indicated the predominance of particular phyla/genera with presumptive functions. Practically, the culturable approach gives beneficial microbes in hand for direct use, whereas the unculturable approach gives the perfect theoretical information about the taxonomy and metabolic potential of well-colonized major microbial groups associated with the plants. To capitalize on such beneficial, endemic, and functionally diverse microbiome, the strategic approach of concomitant use of culture-dependent and culture-independent techniques would help in designing novel "biologicals" for various crops. The designed biologicals (or bioinoculants) should ensure the community's persistence due to their genomic and functional abilities. Here, we discuss the current paradigm on plant-microbiome-induced adaptive functions for the host and the strategies for synthesizing novel bioinoculants based on functions or phylum predominance of microbial communities using culturable and unculturable approaches. The effective crop-specific inclusive microbial community bioinoculants may lead to reduction in the cost of cultivation and improvement in soil and plant health for sustainable agriculture.

Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris)

The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon’s diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land.

Beneficial Microbes and Molecules for Mitigation of Soil Salinity in Brassica Species: A Review

Salt stress results from excessive salt accumulation in the soil can lead to a reduction in plant growth and yield. Due to climate change, in the future climatic pressures, changed precipitation cycles and increased temperature will increase the pressures on agriculture, including increasing severity of salt stress. Brassica species contains oilseed and vegetable crops with great economic importance. Advances in understanding the mechanisms of salt stress in Brassica plants have enabled the development of approaches to better induce plant defense mechanisms at the time of their occurrence through the use of beneficial microorganisms or molecules. Both endophytic and rhizospheric microbes contribute to the mitigation of abiotic stresses in Brassica plants by promoting the growth of their host under stress conditions. In this review we summarized so far reported microorganisms with beneficial effects on Brassica plants and their mode of action. Another approach in mitigating the harmful effect of soil salinity may involve the application of different molecules that are involved in the stress response of Brassica plants. We reviewed and summarized their potential mode of action, methods of application and pointed out further research directions.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.