A river confluence is an important ecosystem to investigate the microbial community and functional profile. Even after the enormous applications of trace elements and antibiotics, their release into the environment causes pollution and selective pressure that facilitate the proliferation and dissemination of resistance genes against antibiotics, metals and biocides among bacterial communities. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights for the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity could aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors in the microbial community of Saryu River water using high-throughput metagenomics coupled with bioinformatic analyses. The highly dominant antibiotic resistance gene (ARG) types identified were rifampin, tetracycline, macrolide, polymyxin and rifampicin multidrug/efflux. ARGs such as rpoB2, Txr, adeF, tetB(P), and acrB were found to be abundant in Saryu River water. Among the detected MRG subtypes, namely, ruvB and arsB, the most abundant are in water. Further, the biocides against which the resistance was identified were ethidium bromide, triclosan, sodium dodecyl sulfate, etc. Among the virulence factors, tufa, htpB (adherence), Gmd (immune-modulation), cheD (motility), and clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota, followed by Pseudomonadota (Proteobacteria) and Bacteroidota were the dominant phyla in the river water. Microcystis was the most dominant genus, followed by Desulfomicrobium and Dechloromonas. The present study shows that antibiotics and metals are the major sources of resistance genes development and dissemination in the environment.. Further, this is a preliminary study based on a single composite sample, representing a "snapshot" at a specific time and location. The present study highlights the persistence of ARGs, MRGs, biocides, and virulence factors in Saryu River water and provides valuable baseline data for risk assessment.

Endophytic microbes, especially bacteria belonging to the genus Bacillus, have received considerable attention worldwide. Different species of Bacillus have been documented for potential implications in agriculture, environment, and medicine. Endophytic Bacillus role has been well acknowledged in the alleviation of different non-biological stressors such as salinity, drought, high and low temperature, in addition to the presence of different heavy metals. The successful application of endophytic Bacillus would have profound role in enhancing the agricultural productivity despite of changing climatic conditions. The elucidation of detailed mechanisms of action responsible for offering tolerance to varied environmental factors could open new avenues in maximizing the application of endophytic bacilli not only as biofertilizers, but also as effective biocontrol agent towards sustainable agriculture. The plethora of researches has shown bioremediation potential of organic and inorganic contaminants by endophytic Bacillus. Moreover, endophytic Bacillus has been proven as important resources of valuable compounds and synthesis of metal nanoparticles holding antimicrobial activities with usefulness in the management of human diseases. Nevertheless, the full potential of endophytic Bacillus has yet to be achieved by extensive in vivo and in vitro experiments. The isolation and characterization of endophytes from newer hosts and habitat could offer more opportunities in the application of such microbial candidate for intended purposes.

Currently, the treatment of various human ailments is based on different therapeutic approaches including traditional and modern medicine systems. Precision nutrition has come into existence as an emerging approach considering the diverse aspects such as age, sex, genetic and epigenetic makeup, apart from the pathophysiological conditions. The continuously and gradually evolving disciplines of genomics about nutrition have elucidated the importance of genetic variations, epigenetic information, and expression of myriads of genes in disease progression apart from the involvement in modulating therapeutic responses. Further, the investigations have presented the considerable role of gut microbiota comprising of commensal and symbionts performing innumerable activities such as release of bioactive molecules, defense against pathogenic microbes, and regulation of immunity. Noteworthy, the characteristics of the microbiome change depending on host attributes, environmental factors, and habitat, in addition to diet, and therefore can be employed as a biomarker to unravel the response to given food. The specific diet and the components thereof can be suggested for supporting the enrichment of the desired microbial community to some extent as an important part of precision nutrition to achieve not only the goal of human health but also of healthy aging.

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Plant natural products or secondary metabolites have gained significant attention globally because of discoveries of semi-synthetic drugs novel bioactive compounds. Currently, a large part of global population relies on natural products to cure ailments and even chronic diseases and to enhance their immune system. Interestingly, the commonly used drugs for the treatment of some common human diseases like cancer, ulcer, tuberculosis, asthma, etc., have been reported to be of plant origin and recognized to elicit beneficial effects in virulent factors of diseases in vivo and in vitro. The herbal drugs are economical and considered as safe upto certain extent from major side effects. But, still there is need of rapid collection, characterization, taxonomy, certification, and storage for broad, efficient and effective use in drug design or discovery. In this review, we summarized the plants derived secondary metabolites used in treating common human diseases and emphasised the protein-ligand interactions between virulent factors of diseases namely Insulin, p53, Proteasome-associated ATPase, Enterotoxin, Choleragen, IgE with secondary metabolites Aloin, Sesamin, Alliin, Flavanon, Salannin Octyl-β-d-Glucopyranoside of plants respectively, through molecular docking. This study will play a valuable and effective role in drug designing and screening plant-derived metabolites for drug designing.

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

The disposal of municipal solid waste (MSW) directly at landfills or open dump areas, without segregation and treatment, is a significant concern due to its hazardous contents of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and metal resistance genes (MGEs). The released leachate from landfills greatly effects the soil physicochemical, biological, and groundwater properties associated with agricultural activity and human health. The abundance of ARB, ARGs, and MGEs have been reported worldwide, including MSW landfill sites, animal husbandry, wastewater, groundwater, soil, and aerosol. This review elucidates the occurrence and abundance of ARB, ARGs, and MRGs, which are regarded as emerging contaminants (ECs). Recently, ECs have received global attention because of their prevalence in leachate as a substantial threat to environmental and public health, including an economic burden for developing nations. The present review exclusively discusses the demands to develop a novel eco-friendly management strategy to combat these global issues. This review also gives an intrinsic discussion about the insights of different aspects of environmental and public health concerns caused due to massive leachate generation, the abundance of antibiotics resistance (AR), and the effects of released leachate on the various environmental reservoirs and human health. Furthermore, the current review throws light on the source and fate of different ECs of landfill leachate and their possible impact on the nearby environments (groundwater, surface water, and soil) affecting human health. The present review strongly suggests the demand for future research focuses on the advancement of the removal efficiency of contaminants with the improvement of relevant landfill management to reduce the potential effects of disposable waste. We propose the necessity of the identification and monitoring of potential environmental and human health risks associated with landfill leachate contaminants.

Microbes releasing varieties of organic compounds considered as "signature markers" are known to play an important role in intra- and interkingdom interactions in below- and aboveground zones. The majority of volatile compounds released from the rhizosphere interface have shown possible roles in pathogen suppression. The production of microbial volatile organic compounds (mVOCs) in soil is influenced by various factors including the growth stage of the microbes, nutrient availability, temperature, oxygen availability, pH, and soil moisture content. Recent research has suggested that these signature molecules of microbial origin are insect repellant in nature, and have potential opportunities in managing crop losses occurring through insect pest infestation. Concerning the implementation of mVOCs, our knowledge on the potential use of such volatile compounds in large-scale agricultural and horticultural activities is still limited. In agricultural systems, mVOCs need to be applied under open-field conditions, which are very different from the in vitro conditions currently used in most studies. Despite the potential role of mVOCs in agriculture, field trials are still a big challenge due to several constraints. The present chapter explores the chemical diversity of mVOCs, interventions in plant–microbe and microbe–microbe interactions, as well as application potential in sustainable management of agricultural productivity.

Microorganisms that are capable of live and adapt in hostile habitats of different environmental factors such as extremes temperature, salinity, nutrient availability and pressure are known as extremophiles. Exposure to xenobiotic compounds is global concern influencing the world population as a health hazard. Hence their removal is warranted using biological means that is very sustainable, potentially cost-effective and eco-friendly. Due to adaptation in extreme environments and unique defense mechanisms, they are receiving more attention for the bioremediation of the xenobiotic compounds. They possess robust enzymatic and biocatalytic systems that make them suitable for the effective removal of pollutants from the contaminated environment. Additionally, the extremophiles act as microfactories having specific genetic and biotechnological potential for the production of biomolecules. This mini review will provide an overview of microbial degradation metabolic pathways for bioremediation along with the molecular and physiological properties of diverse extremophiles from variety of habitats. Furthermore, the factors affecting the bioremediation process is also summarized.

Control of plant disease is primarily reliable on the indiscriminant use of chemical pesticides including the bactericides, fungicides, and insecticides that are harmful for plant pathogens, or plant disease vectors. However, negative effect of these chemicals and their degradation products may pose hazardous effect to the environment and human beings that paved the researchers and growers for exploring the new and eco-friendly mode of disease control. To date, use of alternative methods such as, plant growth promoting rhizobacteria (PGPR) as biological control agents, have been found effective and are being increasingly applied in the field. PGPR directly and indirectly enhances the plant growth and reduces the disease development in plant system by various mechanisms that include: Production of antimicrobial metabolites, volatile compounds, induced systemic resistance (ISR), etc. These defense mechanisms can cause substantial changes in the plants structural and functional changes that lead to pathogen resistance. Present review describes the biocontrol mechanism and proteomic perspective of PGPR elicitors in plant disease management.

Anthropogenic climate change is of prime global concern and directly or indirectly affects the plant and microbial diversity of planet Earth. It is evident that anticipated increase in CO2, temperature, and altered precipitation are major consequences of climate change that has added the complexity and uncertainty to the plants and agroecosystem and threaten their sustainable management. Plant–microbe interactions are an important factor that influence the response of plants to alterations in climatic conditions. However, there are some beneficial plant-associated rhizobacteria and mycorrhiza that play an important role in reducing the ill-effects of climate change, such as drought, salinity, and plant diseases, etc. Apparently, it has been determined that climate change indirectly influences crop quality and plant–microbe relationships through the anthropogenic introduction of xenobiotics (pesticides, polycyclic aromatic hydrocarbons, etc.,) in terrestrial environments, posing risks to soil health by disturbing soil microbial enzyme activities and community structures. Considering the long-term effects of global climate change, it is essential to review the impacts of climate change on various life form sustaining components including soil–plant–microbe relationships with special reference to the belowground environment. This chapter could also help in predicting how plant–microbe interactions respond to climate change as well as the selection of suitable crops that would be able to produce more yields even under multistress conditions.

Recent progress in the sequencing technologies and other omics approaches have had a profound impact on microbiology and helped to develop a more complete picture of the microbial composition and function of different ecosystems. One of the observations from meta-omics research is some microbes are ubiquitous in diverse ecosystems and that such shared microbiota could act as a backbone to support ecosystem function. This chapter describes current meta-omics projects studying this issue and addresses the potential of publicly available data to (i) identify the shared microbes that inhabit different environments and to (ii) study the microbial-core functions. We also discuss key challenges, gaps, and perspectives of meta-omic studies to help researchers to take the next steps forward.

Currently, rapid industrialization, overuses of chemical pesticides in the agriculture and other anthropogenic activities directly or indirectly lead to heavy metals contamination. Normal physiological functioning of plants and humans require metals, but their excessive accumulations have severe toxic effects on ecosystem and ecology of plants, and human. Therefore, there is an urgent need for the mitigation of heavy metals through eco-friendly means. Applications of plant growth promoting bacteria (PGPB) have appeared as a promising approach in the mitigation process of heavy metal tolerance. Pseudomonas is one of the most diversified bacterial genera broadly used as biocontrol, plant growth promoting agents as well as in the mitigation process of xenobiotics and heavy metals. Heavy metal tolerance involves some of the standard mechanisms like the transformation of metals into bioavailable and soluble form, bioaccumulation, production of extracellular polymeric substances (EPSs), siderophores production, etc. Also, Pseudomonas sp. possess plant growth promotion activity, such as synthesis of phytohormones, phosphorus solubilization, production of ammonia, HCN, and siderophore. Present review focused on the impact of heavy metals on the plant growth, and vis a vis the role of Pseudomonas sp. in the mitigation of heavy metal toxicity.

Recent progress in the sequencing technologies and other omics approaches have had a profound impact on microbiology and helped to develop a more complete picture of the microbial composition and function of different ecosystems. One of the observations from meta-omics research is some microbes are ubiquitous in diverse ecosystems and that such shared microbiota could act as a backbone to support ecosystem function. This chapter describes current meta-omics projects studying this issue and addresses the potential of publicly available data to (i) identify the shared microbes that inhabit different environments and to (ii) study the microbial-core functions. We also discuss key challenges, gaps, and perspectives of meta-omic studies to help researchers to take the next steps forward.