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Microorganisms dwell in diverse plant niches as non-axenic biotic components that are beneficial as well pathogenic for the host. They improve nutrients-uptake, stress tolerance, phytohormone synthesis, and strengthening the defense system through phyllosphere, rhizosphere, and endosphere. The negative consequences of the microbial communities are largely in the form of diseases characterized by certain symptoms such as gall, cankers, rots etc. Uncultivable and unspecified nature of different phytomicrobiomes communities is a challenge in the management of plant disease, a leading cause for the loss of the plant products. Metagenomics has opened a new gateway for the exploration of microorganisms that are hitherto unknown, enables investigation of the functional aspect of microbial gene products through metatranscriptomics and metabolomics. Metagenomics offers advantages of characterizing previously unknown microorganisms from extreme environments like hot springs, glaciers, deep seas, animal gut etc. besides bioprospecting gene products such as Taq polymerase, bor encoded indolotryptoline, hydrolases, and polyketides. This review provides a detailed account of the phytomicrobiome networks and highlights the importance and limitations of metagenomics and other meta-omics approaches for the understanding of plant microbial diversity with special focus on the disease control and its management., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)

Background and Objectives: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51"N 75°32'07"E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics. Materials and Methods: In the present study, physiochemical parameters including temperature (65-75oC), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis. Results: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs). Conclusion: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries. [ABSTRACT FROM AUTHOR]

Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow degradation of plastics, MPs show an increased biomagnification probability of persistent, bioaccumulative, and toxic substances thereby creating a threat to environmental biota. Thus, remediation of MP-pollutants requires efficient strategies to circumvent the mobilization of contaminants leaching into the water, soil, and ultimately to human beings. Over the years, several microorganisms have been characterized by the potential to degrade different plastic polymers through enzymatic actions. Metagenomics (MGs) is an effective way to discover novel microbial communities and access their functional genetics for the exploration and characterization of plastic-degrading microbial consortia and enzymes. MGs in combination with metatranscriptomics and metabolomics approaches are a powerful tool to identify and select remediation-efficient microbes in situ. Advancement in bioinformatics and sequencing tools allows rapid screening, mining, and prediction of genes that are capable of polymer degradation. This review comprehensively summarizes the growing threat of microplastics around the world and highlights the role of MGs and computational biology in building effective response strategies for MP remediation. [ABSTRACT FROM AUTHOR]

The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms. [ABSTRACT FROM AUTHOR]

Understanding the microbial diversity and research trends using metagenomics is important for biotechnological and environmental applications. In this study, we carried out bibliometric analysis on hot metagenomics to study the research trends. The high-throughput metagenome sequencing was used to investigate the taxonomic profile of Rajouri hot spring (RHS) located at 33.1829° N, 75.1441° with 3445 feet above the sea level. The isolated metagenomic DNA (mDNA) was subjected to sequencing using Illumina technology, and the data was processed using QIIME for taxonomic classification and diversity analysis. The results showed a high level of diversity within the microbial communities with Proteobacteria (41.03%), Actinobacteria (16.7%), and Firmicutes (7.42%) as the dominant phyla. The Shannon (3.28), Simpson (0.053), and Chao1 (198.5) indices indicate the microbial richness in RHS suggesting a more stable and resilient ecosystem. The Trehalose synthase (TreS) gene, responsible for catalyzing the conversion of maltose to trehalose, was subjected to PCR amplification, DNA sequencing, and subsequent computational analysis. Through these investigations, it was determined that the TreS protein is composed of 169 amino acids, displaying a globular conformation and possessing hydrophilic characteristics. The advancements in high-throughput sequencing technology will enable more comprehensive and accurate analysis of the hot spring metagenome, leading to a deeper understanding of the microbial communities and their interactions. • Metagenomics offers valuable genetic insight into the diverse unculturable microorganisms. • Proteobacteria (41.03%), and Actinobacteria (16.7%) phyla are dominant in RHS. • Trehalose synthase (TreS), a globular protein, is present in RHS metagenomic DNA. • TreS , a hydrophilic protein, is localized in cytoplasm with highest percentage of leucine (11.8%). [ABSTRACT FROM AUTHOR]

This study explored the metagenome of the Pir Panjal Hot Spring (PPHS) to identify thermostable hydrolases. The carboxypeptidase (CarP) gene was successfully amplified and cloned into Escherichia coli DH5-α cells, followed by expression in E. coli BL21-DE3 cells. The CarP enzyme was comprehensively characterized in vitro. Sequencing analysis revealed an open reading frame encoding a functional protein of 504 amino acids, with a molecular weight of 58.65 kDa and an isoelectric point of 4.81. The CarP protein was purified using Ni-His affinity chromatography, and the experimental molecular weight matched in silico predictions. The enzyme exhibited significant thermostability and alkaliphilic properties, with optimal activity at 70 °C and pH 10.0. Additionally, the presence of Zn+2 ions at concentrations of 5 and 10 mmol/L enhanced protease activity by 1.4 and 1.5-fold, respectively. This study reports the discovery of a novel, multifunctional, and thermostable CarP from hot-spring metagenomes. The enzyme's stability against high temperatures, metal ions, surfactants, and inhibitors, along with its specific substrate interactions, highlights its potential for various biotechnological applications. [Display omitted] • Metagenomics allows access to the genetic material of unculturable microorganisms. • Carboxypeptidase (1515 bp) gene was successfully cloned and expressed in pJET1.2 and pET28a respectively. • His-tagged CarP protein (58.65 kDa) was purified using nickel column affinity chromatography. • CarP exhibits a pI and GRAVY of 4.81 and −0.447 respectively. • Zn2+ positively affects the activity of thermostable (70 °C) and alkalophilic (10.0) CarP. [ABSTRACT FROM AUTHOR]

Rhizosphere is a dynamic and complex environment shaped by intricate interactions between plants and a diverse microbial community. The rhizosphere microbiome is crucial for plant growth, nutrition, and health in agro-ecosystems. Recent advancements in metagenomics, especially through shotgun sequencing, offer unprecedented opportunities to unravel the complexities of rhizosphere microbial dynamics. Sequence and function-based metagenomic approaches enhance our understanding of plant-microbe relationships and serve as transformative tools for sustainable agriculture. They offer insights into precision microbiome engineering and ecosystem management by capturing the genomic landscape of microbial communities, revealing their taxonomic composition and functional potential. The integration of computational tools and machine learning approaches provides a powerful analytical framework to interpret vast and intricate metagenomic datasets. This paper comprehensively explores the rhizosphere using cutting-edge shotgun sequencing techniques to capture a holistic view of microbial communities in this crucial zone. Additionally, it delves into the emerging domain of virus-rhizosphere interactions, elucidating the impact of viral dynamics on rhizosphere microbial composition. To date, significant achievements in rhizosphere biology through metagenomics include detailed characterizations of microbial diversity, functional profiling of microbial communities, and identification of key microbial players in plant health and nutrient cycling. These advances underscore the critical role of metagenomics in advancing our understanding of rhizosphere biology and its applications in sustainable agriculture. The novel application of these advanced metagenomic techniques presents both opportunities and challenges, offering deeper insights into the rhizosphere while highlighting the need for improved data integration and interpretation methods. [Display omitted] • Metagenomics is a tool for studying rhizosphere microbial community genetics. • Shotgun sequencing is a common high-throughput method in metagenomics. • Metagenomics explores plant-microbe ecological interactions, including viruses. • Computational tools process and analyze large metagenomic data sets. • Metagenomics reveals insights into metabolic pathways, nutrient cycling, and plant interactions. [ABSTRACT FROM AUTHOR]

Zoonotic viral infections continue to pose significant threats to global public health, as highlighted by the COVID-19 pandemic caused by the SARS-CoV-2 virus. The emergence of SARS-CoV-2 served as a stark reminder of the potential for zoonotic transmission of viruses from animals to humans. Understanding the origins and dynamics of zoonotic viruses is critical for early detection, prevention, and effective management of future outbreaks. Metagenomics has emerged as a powerful tool for investigating the virome of diverse ecosystems, shedding light on the diversity of viral populations, their hosts, and potential zoonotic spillover events. We provide an in-depth examination of metagenomic approaches, including, NGS metagenomics, shotgun metagenomics, viral metagenomics, and single-virus metagenomics, highlighting their strengths and limitations in identifying and characterizing zoonotic viral pathogens. This review underscores the pivotal role of metagenomics in enhancing our ability to detect, monitor, and mitigate zoonotic viral infections, using SARS-CoV-2 analogues as a case study. We emphasize the need for continued interdisciplinary collaboration among virologists, ecologists, and bioinformaticians to harness the full potential of metagenomic approaches in safeguarding public health against emerging zoonotic threats. [Display omitted] • zoonotic viral infection spillover from animals to humans is global health concern. • Metagenomics allows comprehensive analysis of genetic material for early detection. • NGS and shotgun metagenome sequencing ensure early virome analysis in complex biological samples. • The development of advanced bioinformatics tools can help in pandemic preparedness and response. [ABSTRACT FROM AUTHOR]