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Aquaculture, a rapidly expanding sector, meets the global surging demand for aquatic food. Pangasius, a highly valued freshwater species, has seen a significant increase in demand due to its adaptability and potential for high yields, making it a promising candidate for aquaculture in India. This study investigates the gut microbiome composition of Pangasius pangasius fish cultured in three different systems (biofloc, cage, and pond). Metagenomic DNA extraction and 16S rRNA gene-targeted sequencing were performed. Outcomes revealed distinct microbial compositions across culture types, with significant differences in species richness and diversity, specifically in the biofloc system, compared to cages and ponds. Taxonomic analysis identified prevalent phyla such as Firmicutes and Fusobacteriota, with varying abundances among culture systems. The genus-level analysis highlighted dominant genera such as Cetobacterium and WWE3. Functional profiling indicated differences in enzymatic activity and metabolic pathways, emphasizing each culture sample type's unique microbial community structures. Notably, the microbiota from BF samples exhibited significant differences and unique metabolic pathways compared to the microbiota from C and P samples, which showed greater similarity and shared several common metabolic pathways. These findings highlight substantial differences in microbial diversity across the culturing systems, reflecting the microbiota's ability to adapt to specific environments and their potential role in promoting fish growth within those environments. Overall, this study provides insights into the gut microbiome diversity and functionality in Pangasius pangasius across different aquaculture environments, contributing to a better understanding of host-microbe interactions and aquaculture management strategies. [ABSTRACT FROM AUTHOR]

The colonisation of building materials by microorganisms is the first step in terms of a subsequent biodeterioration and an occurrence of potential building-associated health hazards. Contrary to many studies to date, focusing mainly on old buildings with symptoms of biocorrosion, this research focuses on the bioreceptivity of selected unused building materials and the factors determining the intensity of their colonisation. The experiments were carried out in parallel in India and Poland, with the use of indigenous microflora from a given region. They revealed the similar dynamics of the microbial multiplication in concrete and plasterboard and the extreme intensity of the process: after only 10 weeks under favorable conditions, the number of bacteria and fungi reached 107 CFU/g of dry weight of the material. The stimulation of microbial growth by individual environmental factors was slightly different in Indian and Polish studies: in India, the strongest stimulating factor was the periodic increase in humidity, while in Poland, the highest intensification of growth was observed in samples enriched with organic matter. Mould biodiversity turned out to be higher in India, although some types of fungi common to both regions were isolated. [ABSTRACT FROM AUTHOR]

The formation of oxygen-depleted zones in the bottom waters is one of the most widespread phenomena in coastal areas. Upwelling episodes along India's west coast due to the southwest monsoon increase biological productivity, further lowering the dissolved oxygen in the upwelled waters, which intensifies annually between June and October. Here, we have determined the changes in the microbial community in response to the varying oxygen levels and other physicochemical parameters at the Candolim Time Series Station using highthroughput sequencing. Amplicon Sequence Variants across all the samples collected in different seasons were mostly affiliated to the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Firmicutes and Planctomycetes, with the most dominant being Proteobacteria (21-41%). Statistical analysis revealed that microbial diversity differed significantly with changing DO, ammonia, nitrate and nitrite concentrations during different seasons. The microbial community shift due to seasonal hypoxia results in the differential biogeochemical cycling of essential nutrients, with certain years seeing redox conditions up to sulphate reduction while certain years seeing only nitrogen loss. Future global warming scenarios will serve as a big challenge for understanding the role of microbial diversity and its implications in the cycling of natural elements. [ABSTRACT FROM AUTHOR]

Phytophthora gummosis, foot rot, and root rot are considered major challenges to the citrus industry worldwide. Little is known about the Phytophthora–microbiome interaction, despite several studies demonstrating changes in the microbial composition of the rhizosphere following challenges by a pathogen. In the present study, we studied the microbial diversity and community structure in healthy rhizospheres and Phytophthora-infected rhizospheres of Khasi mandarin (Citrus reticulata Blanco), a commercial cultivar extensively grown in the northeast of India. An exploratory study was conducted to identify Phytophthora-infected orchards of Khasi mandarin, and the isolated pathogen was confirmed as P. nicotianae based on its morpho-cultural and molecular characteristics coupled with pathogenicity tests. This study on culturable microbes established the dominance of Trichoderma spp. in the healthy rhizosphere, while the diseased rhizosphere showed the presence of Fusarium spp. A metagenomic study further revealed that the rhizospheres of Phytophthora-infected plants were dominated by species such as Bacteroidia spp., Patescibacteria spp., and Pythium spp., while the healthy Khasi mandarin rhizospheres had a more diverse community predominantly represented by Trichoderma, Penicillium, Linnemannia, Mortierella, Talaromyces, Saitozyma, Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Terrabacteria and FCB (Fibrobacterota, Chlorobiota, and Bacteroidota groups) were found to exist in higher relative abundance in disease-free soils than in Phytophthora-infected soils, while phylum Proteobacteria showed identical relative abundance in all soil types. The phyla represented by Pseudomonas, Flavobacteriia, Candidatus, Mycobacterium, Rhizobium, Mesorhizobium, Sphingomonas, and Cytophagia were the most common bacterial phyla in all soil samples, but healthy soil exhibited a greater abundance of Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Our study suggests that the presence of Phytophthora spp. in the rhizosphere alters microbial community structure, having potentially strong implications for plant health and productivity. These rhizosphere microbiome-derived citrus responses shed light on exploring effective management strategies for Phytophthora gummosis disease ailing Khasi mandarin. [ABSTRACT FROM AUTHOR]

Background: Rice is a vital staple food for a large part of the global population and zinc deficiency poses health risks, particularly in rice-dependent regions. Studying genotypic differences in rice seed zinc content is vital for breeding zinc enriched varieties to address malnutrition and enhance food security. In the plant microbe partnership exploring the role of seed bacterial endophytes in influencing the plant physiology holds promise for Zn accumulation contributing to the broader goals of enhancing food quality, nutrition and crop production in a world facing increasing agricultural demands and challenges. Methods: Rice genotypes were surveyed and their seed zinc content was analysed using non-destructive X-ray fluorescence spectrometry. Surface sterilization of rice seed samples was performed to isolate endophytic bacteria, involving a series of treatments with distilled water, ethanol and sodium hypochlorite to remove surface microflora. The sterilized seeds were then macerated and diluted to obtain a countable number of colonies, which were subsequently spread-plated on nutrient agar, tryptic soy agar and soil extract agar to enumerate the different nutritional types of seed endophytic microflora. Result: In this study, 34 different rice genotypes, comprising traditional landraces and modern cultivars, were collected and analysed for their inherent zinc content. One variety in each category of low, medium and high seed Zn content was selected. The occurrence of all nutritional types of bacterial and their population was highest in the genotype Karuppunel followed by CO51 and ADT 39. Nutrient agar was found to promote a higher count of culturable bacterial endophytes compared to Tryptic soy agar and Soil extract agar. [ABSTRACT FROM AUTHOR]

Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial community structure and their metabolic potential in such beverages is necessary to define product quality, safety, and consistency, as well as to explore associated biotechnological applications. In the present investigation, Illumina-based (MiSeq system) whole-genome shotgun sequencing was utilized to characterize the microbial diversity and conduct predictive gene function analysis of keem, a starter culture employed by the Jaunsari tribal community in India for producing various traditional alcoholic beverages. A total of 8,665,213 sequences, with an average base length of 151 bps, were analyzed using MG-RAST. The analysis revealed the dominance of bacteria (95.81%), followed by eukaryotes (4.11%), archaea (0.05%), and viruses (0.03%). At the phylum level, Actinobacteria (81.18%) was the most abundant, followed by Firmicutes (10.56%), Proteobacteria (4.00%), and Ascomycota (3.02%). The most predominant genera were Saccharopolyspora (36.31%), followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (8.75%), Bacillus (4.59%), and Brachybacterium (3.42%). At the species level, the bacterial, fungal, and viral populations of the keem sample could be categorized into 3347, 57, and 106 species, respectively. Various functional attributes to the sequenced data were assigned using Cluster of Orthologous Groups (COG), Non-supervised Orthologous Groups (NOG), subsystem, and KEGG Orthology (KO) annotations. The most prevalent metabolic pathways included carbohydrate, lipid, and amino acid metabolism, as well as the biosynthesis of glycans, secondary metabolites, and xenobiotic biodegradation. Given the rich microbial diversity and its associated metabolic potential, investigating the transition of keem from a traditional starter culture to an industrial one presents a compelling avenue for future research. [ABSTRACT FROM AUTHOR]

Background: Eu is a lesser-known and traditional millet-based fermented brew of the Toto tribe from West Bengal, India. The starter culture used in this brew consists of diverse microflora. Identifying those microbes will not only help us gain a deeper understanding of the brew, but also quantify the impacts of this brew on the human system after consumption. Due to the progress in Illumina sequencing technology, the meta-profiling of 16S rRNA has emerged as a valuable resource for exploring the microbiome of any sample. We have utilised this tool (V3–V4 region) to study the microbiome population of Eu. Results: The microbial diversity present in the brew was mainly constituted of probiotic and fermenting bacteria. The nutrient profiling of Eu estimated the amount of protein, carbohydrate, free amino acid, and free fatty acid. The nutritional substance present in the brew probably supports the growth of the probiotic microflora. Reverse ecology-based network analysis revealed considerable complementary interaction between humans and the microflora present in the Eu. GC–MS outlining enlisted thirteen potent compounds from Eu, and a comprehensive network pharmacological study on those compounds revealed the anti-cancerous properties of Eu, especially against gastrointestinal malignancy, by reducing the proliferation of malignant cells and forming pro-inflammatory cytokines. Conclusions: The current study focuses on the meta-profiling and nutritional characteristics of Eu, which highlight the beverage's potential as a probiotic health drink. Reverse ecology analysis demonstrated that the probiotic microflora competes strongly against pathogenic bacteria. Additionally, in silico network pharmacological research identified the drink as a potentially health-promoting and anti-cancer beverage. [ABSTRACT FROM AUTHOR]

This metagenomic study delves into the microbial diversity and functional potential of sediment samples from the Pichavaram and Parangipettai mangrove ecosystems. The dataset, initially comprising millions of base pairs and sequences, undergoes meticulous quality control, revealing refined characteristics post-artificial duplicate read identification. Taxonomic analyses unveil a rich microbial landscape, dominated by bacteria, with intriguing presence of Eukaryota, Archaea, and unclassified sequences. The intricate community structures, highlighted through phylogenetic distributions, showcase the diversity and unexpected taxa, providing a nuanced understanding of microbial dynamics. Functional gene exploration uncovers key enzymes driving biosynthesis of secondary metabolites and metabolic pathways, shedding light on the microbial community's ecological roles and biotechnological potential. This comprehensive metagenomic analysis serves as a foundation for further ecological assessments, taxonomic refinements, and investigations into the adaptive strategies of these microbial communities in mangrove sediments. [ABSTRACT FROM AUTHOR]

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]

Background The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge. Results To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances. Conclusion Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section. [ABSTRACT FROM AUTHOR]

The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites. [ABSTRACT FROM AUTHOR]

Since the natural resources have been over-utilized, aquaculture has emerged as the food industry with the highest rate of growth worldwide and established itself as a source of high-quality protein. India is second in the world in terms of fish resource culture. The Indian economy depends heavily on the fishing industry for possibilities on how the rural and poor might make a living. Omnipotent bacteria are present in water as microflora and may play a significant role in harming the fish farming sector. The future growth of aquaculture depends on early illness detection and the development of effective vaccinations. From water samples taken in the Meja Regions of Uttar Pradesh, the current research sought to isolate and maybe identify bacteria with the potential for growth. Materials and Techniques 20 different ponds’ worth of water samples. The samples that were gathered were located and examined. Using the agar plate technique, the bacterial load in the samples was assessed for the potential indicator species. According to a preliminary investigation, the majority of the water samples included potential Vibrio cholerae, E. coli, S. thyphimurium. In the chosen fishponds, other bacteria such as Staphylococcus, Micrococcus and E. coli were also found. It was discovered that the ponds were severely polluted with harmful microorganisms, particularly bacteria that pose a significant danger to fish kept in captivity. [ABSTRACT FROM AUTHOR]

Halotolerant plant growth promoting rhizobacteria (PGPR) are beneficial microorganisms utilized to mitigate the biotic and abiotic stresses in plants. The areas of Sundarban mangroves of West Bengal, India have been reported to be rich in halotolerant microflora, yet major area remains unexplored. The present study, therefore, aims to map down the region-specific native microbial community potent of salt tolerance, plant growth promoting (PGP) activity and antagonistic activity against fungal pathogens. Bacterial samples were isolated from the saline soil of the Sundarban mangroves. A total of 156 bacterial samples were isolated and 20 were screened for their salt tolerance potential. These isolates were characterised using morphological, biochemical, and molecular approaches. Based on 16s rRNA sequencing, they were classified into 4 different genera, including Arthrobacter sp. (01 isolate), Pseudomonas plecoglossicida (01 isolate), Kocuria rosea (01 isolate), and Bacillus (17 isolates). The halotolerant isolates which possessed plant growth promoting traits including phosphate, and zinc solubilization, indole acetic acid production, siderophore, and ammonia generation were selected. Further, the effect of two halotolerant isolates GN-5 and JR-12 which showed most prominent PGP activities was evaluated in pea plant under high salinity conditions. The isolates improved survival by promoting germination (36 to 43%) and root-shoot growth and weight of pea plant in comparison to non-inoculated control plants. In a subsequent dual culture confrontation experiment, both these halo-tolerant isolates showed antagonistic activities against the aggressive root rot diseasecausing Macrophomina phaseolina (Tassi) Goid NAIMCC-F-02902. The identified isolates could be used as potential bioagents for saline soils, with potential antagonistic effect on root rot disease. However, further studies at the physiological and molecular level would help to delineate a detail mechanistic understanding of broad-spectrum defence against salinity and potential biotic pathogen. [ABSTRACT FROM AUTHOR]

The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics). [ABSTRACT FROM AUTHOR]

Smokeless tobacco (ST) consumption keeps human oral health at high risk which is one of the major reasons for oral tumorigenesis. The chemical constituents of the ST products have been well discussed; however, the inhabitant microbial diversity of the ST products is less explored especially from south Asian regions. Therefore, the present investigation discusses the bacteriome-based analysis of indigenous tobacco products. The study relies on 16S amplicon-based bacteriome analysis of Indian smokeless tobacco (ST) products using a metagenomic approach. A total of 59,15,143 high-quality reads were assigned to 34 phyla, 82 classes, 176 orders, 256 families, 356 genera, and 154 species using the SILVA database. Of the phyla (> 1%), Firmicutes dominate among the Indian smokeless tobacco followed by Proteobacteria, Bacteroidetes, and Actinobacteria (> 1%). Whereas, at the genera level (> 1%), Lysinibacillus, Dickeya, Terribacillus, and Bacillus dominate. The comparative analysis between the loose tobacco (LT) and commercial tobacco (CT) groups showed no significant difference at the phyla level, however, only three genera (Bacillus, Aerococcus, and Halomonas) were identified as significantly different between the groups. It indicates that CT and LT tobacco share similar bacterial diversity and poses equal health risks to human oral health. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt 2.0) based analysis uncovered several genes involved in nitrate/nitrite reduction, biofilm formation, and pro-inflammation that find roles in oral pathogenesis including oral cancer. The strong correlation analysis of these genes with several pathogenic bacteria suggests that tobacco products pose a high bacterial-derived risk to human health. The study paves the way to understand the bacterial diversity of Indian smokeless tobacco products and their putative functions with respect to human oral health. The study grabs attention to the bacterial diversity of the smokeless tobacco products from a country where tobacco consumers are rampantly prevalent however oral health is of least concern. [ABSTRACT FROM AUTHOR]

Chasmophytes are a group of diverse plants growing on cracks and crevices of rocks. They survive under nutrient and water-limited conditions. Microorganisms associated with chasmophytes may play a critical role in their survival. In the present study, 263 bacterial isolates were obtained from chasmophytic wild Chenopodium collected from Tsomoriri, Ladakh. Members of Enterobacter, Pseudomonas, Pantoea, and Alcaligenes comprised ~ 90% of the Gram-negative bacteria, while among Gram-positive, Bacillus, Solibacillus, Fictibacillus, Microbacterium, and Micrococcus were most abundant. When evaluated for various plant growth-promoting traits, 36 bacteria could solubilize insoluble phosphate, 10 bacteria could release potassium from silicate minerals, and 25 bacteria could solubilize ZnO, while 124 bacteria produced siderophores. ACC deaminase activity was present in 31 isolates, while 46 bacteria could produce IAA (10.40–232.0 μg/mL). Furthermore, more than 64% of the isolates could grow at 50 °C, while ~ 60% could grow at 4 °C. Similarly, ~ 50% isolates were able to grow with > 1.7 M NaCl and ~ 70% could grow under high osmolarity (~ 67 mOsmol/L). The ability of these microorganisms to grow under such a wide range of temperature, salinity, and osmolarity offers adaptive advantage to colonize plants surviving under harsh environmental conditions. A large number (30–49%) of these isolates could produce acids from various sugars and sugar alcohols which is crucial to release mineral nutrients trapped in the rocks. The results indicated that genetically and functionally diverse microflora associated with wild Chenopodium might be helping these plants to effectively mine nutrients and water under extreme conditions. [ABSTRACT FROM AUTHOR]

An experiment was executed at field condition to evaluate ecological impact of Bt cotton (Mech 162 + Bt) on soil microbes and Bt protein behavior in soil. Root exudates of Bt cotton plant containing Bt protein enter into soil which persisted in soil for atleast 235 days after sowing (DAS). During vegetative and flowering stage, Bt protein was not detectable in both qualitative and quantitative assay but, during onset of boll formation at 150 DAS, a level of 0.0013 μg/g of Cry 1Ac protein was quantified in rhizospheric soil which further increased exponentially up to 0.0033 μg/g at 195 DAS and then maintained at the same level till 235 DAS with Cry1Ac expression level of 0.0029 μg/g soil. Rhizospheric soil of Bt cotton had significantly higher (p < 0.05) abundance of Fatty Acid Methyl Esters (FAME) of gram positive bacteria. Abundance of polyunsaturated FAMEs that are indicators of fungi, were slightly higher in Bt as compared to non-Bt cotton soils. The metabolic profiling, also called community level physiological profiling (CLPP) showed more microbial functional diversity (Shannon–Wiener Diversity) in soil samples of different growth stages of Bt cotton than its corresponding non-Bt variety. Our results showed that Cry 1AC Bt protein persists in clay loamy soil even after harvesting and significantly altered microbial community composition and functional diversity in rhizospheric soil of Bt cotton than non-Bt. Any possible and unintentional changes in composition of root exudes of Bt cotton could regulate the selection of different microbial communities and thus can alter functional responses. [ABSTRACT FROM AUTHOR]

Summary: Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under‐represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation‐based analyses. Gene sequences 16S rRNA (7.37 × 106) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co‐occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood–Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient‐ and energy‐limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy. [ABSTRACT FROM AUTHOR]

Smokeless tobacco product (STP) consumption is a significant public health threat across the globe. STPs are not only a storehouse of carcinogens and toxicants but also harbor microbes that aid in the conversion of tobacco alkaloids to carcinogenic tobacco-specific nitrosamines (TSNAs), thereby posing a further threat to the health of its consumers. The present study analyzed the bacterial diversity of popular dry and loose STPs by 16S rRNA gene sequencing. This NGS-based investigation revealed four dominant phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria and identified 549 genera, Prevotella, Bacteroides, and Lactobacillus constituting the core bacteriome of these STPs. The most significantly diverse bacteriome profile was displayed by the loose STP Mainpuri kapoori. The study further predicted the functional attributes of the prevalent genera by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm. Genes encoding for nitrate and nitrite reduction and transport enzymes, antibiotic resistance, multi-drug transporters and efflux pumps, secretion of endo- and exotoxin, and other pro-inflammatory molecules were identified. The loose STPs showed the highest level of nitrogen metabolism genes which can contribute to the synthesis of TSNAs. This study reveals the bacteriome of Indian domestic loose STPs that stagger behind in manufacturing and storage stringencies. Our results raise an alarm that the consumption of STPs harboring pathogenic genera can potentially lead to the onset of several oral and systemic diseases. Nevertheless, an in-depth correlation analysis of the microbial diversity of STPs and their elicit impact on consumer health is warranted. Key points: • Smokeless tobacco harbors bacteria that aid in synthesis of carcinogenic nitrosamines. • Most diverse bacteriome profile was displayed by loose smokeless tobacco products. • Pathogenic genera in these products can harm the oral and systemic health of users. [ABSTRACT FROM AUTHOR]

The microbial life indigenous to mineral deposits are generally regarded as extremophiles as they are tolerant to extreme conditions. The microorganisms that thrive in such environments survive by modifying their metabolic pathway or mechanisms. The microbiome associated with ore deposits remain poorly studied. The present study is the first attempt to explore the taxonomic composition of the bacterial community associated with the muscovite ore deposit from Southern India by using high throughput Illumina sequencing employing the V3 and V4 region of the16S rDNA and bioinformatics channel. A total of 20 bacterial phyla with 55 classes, 96 orders, 192 families, 382 genera and 462 species were recovered in the study. The alpha diversity index suggests that muscovite ore deposits harbored highly variable bacterial communities. Among the bacterial communities, Proteobacteria (33%), Actinobacteria (29.9%), Firmicutes (25.4%), Bacteroidetes (5.5%) and Chloroflexi (2.7%) were the dominate phyla. A total of 156 abundant species and 306 rare species were observed and is an indication of the presence of novel species. This study helps to understand the survival strategy of oligotrophs, which are an important aspect of microbial ecology. [ABSTRACT FROM AUTHOR]

An improved understanding of the vegetation and microbial diversity across different coastal landscape and it's interlink with ecosystem multifunctionality are vital for sustaining the ecosystem services. In view of this, the present study was carried out in Andaman Island, India creating three representatives transects covering four major ecosystem types by subplot sampling and ecosystem multifunctionality was computed from eleven related soil properties after Z-score transformation. We have estimated the vegetation and soil microbial diversity, examined individual effects of edaphic factors on vegetation and soil microbial diversity, extracellular enzyme activities and also investigated the combined effects on ecosystem multiple functions as matrices by Mantel tests. The results suggested that above ground vegetation diversity (2.4–4.9) exhibited significant effect on soil microbial diversity (1.07–1.47) due to difference in species richness and organic matter addition. In turn microbial diversity played a critical role in enzyme activities and nutrient recycling, both constituted the vital coastal ecosystem functions. Amongst the different ecosystems, highest species richness and microbial diversity was found in littoral forest and moist deciduous forest, respectively whilst agro-ecosystem recorded the lowest values. Soil organic carbon, excluding agriculture, increased downward the topography from moist deciduous forest in the hill top to the mangroves in the coastal lowlands while soil enzymes, total N and microbial biomass C and N followed the trend as in soil organic C. The study also observed large endemism and constraints to diversity in mangrove ecosystem due to specific environmental conditions. Our findings provided empirical evidence that above ground and below ground diversity conditioned by edaphic factors constituted the primary drivers for ecosystem multifunctionality in different coastal ecosystem types. [ABSTRACT FROM AUTHOR]

The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8–3.7 ppm), COD (23–29.2 ppm) and organic carbon (0.18–0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem. [Display omitted] • Metagenomic study of microbial communities in sediments of river Ganga stretches. • Highest concentrations of Mn, Fe, and Cr were observed in the polluted sites. • Bacteroidota and Chloroflexota were predominant in all sediment samples. • First report reveals the presence of 13 plastic & 18 xenobiotic degradation enzymes. [ABSTRACT FROM AUTHOR]

Mangrove wetlands are a unique transitional coastal zone between terrestrial and aquatic ecosystems along the subtropical and tropical coastlines. The abundant biodiversity of mangroves facilitates their various ecological functions, including pollution control and nitrogen cycling. However, the comparison of specific nitrogen metabolic pathways and microbial communities in mangrove ecosystems of different countries is scarce. In this study, microbial communities and functional genes involved in nitrogen cycling were analyzed and compared by Illumina sequencing technique of collected surface and bottom sediments from mangroves in China, India, and Malaysia. The results revealed the highest microbial diversity in India (3310 OTUs), followed by China (2589 OTUs) and Malaysia (1811 OTUs). Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were the main nitrate reduction pathways in mangrove sediments. Anammox was significantly more active in Odisha and Goa of India than in all other samples. Woeseia and Desulfococcus in China, Robiginitalea and Tenacibaculum in India, and Woeseia in Malaysia were identified as the active organisms involved in the nitrogen cycle. The results provided a basis for preliminarily understanding the microbe-driven nitrogen conversion in mangroves of different regions. • Denitrification and DNRA are the main nitrate reduction in mangroves. • The anammox and assimilatory nitrate reduction are more active in India mangrove. • Woeseia in China and Malaysia, Robiginitalea in India are active bacteria participating in the nitrogen cycle, respectively. • The archaea Thermoplasmatales and Thermoprotei in Malaysia play an important role in the nitrogen cycle. [ABSTRACT FROM AUTHOR]

Simple Summary: We present a systematic investigation of the distribution of microbial communities in arid and semi-arid regions of Thar Desert Rajasthan, India. Their responses in multiple environmental stresses, including surface soil, surface water and underground water were evaluated. We further assess the biotechnological potential of native microorganisms and discover functional species with results providing a detailed understanding of the abundance of microbial communities in these regions, associated with various stress-related biogeochemical and biotechnological processes. We hope our work will facilitate the development of effective future strategies for the use of extremophiles in complex environments. The arid and semi-arid regions of Rajasthan are one of the most extreme biomes of India, possessing diverse microbial communities that exhibit immense biotechnological potential for industries. Herein, we sampled study sites from arid and semi-arid regions of Thar Desert, Rajasthan, India and subjected them to chemical, physical and metagenomics analysis. The microbial diversity was studied using V3–V4 amplicon sequencing of 16S rRNA gene by Illumina MiSeq. Our metagenomic analyses revealed that the sampled sites consist mainly of Proteobacteria (19–31%) followed by unclassified bacteria (5–21%), Actinobacteria (3–25%), Planctomycetes (5–13%), Chloroflexi (2–14%), Bacteroidetes (3–12%), Firmicutes (3–7%), Acidobacteria (1–4%) and Patescibacteria (1–4%). We have found Proteobacteria in abundance which is associated with a range of activities involved in biogeochemical cycles such as carbon, nitrogen, and sulphur. Our study is perhaps the first of its kind to explore soil bacteria from arid and semi-arid regions of Rajasthan, India. We believe that the new microbial candidates found can be further explored for various industrial and biotechnological applications. [ABSTRACT FROM AUTHOR]

Probiotics are potential health-promoting microorganisms representing a significant health aid with diverse pharmaceutical applications. But its role in modulating the human gut microbiome necessities a profound analysis. Undoubtedly, the human gut is a reservoir of infinite species such as bacteria, viruses, fungi, etc. But host with chronic illness bids enrichment of the pathogenic strain which may alter the composition gut microbiome. Culture-based techniques are providing unclear taxonomic data where the possibility of the discrepancy is very high. Therefore the use of next-generation sequencing (NGS) analysis helps to explore depth understanding of the curd microbiome and can generate big genomic data. The present investigation aims to explore the microbial diversity of curd samples from different local dairy farms of Odisha, India using a metagenomic approach. The data read comprising 304,725 sequences totaling 148,546,295 base pairs were interpreted. Taxonomical distribution at different levels unfolded the absolute abundance of phylum, class, order, family, genus, and species within each microbial community. The most dominant species found to be Lactobacillus at order level is 49%, whereas phyla proteobacteria and firmicutes have shown taxonomic percentage abundance of 50.01% and 48.77%, respectively. However, nearly 26.41% of unclassified species from the Lactococcus genus were identified in the sample at different taxonomic levels. The metagenomics sequence data has been deposited to sequence read archive (SRA) of NCBI database under Bioproject PRJNA383620. The present study has vital implications in understanding the microbial diversity in curd samples with their role in human health and application in future pharmaceutical probiotic research. [ABSTRACT FROM AUTHOR]

The current study deals with the diversity and distribution of culturable cold-adapted bacteria in Himalayan Thajwas glacial soil. The total bacterial count of the seven soil samples collected near glacier snout at different altitudes was investigated through a culture-dependent method. The highest cfu/g (6.8±2 × 107) was recorded at site I, and the lowest cfu/g (4.6±2 × 103) was recorded at site VII on nutrient agar (NA) media. The 31 isolated strains were identified using 16S rRNA gene sequencing. Based on their optimum growth at different temperatures, these bacterial isolates were categorized into two overlapping groups: psychrophiles (optimum growth ≥15°C) and psychrotrophs (optimum growth ≥20°C). Besides, these bacterial strains were screened for their cold-active enzyme activity. Further, the microbial diversity was affected by higher incubation temperature, which reduced the richness due to the selection of psychrotrophic microorganisms. Variation in microbial diversity may be related to soil physicochemical properties since a high positive correlation was observed with water content, total nitrogen and organic carbon. This is the first research to look at microbial communities from the Thajwas Glacier, and it adds to our knowledge of the microbial diversity found in Himalayan cold ecosystems. [ABSTRACT FROM AUTHOR]

This paper presents a pioneer study on the microbial diversity and antibacterial potential of hive bees (Apiscerana and A.mellifera) honey collected from Himachal Pradesh. In total, 26 bacteria (14 from A.cerana and 12 from A.mellifera) but no fungal isolate were recovered. Bee species and locations comparison in terms of bacterial load (log CFU/g) revealed maximum loads of 3.74 and 3.99 in the honey from A.cerana and Mandi location, respectively. The most prevalent strains (HC3, HC5, HC6, HC8 and HM2) were identified (16S rRNA ribotyping) as Staphylococcushaemolyticus (MT742636), "Bacillussubtilis subsp. stecoris" (MT742637), Bacillussafensis subsp. safensis (MT742638), "Bacilluszanthoxyli" (MT742639) and Bacillussafensis subsp. safensis (MT938911). The apiary honey displayed good to excellent inhibitory activity against Escherichiacoli ATCC1041 whereas, fair to good against Bacillussubtilis ATCC6633, Pseudomonasaeruginosa ATCC10662, Salmonellatyphi NCTC786 and Klebsiellapneumoniae ATCC13883, highlighting its use as a therapeutic agent. Furthermore, it can be effective in minimizing numerous side effects associated with the consumption of synthetic drugs for treating bacterial infections thereby signifying the role of honey as a healthier substitute for synthetic drugs. [ABSTRACT FROM AUTHOR]

Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min−1 mg−1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites. [ABSTRACT FROM AUTHOR]

In the last two decades, the productivity of the rice–wheat growing system (RWGS) in the upper Indo‐Gangetic Plains of India has come to a plateau, and, as a result, farmers are now shifting to other crop growing systems (cropping sysytems) to achieve a higher net productivity. Inclusion of other cropping systems in place of the rice–wheat system affects overall crop productivity; however, there is dearth of information with respect to nutrient index (NI), microbial diversity, and soil quality. This study was carried out to assess how NI, microbial diversity, and soil quality changed after replacement of rice–wheat by a vegetable growing system (VGS), pulse growing system (PGS), potato growing system (PoGS), and a mustard growing system (MGS). An analysis of 307 soil samples from these crop growing systems revealed a soil pH range of 6.58–8.87 with 75.3% soils falling within the low category of mineralized N, and low NI (<1.67). The highest NI, enzymatic activity, and microbial diversity was recorded under PGS, which restored 34.2, 24.1, and 10.2% greater soil organic carbon (SOC) than other systems, and had a better carbon substrate oxidation rateand mineralized N than PoGS. The diversity indices peaked under PGS followed by VGS due to greater SOC, mineralized N, higher microbial counts, and more soil enzymes. Among the different crop growing systems the soil quality index (SQI) ranged from 0.647 (for PoGS) to 0.783 (for VGS). The silt content, SOC, Zn, TN, acid phosphatase activity, available P, and total culturable fungi were the key soil indicators across all the crop growing systems. SOC is the most important and viable indicator for all the crop growing systems that affected microbial dynamics and soil quality. The greater SQI under VGS was due to the addition of organic manure and augmented SOC, P, and Zn availability. In contrast, the highest microbial and enzymatic activities, and functional diversity was recorded under PGS mainly due to greater edaphic variables. It is concluded that the pulse growing system (PGS) is the best for maintaining higher NI, and improving microbial and functional diversity. [ABSTRACT FROM AUTHOR]

Thermal springs have been the most resourceful ecological niches to understand the intricacies of the microbial community structure building. In the present study, the microbial community structure was investigated in five ecologically different hot springs. The highest number of OTUs was observed at low temperatures (42 °C) whereas an increasing number of unclassified bacteria was observed with a temperature rise. The statistical correlation predicted that temperature, total dissolved solids and ions were the primary environmental factors in controlling the community composition and diversity. The relative abundance of Proteobacteria, Cyanobacteria showed a positive correlation with moderate temperature whereas growth of Chloroflexi and Nitrospira was unstable at 65 °C. The observed LCBD was negatively correlated to the bacteria richness. A high relative abundance of Planctomycetes was restricted to Odisha hot springs (AT, TP, and DJ). We further hypothesize that abundance of most common cellulose-degrading bacteria such as Acinetobacter, Pseudomonas and Aeromonas only in DJ hot spring is possibly due to the high carbon content of the runoff water received from dense pandanus forest around it and could be a prospective source of industrially relevant cellulase after detailed characterization. The present study concludes that the association of physicochemical components with key species drive the microbial community structure. [ABSTRACT FROM AUTHOR]

Bacterial diversity of Bhitarkanika mangrove was studied by both the culture-dependent and culture-independent methods. The variation of culture-dependent bacterial population with respect to different physico-chemical parameters was also observed seasonally (summer and monsoon) from five stations—Dangmal, Ekakula, Gupti, Habalikhati and Kalibhanjadiha. Overall, culture-dependent total heterotrophic bacteria varied from 2.16 ± 0.5 to 168.25 ± 1.73 × 103 cfu/g in sediment and 1.53 ± 0.915 to 38.33 ± 0.108 × 103 cfu/ml in water. Major regulatory factors for bacterial abundance of water were nitrate phosphate, conductivity, dissolved oxygen in different seasons while no such clear influence was observed on sediment bacterial abundance. Culture-dependent study revealed that Bacilli, Gammaproteobacteria and Betaproteobacteria were dominant bacterial classes. Culture-independent study revealed that the operational taxonomic unit varied from 5077 to 21,207 in sediment and 14,213 to 17,501 in water. Majority of the bacterial community were found to be under the class Gammaproteobacteria followed by Alphaproteobacteria and Bacilli. In sediment, highest and lowest species richness as well as evenness was recorded at Dangmal and Ekakula, respectively, while in water, both the parameters were more or less similar in all the sampling sites. Maximum species diversity was observed at Dangmal sediment (Shannon diversity index: 10.43) and Habalikhati water (Shannon diversity index: 7.45). Principal Coordinate Analysis (PCoA) revealed that Ekakula, Kalibhanjadiha and Gupti, Habalikhati sediment had similar species composition in culture-dependent and independent analysis, respectively. Dangmal sediment had the unique species composition, whereas bacterial species composition in water varied greatly within different sites in both the cases. This study depicts the highly rich bacterial diversity of Bhitarkanika. [ABSTRACT FROM AUTHOR]

The agricultural practices are known to affect the soil ecosystem, which ultimately influences the environment and human health. In this perspective, soil nutrient status and microbial diversity of ten year's long organically managed soil were compared with its conventional counterpart at Pantnagar, India (29.03° N/79.46° E). A combination of farmyard manure and vermicompost was used under an organic farming system along with a mixture of neem oil and cow urine as a biopesticide. Organic amendments have improved carbon, nitrogen, and phosphorus content in the soil. Moreover, the copy numbers of diazotrophs and phosphate solubilizers were also found to increase under the organic system which can be evident from their dominance in the organic soil metagenome. Further, several clinically important bacterial genera viz. Corynebacterium, Mycobacterium, Enterococcus, Staphylococcus, Ruminococcus, Prevotella, Coxiella, Neisseria, Haemophilus, Actinobacillus, Treponema, and Mycoplasma were observed only in conventional soil and were completely absent in organic soil sample. These findings revealed that besides enhancing soil fertility and microbial diversity, organic practices have an impact on the soil-borne pathogens and, in general, on the soil microbiome. It will impart value addition to the organic products and lead us towards healthy agricultural practices and products. [ABSTRACT FROM AUTHOR]

Wheat is a staple food crop, primarily grown in India's Indo-Gangetic plains, crucial for sustaining the region. Soil quality, vitality, and microbial inhabitants' interplay are pivotal. However, very little information is available on the impacts of agricultural practices, such as crop rotation and cropping systems, on the diversity of both bulk soil (BS) and rhizospheric soil (RS) microbiota. The impact of two different cropping systems, rice-wheat (RW) and sugarcane-wheat (SW) on soil properties, microbial diversity, and plant growth-promoting bacteria (PGPB) in wheat cultivation was investigated in the Indo-Gangetic plains of India. Microbial richness and diversity were analyzed using 16S rRNA sequencing, which reveals distinct clustering patterns between RS and BS, with higher diversity in BS of RW and higher richness in RS of SW. Notably, Proteobacteria dominated across all samples, along with Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Firmicutes, Planctomycetes, candidate division TM7, Cyanobacteria, and Nitrospirae. Intriguingly, the RS associated with the SW system exhibited the presence of 67 distinct genera, whereas the RS under the RW system showed 48 such genera. Within the realm of specific microbial genera exhibiting plant growth-promoting (PGP) activity, a higher abundance was noted in the RS (17.48%), as opposed to the BS (15.21%). Moreover, certain genera such as Haliangium, Iamia, Bacillus, Gaiella, Candidatus _Entotheonella , Anaerolinea , and Anaeromyxobacter, were found to be positively correlated with the availability of nitrogen, phosphorus, potassium, iron, and sulfur. The study sheds light on the intricate relationships between cropping practices, soil properties, and microbial dynamics, contributing to the development of sustainable agricultural practices for wheat cultivation. [Display omitted] • Soils in upper IGP under both cropping systems are represented by well-known plant growth-promoting genera. • Cropping system has significant effects on the richness and diversity of microbiota. • Bulk soil of rice-wheat system recorded higher diversity; rhizospheric soils of sugarcane-wheat recorded higher richness. • A higher abundance of genera exhibiting plant growth promotional activities was noted in rhizospheric soil. [ABSTRACT FROM AUTHOR]

Geomicrobiology of mine tailing from Asia's largest open-cast Cu mine at Malanjkhand was established, emphasizing the roles of microorganisms in acidification process using 16S rRNA gene amplicon and shotgun metagenomics. Mine tailings collected from five different locations portrayed the characteristic oligotrophic geochemical nature, with varying pH (pH 1.9–7.2), high heavy metals (Fe, Cu, Zn, Ni) and sulfate, but reduced, carbon, nitrogen and phosphate content. Iron-oxides and sulfate mineral phases were detected. Highly acidophilic, iron- and sulfur-oxidizing microorganisms including Sulfobacillus, Acidithiobacillus, Leptospirillium, Ferrimicrobium, Ferrithrix, etc. encoding the genes necessary for chemolithoautotrophic metabolism (sqr, sox, cbbL, cox, cyc1, etc.), resistance to low pH (sqh, kdp, gadB, etc.) and heavy metal stress (cop, cus, czc, chr, etc.) predominated the oxidized tailings. A markedly different microbial community represented by Thiobacillus, Sphingomonas, Meiothermus, Sulfurifustis, and members of Hydrogenophilaceae, Acidiferrobacteraceae, Gaiellales, Gemmatimonadetes, Ignavibacteriales, KD4-96, etc. predominated the fresh tailings. Metagenome of the fresh tailings confirmed presence of similar sets of genes as found in oxidized tailings, however, taxonomic affiliations of most of these functional genes vary between the two habitats, indicating differential taxa recruitment under the two contrasting ecological conditions. The study provided an in-depth understanding of Cu mine tailings microbial community and their role in acidification process. [ABSTRACT FROM AUTHOR]

One plant and one to two ratoon crops are the predominant patterns of sugarcane cultivation in sub-tropical part of India. Despite high agricultural inputs, yield of ratoon crop gets dwindled in the subsequent years. The microbial community, particularly bacteria and fungi, in the rhizosphere and their interaction with the root system, in general influences plant productivity. For the present study, an early maturing sugarcane variety (CoLk 94184), was used to establish plant and winter-initiated ratoon crops in 2016–2018. Soils pertaining to both plant and ratoon rhizospheres were subjected to biochemical analysis, microbial DNA isolation and high-throughput sequencing of 16S rRNA genes to assess the microbial diversity and associated characteristics impacting cane yield. Although alpha diversity of bacterial community was observed high in the soils of both plant and ratoon crops, the species richness/diversity was more in plant crop. Bacterial community structure in the rhizosphere of plant crop was predominantly consisted of phyla Actinobacteria (35.68%), Gemmatimonadetes (29.26%), Chloroflexi (26.73%) and Proteobacteria (16.68%), while ratoon rhizosphere revealed dominance of Acidobacteria (20.77%) and Bacteroidetes (10.7%). Though studies revealed the presence of rich bacterial community in the rhizospheres of both plant and ratoon crops of sugarcane, dominance of Acidobacteria and meager proportion of Actinobacteria and Proteobacteria in ratoon crop possibly limited its productivity. Along with high total phenols (7.27 mg/g dry wt), ratoon crop depicted less active root system as revealed by scanning electron microscopy. Dominance of thermophilic bacterial phyla Chloroflexi and Gemmatimonadetes which was observed in sugarcane rhizosphere supports better crop growth in drought. However, management of soil microbial community is required to improve the ratoon crop productivity. [ABSTRACT FROM AUTHOR]

To accelerate the monitoring and counting of biodiversity of various species, there is a need for automating the process of computing biodiversity. The calculations of the alpha and beta biodiversity indexes are fundamental for the analysis of ecological and biodiversity studies. Sukhna and Dhanas lakes, India are critical for the maintenance of the health of the residents and aquatic life thriving in them. Both lakes are prone to pollution. Due to these factors, there is a need for building digitized infrastructure for monitoring the health of these lakes. Hence in this research work, an automated algorithm has been devised for the computation of biodiversity of microorganisms. The work focuses on the surface water of both these lakes. The automation of biodiversity computation is done with image processing algorithms and is applied to the primary data collected. From this study, it is apparent that the counting of microorganisms using image processing algorithms is an easier and efficient way for biodiversity studies as compared to the manual process of estimating the population of microbes. The results show that the species richness of Dhanas Lake is more as compared to Sukhna Lake. The dissimilarity between the two lakes is five species as per the primary data collected. This shows that the biodiversity of Dhanas Lake is better than the Sukhna Lake but it is prone to harmful algal blooms. This may be attributed to the fact that Dhanas Lake may have multiple sources of pollution that need to be identified. [ABSTRACT FROM AUTHOR]

Western Ghats is considered as one of the most important biogeographic zones of India and also major tropical evergreen-forested region that possesses enormous biodiversity. Challenging biodiversity due to decreasing forests and thereby related habitat loss triggered us to give a hand on conservation of microbial diversity in such regions. Vanda testacea a vulnerable epiphytic orchid from Kodagu, is in the heart of Western Ghats which was used for endophyte isolation and characterization in the current study. From leaves of V. testacea fungal and bacterial strains were isolated. Further, by using molecular methods, the genomic DNA of isolated strains was extracted. The ITS region from fungi and 16S rDNA from bacteria were amplified by PCR, and then sequenced. Nucleotide sequences were compared with the known sequences available in NCBI database. Sequence similarity matrix were prepared with closely related species and phylogenetic tree was also generated for homology comparison. Identity of isolated strains was established as two different endophytic fungi, Cladosporium perangustum and Pestalotiopsis maculans and two different strains of Bacillus pumilus upto its genotypic level from the epiphytic orchid, V. testacea. Studies related to endophyte from orchids and identifying them by comparing its sequence are meagre. However, further rigorous trials are necessary to identify diversified endophytes from the epiphytic vulnerable orchid plant habitat and so as to make strategies for biodiversity conservation of Western Ghats, one of the hottest biodiversity hotspots of the World. [ABSTRACT FROM AUTHOR]

The microbial fluctuations along an increasing salinity gradient during two different salt production phases – initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na+) and chloride (Cl–) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum , Haloarcula , Halorhabdus , and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum , and Halorhabdus decreased while Haloarcula , Haloplanus , and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes , Proteobacteria , and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria , Alphaproteobacteria , and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira , Desulfovermiculus , and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame. [ABSTRACT FROM AUTHOR]

Scientific deep drilling of the Koyna pilot borehole into the continental crust up to a depth of 3000 m below the surface at the Deccan Traps, India, provided a unique opportunity to explore microbial life within the deep granitic bedrock of the Archaean Eon. Microbial communities of the returned drilling fluid (fluid returned to the mud tank from the underground during the drilling operation; designated here as DF) sampled during the drilling operation of the Koyna pilot borehole at a depth range of 1681–2908 metres below the surface (m b.s.) were explored to gain a glimpse of the deep biosphere underneath the continental crust. Change of pH to alkalinity, reduced abundance of Si and Al, but enrichment of Fe, Ca and SO42- in the samples from deeper horizons suggested a gradual infusion of elements or ions from the crystalline bedrock, leading to an observed geochemical shift in the DF. Microbial communities of the DFs from deeper horizons showed progressively increased abundance of Firmicutes, Gammaproteobacteria and Actinobacteria as bacterial taxa and members of Euryarchaeota as the major archaeal taxa. Microbial families, well known to strive in strictly anaerobic and extremophilic environments, (e.g. Thermoanaerobacteraceae , Clostridiaceae , Bacillaceae , Carnobacteriaceae , Ruminococcaceae), increased in the samples obtained at a depth range of 2000 to 2908 m b.s. Phylogenetic analysis of common and unique operational taxonomic units (OTUs) of DF samples indicated signatures of extremophilic and deep subsurface relevant bacterial genera (Mongoliitalea , Hydrogenophaga , Marinilactibacillus , Anoxybacillus , Symbiobacterium , Geosporobacter , Thermoanaerobacter). Thermophilic, obligatory anaerobic sulfate-reducing bacterial taxa known to inhabit the deep subsurface were enriched from DF samples using sulfate as a terminal electron acceptor. This report on the geomicrobiology of the DF obtained during drilling of the deep subsurface of the Deccan Traps showed new opportunities to investigate deep life from terrestrial, granite-rock-hosted habitats. [ABSTRACT FROM AUTHOR]

The study aim was assessment of physicochemical characteristics along with the microbial diversity of samples of water collected from three important thermal springs of Uttarakhand state in India for two continuous years (2015 - 2016) with two samples taken each year. Some parameters were assessed at the sampling sites and the others in the laboratory. Microbial diversity was explored by using morphological, biochemical, MALDI-TOF-mass spectrometry and molecular approaches. The a-diversity of Gauri Kund was 24 with 14 strains of bacteria, five strains of actinomycetes and five strains of fungi. The a-diversity of Gangnani Kund was 22 with 10 strains of bacteria, five strains of actinomycetes and seven strains of fungi. The a-diversity of Tapovan Kund was 18 with eight strains of bacteria, four strains of actinomycetes and six strains of fungi. The current study can be a good reference for further similar studies. The available data will also help to understand the reasons behind the curative properties of these hot water springs. It also helps the government and local administration to take preventive measures for the conservation and management of these hot water springs. [ABSTRACT FROM AUTHOR]

The deterioration of water quality of river Ganga is a huge concern for Govt. of India. Apart from various pollution sources, the religious and ritualistic activities also have a good share in deteriorating Ganga water quality. Thus, the aim of the present study was to evaluate the changes in physico-chemical properties, microbial diversity and role of bacteriophages in controlling bacterial population of Ganga water during mass ritualistic bathing on the occasion of Maha-Kumbh in 2013. The BOD, COD, hardness, TDS and level of various ions significantly increased, while DO decreased in Ganga water during Maha-Kumbh. Ganga water was more affluent in trace elements than Yamuna and their levels further increased during Maha-Kumbh, which was correlated with decreased level of trace elements in the sediment. The bacterial diversity and evenness were increased and correlated with the number of devotees taking a dip at various events. Despite enormous increase in bacterial diversity during mass ritualistic bathing, the core bacterial species found in pre-Kumbh Ganga water were present in all the samples taken during Kumbh and post-Kumbh. In addition, the alteration in bacterial population during mass bathing was well under 2 log units which can be considered negligible. The study of bacteriophages at different bathing events revealed that Ganga was richer with the presence of bacteriophages in comparison with Yamuna against seven common bacteria found during the Maha-Kumbh. These bacteriophages have played a role in controlling bacterial growth and thus preventing putrefaction of Ganga water. Further, the abundance of trace elements in Ganga water might also be a reason for suppression of bacterial growth. Thus, the current study showed that Ganga has characteristic water quality in terms of physico-chemical property and microbial diversity that might have a role in the reported self-cleansing property of Ganga; however, the increased pollution load has surpassed its self-cleansing properties. Since water has been celebrated in all cultures, the outcome of the current study will not only be useful for the policy maker of cleaning and conservation of Ganga but also for restoration of other polluted rivers all over the world. [ABSTRACT FROM AUTHOR]

Introduction: Urbanization is a globally pervasive trend. Although urban settings provide better access to infrastructure and opportunities, urban lifestyles have certain negative consequences on human health. A number of recent studies have found interesting associations between the structure of human gut microbiota and the prevalence of metabolic conditions characterizing urban populations. The present study attempts to expand the footprint of these investigations to an Indian context. The objectives include elucidating specific patterns and gradients based on resident habitat and lifestyles (i.e., tribal and urban) that characterize gut microbial communities. Methods: Available 16S rRNA sequence datasets corresponding to the gut microbiota of urban and tribal populations from multiple regions of India have been rigorously compared. This analysis was carried out to understand the overall community structure, resident taxa, and their (inferred) functional components as well as their correlations with available meta-information. Results: The gut microbiota of urban and tribal communities are observed to have characteristically different signatures with respect to diversity as well as taxonomic and functional composition. Primarily, the gut microbiota in tribal communities is found to harbor significantly higher species diversity and richness as compared to that in urban populations. In spite of geographical segregation and diet-related differences, gut microbial diversity was not found to differ significantly between tribal groups. Furthermore, while the taxonomic profiles of different tribal communities cluster together irrespective of their geographic location, enterotype analysis indicates that samples from urban communities form two distinct clusters. Taxonomic analysis of samples in one of these clusters reveals the presence of microbes that are common to both urban and tribal cohorts, indicating a probable transient evolutionary state. Prevotella , previously reported to be the dominant genus resident in Indian gut microbiota, is found to have distinct OTUs and strain-specific oligotypes characterizing resident habitats and diet patterns. Certain interesting associations between microbial abundances and specific metadata have also been observed. Overall, urban lifestyle and diet appear to impact the structure and function of gut microbial communities, and the results of this study provide further evidence of this likely detrimental association. Conclusion: This study attempts to analyze, in an Indian context, the impact of urbanization on the human gut microbiota. Overall, the analysis elucidates interesting taxonomic and functional signatures characterizing the evolutionary transition in gut microbiota from tribal to urban. [ABSTRACT FROM AUTHOR]

Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial communities of deep subsurface of KG basin and their relationship with the geochemical environment. Elemental and mineralogical characterization of the sediments highlighted the presence of carbon and nitrogen deprived conditions along with the abundance of metalliferous minerals, especially rich in valuable elements like zirconium, vanadium, cesium, and rare earth elements. Diversity analysis based on Illumina MiSeq high-throughput sequencing platform revealed the predominance of Firmicutes (44.24%), Proteobacteria (34.17%), Bacteroidetes (15.18%), and Actinobacteria (3.81%) in the deep subsurface of this basin. 'Abundant' and 'rare' sub-communities analysis indicated that a large number of phyla like Acidobacteria, Armatimonadetes, Chloroflexi, and Deinococcus-Thermus were exclusively present as a rare community. Statistical analyses demonstrated that geochemical parameters, especially depth, pH, and metal content, showed significant influence on the microbial community structure. The present study should help future investigations for microbial mediated sustainable utilization of mineral-rich sediments of the region. [ABSTRACT FROM AUTHOR]

The quality of the indoor environment significantly impacts human health and productivity, especially given the amount of time individuals spend indoors globally. While chemical pollutants have been a focus of indoor air quality research, microbial contaminants also have a significant bearing on indoor air quality. This review provides a comprehensive overview of microbial contamination in built environments, covering sources, sampling strategies, and analysis methods. Microbial contamination has various origins, including human occupants, pets, and the outdoor environment. Sampling strategies for indoor microbial contamination include air, surface, and dust sampling, and various analysis methods are used to assess microbial diversity and complexity in indoor environments. The review also discusses the health risks associated with microbial contaminants, including bacteria, fungi, and viruses, and their products in indoor air, highlighting the need for evidence-based studies that can relate to specific health conditions. The importance of indoor air quality is emphasized from the perspective of the COVID-19 pandemic. A section of the review highlights the knowledge gap related to microbiological burden in indoor environments in developing countries, using India as a representative example. Finally, potential mitigation strategies to improve microbiological indoor air quality are briefly reviewed., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Chawla, Anand, Garg, Bhagat, Varmani, Bansal, McBain and Marwah.)

• Formation water of Jharia coal bed methane reservoir showed presence of methanogens. • Thermophilic methanogens and syntrophic bacteria were predominant in the formation water. • Upon enrichment, indigenous microbial consortium TERIOJ1 showed methane generation from coal at 45 °C. • Dominance of acetoclastic methanogens along with syntrophic bacteria were observed in consortium. • Microbial enhanced CBM can be realized by enriching native microbes of Jharia CBM reservoir. Microbial enhanced coal bed methane process has emerged as cheaper, feasible and environment friendly approach for enhancing coal bed methane (CBM) generation worldwide. Despite the fact that India has tremendous potential for CBM, there are many challenges towards microbial translation of CBM. Therefore, to explore the possibility of microbial enhanced CBM generation from the deep thermogenic CBM reservoir, diversity of the microbial community was investigated using the 16S rRNA gene amplification methods. Additionally, a culture dependent analysis from the formation water of the reservoir was performed to access the ability of the indigenous microbes to produce methane from coal when enriched with suitable nutrient supplements. Culture independent data revealed the nature of communities i.e. bacterial and archaeal domain, majorly from thermophilic profile. The bacterial community was dominated by proteobacterial and Firmicutes taxa, while archaeal community was dominated by Euryarchaeota taxa (acetoclastic methanogens). The enrichment cultures derived from the formation water were able to produce methane (1002 µmol/g coal) at 45 °C. The 16S rRNA gene analysis depicted that the enriched microbial culture was dominated with anaerobic thermophilic fermentative bacteria of Clostridiales family and acetoclastic Methanosarcinales methanogens. The present study depicts the biogenic methane generation in the thermogenic-gas containing CBM reservoir could be enhanced by stimulating the indigenous microorganisms through providing suitable nutrient supplements. Present investigation is likewise the prime response to deliberate about the capability of thermogenic CBM reservoir (temperature > 40 °C) in India for biogenic methane generation through culture independent and culture dependent examination. [ABSTRACT FROM AUTHOR]

The water samples were collected from two different hot water springs (Ringigad and Saldhar) of the Garhwal Himalaya for a period of two years. During the study period, the water sample was collected two times (June and August) each year for the analysis of physico-chemical attributes and isolated microorganisms including bacteria, archaea and fungi. A total of fifteen physico-chemical parameters were studied during the study period that includes the water temperature, dissolved oxygen, pH, conductivity, free carbondioxide, salinity, total dissolved solids, chlorides, total alkalinity, nitrates, sulphates, phosphates, total hardness, calcium and magnesium. Seven bacterial strains along with four archaeal and three fungal strains were isolated and identified in Ringigad thermal spring with αdiversity of 14. However, the α-diversity in Saldhar thermal spring was recorded to be 12 with six bacterial, three archaeal and three fungal strains. The temperature of water ranged between 82°C and 89°C for Ringigad and between 87°C and 92°C for Saldhar. [ABSTRACT FROM AUTHOR]

In this research, we examined the microbial diversity in Sohna hot spring, Haryana, India using shotgun metagenome sequencing based on the Illumina Hiseq 4000 sequencing technology. The raw sequence data from metagenomic paired-end libraries were analysed for taxonomic classification, diversity, and functional annotation using MG-RAST online server. The results showed the presence of total of 57 phyla, 931 genera, and 2068 species, predominantly occupied by Moraxellaceae (Gammaproteobacteria). However, at the species level, we reported the presence of some representative pathogenic taxa, such as Acinetobacter baumannii and Moraxella osloensis. The functional annotation predicted at various levels based on SEED-based subsystem, KEGG ortholog identity (KO), Cluster of Orthologous Groups (COGs) database identified the predominance of genes associated with primary and secondary metabolism along with a crucial role in environmental and genetic signals, cellular communication, and cell signalling. Comparative Genome Analysis (CGA) using The Pathosystem Resource Integration Centre (PATRIC) tool based on genome annotation and assembly of the metagenomic libraries for representative taxon Acinetobacter baumannii (NCBI tax id:470) characterized the reads with a unique genome identifier of 470.20380 (A. baumannii DDLJ4) which is evolutionary closer to A. baumannii ATCC 470.17978 400667.7. In addition, the CARD database results about the presence of potential AMR pathotypes and the prevalence of adeABC, adeIJK, abeM gene-specific clusters that function as multidrug efflux pumps. Overall, the results provided a comprehensive insight into virulence and anti-microbial resistance mechanism and could be useful for developing potential drug targets against the possible AMR pathotypes., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata. Effect on culturable fraction was assessed by enumeration on selective media, while PCR-denaturing gradient gel electrophoresis (DGGE) was employed to capture total bacterial community diversity. This was followed by a metabolic sketch using community-level physiological profiling (CLPP), to obtain a broader picture of the non-target effects on rhizospheric microbial community. Although plant parameters were not significantly affected by pesticide application, the microbial community structure experienced an undesirable impact as compared to control devoid of pesticide treatment. Examination of DGGE banding patterns through cluster analysis revealed that microbial community structure of pesticide-treated soils had only 70% resemblance to control rhizospheric soil even at 45 days post application. Drastic changes in the metabolic profiles of pesticide-treated soils were also detected in terms of substrate utilization, rhizospheric diversity, and evenness. It is noteworthy that the effects exacerbated by biopesticide were comparable to that of synthetic pesticides, thus emphasizing the significance of ecotoxicological assessments before tagging biopesticides as 'safe alternatives.' [ABSTRACT FROM AUTHOR]