Spatio-temporal resolution of taxonomic and functional microbiome of Lonar soda lake of India reveals metabolic potential for bioremediation

Nanopore Environmental Analysis

As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.

Metagenomic approaches in bioremediation of environmental pollutants

Metagenomics has emerged as a pivotal tool in bioremediation, providing a deeper understanding of the structure and function of the microbial communities involved in pollutant degradation. By circumventing the limitations of traditional culture-based methods, metagenomics enables comprehensive analysis of microbial ecosystems and facilitates the identification of new genes and metabolic pathways that are critical for bioremediation. Advanced sequencing technologies combined with computational and bioinformatics approaches have greatly enhanced our ability to detect sources of pollution and monitor dynamic changes in microbial communities during the bioremediation process. These tools enable the precise identification of key microbial players and their functional roles, and provide a deeper understanding of complex biodegradation networks. The integration of artificial intelligence (AI) with machine learning algorithms has accelerated the process of discovery of novel genes associated with bioremediation and has optimized metabolic pathway prediction. Novel strategies, including sequencing techniques and AI-assisted analysis, have the potential to revolutionize bioremediation by enabling the development of highly efficient, targeted, and sustainable remediation strategies for various contaminated environments. However, the complexity of microbial interactions, data interpretation, and high cost of these advanced technologies remain challenging. Future research should focus on improving computational tools, reducing costs, and integrating multidisciplinary approaches to overcome these limitations.

Unveiling the role of emerging metagenomics for the examination of hypersaline environments

Hypersaline ecosystems are distributed all over the globe. They are subjected to poly-extreme stresses and are inhabited by halophilic microorganisms possessing multiple adaptations. The halophiles have many biotechnological applications such as nutrient supplements, antioxidant synthesis, salt tolerant enzyme production, osmolyte synthesis, biofuel production, electricity generation etc. However, halophiles are still underexplored in terms of complex ecological interactions and functions as compared to other niches. The advent of metagenomics and the recent advancement of next-generation sequencing tools have made it feasible to investigate the microflora of an ecosystem, its interactions and functions. Both target gene and shotgun metagenomic approaches are commonly employed for the taxonomic, phylogenetic, and functional analyses of the hypersaline microbial communities. This review discusses different types of hypersaline niches, their residential microflora, and an overview of the metagenomic approaches used to investigate them. Various applications, hurdles and the recent advancements in metagenomic approaches have also been focused on here for their better understanding and utilization in the study of hypersaline microbiome.

Superb green cycling strategies for microbe-Fe0 neural network-type interaction: Harnessing eight key genes encoding enzymes and mineral transformations to efficiently treat PFOA

To address time-consuming and efficiency-limited challenges in conventional zero-valent iron (ZVI, Fe0) reduction or biotransformation for perfluorooctanoic acid (PFOA) treatment, two calcium alginate-embedded amendments (biochar-immobilized PFOA-degrading bacteria (CB) and ZVI (CZ)) were developed to construct microbe-Fe0 high-rate interaction systems. Interaction mechanisms and key metabolic pathways were systematically explored using metagenomics and a multi-process coupling model for PFOA under microbe-Fe0 interaction. Compared to Fe0 (0.0076 day-1) or microbe (0.0172 day-1) systems, the PFOA removal rate (0.0426 day-1) increased by 1.5 to 4.6 folds in the batch microbe-Fe0 interaction system. Moreover, Pseudomonas accelerated the transformation of Fe0 into Fe3+, which profoundly impacted PFOA transport and fate. Model results demonstrated microbe-Fe0 interaction improved retardation effect for PFOA in columns, with decreased dispersivity a (0.48 to 0.20 cm), increased reaction rate λ (0.15 to 0.22 h-1), distribution coefficient Kd (0.22 to 0.46 cm3∙g-1), and fraction f´(52 % to 60 %) of first-order kinetic sorption of PFOA in microbe-Fe0 interaction column system. Moreover, intermediates analysis showed that microbe-Fe0 interaction diversified PFOA reaction pathways. Three key metabolic pathways (ko00362, ko00626, ko00361), eight functional genes, and corresponding enzymes for PFOA degradation were identified. These findings provide insights into microbe-Fe0 "neural network-type" interaction by unveiling biotransformation and mineral transformation mechanisms for efficient PFOA treatment.

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils

Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.

IMPORTANCE

The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.

Industrial and Pharmaceutical Applications of Microbial Diversity of Hypersaline Ecology from Lonar Soda Crater

The unidentified geochemical and physiochemical characteristics of Soda Lakes across the globe make it a novel reservoir and bring attention to scientific civic for its conceivable industrial and pharmaceutical applications. In India, in the Maharashtra state, Lonar Lake is a naturally created Soda Lake by a meteorite impact. Phylogenetic data from this lake explored a diverse array of microorganisms like haloalkaliphilic bacteria and Archaea. Previously reported studies postulated the major microbial communities present in this lake ecosystem are Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria. Furthermore, it also contains Bacteroidetes, Nitrospirae, and Verrucomicrobia. This lake is also rich in phytoplankton, with the predominant presence of the Spirulina plantensis. Unique microbial strains from Lonar Lake ecosystems have fascinated consideration as a source of biological molecules with medicinal, industrial, and biotechnological potential. Recent literature revealed the isolation of antibioticproducing bacteria and alkaline proteases-producing alkaliphilic bacterium, as well as novel species of rare methylotrophs, other bacterial strains involved in producing vital enzymes, and unique actinomycetes are also reported. It indicates that the novel bacterial assemblage not reached hitherto may exist in this modified and unique ecology. This comprehensive review provides information about microbial diversity and its industrial and pharmaceutical interests that exist in Lonar Lake, which could be the future source of bioactive enzymes, biosurfactants, and biofuel and also useful in bioremediation. Furthermore, the novel species of microorganisms isolated from Lonar Lake have applications in the biosynthesis of medicines like antibiotics, antivirals, antifungals, anti-inflammatory agents, and precursors for synthesising valuable products. Data consolidated in the present review will cater to the needs of emerging industrial sectors for their commercial and therapeutic applications.

Recent Advances in Metagenomic Approaches, Applications, and Challenge

Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to conventional techniques providing advanced approach to identify novel and uncultivable microorganisms based on their genetic information derived from a particular environment. Shotgun metagenomics involves investigating the DNA of the entire community without the requirement of PCR amplification. It provides access to study all genes present in the sample. On the other hand, amplicon sequencing targets taxonomically important marker genes, the analysis of which is restricted to previously known DNA sequences. While sequence-based metagenomics is used to analyze DNA sequences directly from the environment without the requirement of library construction and with limited identification of novel genes and products that can be complemented by functional genomics, function-based metagenomics requires fragmentation and cloning of extracted metagenome DNA in a suitable host with subsequent functional screening and sequencing clone for detection of a novel gene. Although advances were made in metagenomics, different challenges arise. This review provides insight into advances in the metagenomic approaches combined with next-generation sequencing, their recent applications highlighting the emerging ones, such as in astrobiology, forensic sciences, and SARS-CoV-2 infection diagnosis, and the challenges associated. This review further discusses the different types of metagenomics and outlines advancements in bioinformatics tools and their significance in the analysis of metagenomic datasets.

Alkaliphilic/Alkali-Tolerant Fungi: Molecular, Biochemical, and Biotechnological Aspects

Biotechnologist interest in extremophile microorganisms has increased in recent years. Alkaliphilic and alkali-tolerant fungi that resist alkaline pH are among these. Alkaline environments, both terrestrial and aquatic, can be created by nature or by human activities. Aspergillus nidulans and Saccharomyces cerevisiae are the two eukaryotic organisms whose pH-dependent gene regulation has received the most study. In both biological models, the PacC transcription factor activates the Pal/Rim pathway through two successive proteolytic mechanisms. PacC is a repressor of acid-expressed genes and an activator of alkaline-expressed genes when it is in an active state. It appears, however, that these are not the only mechanisms associated with pH adaptations in alkali-tolerant fungi. These fungi produce enzymes that are resistant to harsh conditions, i.e., alkaline pH, and can be used in technological processes, such as in the textile, paper, detergent, food, pharmaceutical, and leather tanning industries, as well as in bioremediation of pollutants. Consequently, it is essential to understand how these fungi maintain intracellular homeostasis and the signaling pathways that activate the physiological mechanisms of alkali resistance in fungi.

First report on microplastics contamination in a meteorite impact Crater Lake from India

Microplastic pollution is a worldwide concern affecting all environmental matrices, including pristine lakes. Lentic lakes operate as a sink for microplastics (MPs), which interfere with a biogeochemical cycle and, therefore, deserve immediate attention. We present a comprehensive assessment of MPs contamination in the sediment and surface water of a geo-heritage site, Lonar lake (India). It is the third largest natural saltwater lake and only basaltic crater in the world formed by meteoric impact around 52,000 years ago. Mean MPs abundance in lakeshore sediment and surface water was 14.44 particles/kg and 2.66 particles/L, respectively. Small-sized MPs dominate the hypersaline region of the lake. Transparent and green fragments and filaments morphotypes were abundant. Most of the MPs in Lonar lake were secondary in origin. FTIR-ATR analysis revealed 16 types of polymers in the lake, of which polypropylene, polyvinyl chloride, polyethylene, high-density polyethylene, low-density polyethylene, polystyrene, and polyester were the most common. The overall pollution load index (PLI) for Lonar lake sediment and water was 1.39 and 2.58, respectively. Although all sampling stations had significant MPs pollution (PLI > 1), there was noticeable station-specific variability, which could be linked to anthropogenic activities. Irresponsible tourist behavior and religious activities, coupled with poor waste management are the leading causes of MPs contamination in the lake. The current work fills a gap in the investigation of MP pollution in a crater lake formed by a meteorite impact by being the first to provide a precise estimate of the MPs contamination in the Lonar lake.

Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review

Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.

Insight into the effect of wastewater-derived dissolved organic matter composition on norgestrel degradation in activated sludge: Coupled bacterial community and molecular characteristics

Dissolved organic matter (DOM) mediates the microbial transformation of micropollutants, including norgestrel (NGT) in natural waters. However, little is known of the effect of complex and variable wastewater-derived DOM composition on NGT degradation during wastewater treatment. In this study, the relationship between the compositions of initial DOM and NGT removal efficiencies of 17 wastewater treatment plants (WWTPs) in spring and summer were analyzed. The different molecular composition of DOM was selected in the lab to further explore its effect on NGT degradation by activated sludge. Results indicated that the DOM composition was a substantial driver of NGT removal in WWTPs. The discrepancies in the initial DOM composition contributed to the differences in the kinetics of NGT degradation by activated sludge. The larger rapid decay phase rates of NGT are usually accompanied by a large proportion of labile substances in DOM. High-throughput sequencing and ultrahigh-resolution mass spectrometry were used to further analyze the evolution of bacterial communities and DOM molecular composition were combined with network analysis to reveal the intrinsic relationship that how DOM composition affected NGT degradation by regulating core microbes. Eighty-nine core OTUs were significantly associated with NGT degradation, and 73 occurred in the rapid decay phase, implying that NGT degradation was mainly regulated by the initial composition of DOM. Nine major transformation products were identified in different groups with widely varying concentrations or relative abundances of these transformation products. This work provides valuable insights into the effects of wastewater-derived DOM composition on NGT degradation by activated sludge and innovatively explores the influence mechanisms from the bacterial community and molecular characterization perspectives.

Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context

Bauxite residue is the alkaline byproduct generated during alumina extraction and is commonly landfilled in open-air deposits. The growth in global alumina production have raised environmental concerns about these deposits since no large-scale reuses exist to date. Microbial-driven techniques including bioremediation and critical metal bio-recovery are now considered sustainable and cost-effective methods to revalorize bauxite residues. However, the establishment of microbial communities and their active role in these strategies are still poorly understood. We thus determined the geochemical composition of different bauxite residues produced in southern France and explored the development of bacterial and fungal communities using Illumina high-throughput sequencing. Physicochemical parameters were influenced differently by the deposit age and the bauxite origin. Taxonomical analysis revealed an early-stage microbial community dominated by haloalkaliphilic microorganisms and strongly influenced by chemical gradients. Microbial richness, diversity and network complexity increased significantly with the deposit age, reaching an equilibrium community composition similar to typical soils after decades of natural weathering. Our results suggested that salinity, pH, and toxic metals affected the bacterial community structure, while fungal community composition showed no clear correlations with chemical variations.

Sodium Energetic Cycle in the Natronophilic Bacterium Thioalkalivibrio versutus

As inhabitants of soda lakes, Thioalkalivibrio versutus are halo- and alkaliphilic bacteria that have previously been shown to respire with the first demonstrated Na⁺-translocating cytochrome-c oxidase (CO). The enzyme generates a sodium-motive force (Δs) as high as −270 mV across the bacterial plasma membrane. However, in these bacteria, operation of the possible Δs consumers has not been proven. We obtained motile cells and used them to study the supposed Na⁺ energetic cycle in these bacteria. The resulting motility was activated in the presence of the protonophore 2-heptyl-4-hydroxyquinoline N-oxide (HQNO), in line with the same effect on cell respiration, and was fully blocked by amiloride—an inhibitor of Na⁺-motive flagella. In immotile starving bacteria, ascorbate triggered CO-mediated respiration and motility, both showing the same dependence on sodium concentration. We concluded that, in T. versutus, Na⁺-translocating CO and Na⁺-motive flagella operate in the Na⁺ energetic cycle mode. Our research may shed light on the energetic reason for how these bacteria are confined to a narrow chemocline zone and thrive in the extreme conditions of soda lakes.