Metagenomic insights into novel microbial lineages with distinct ecological functions in the Arctic glacier foreland ecosystems.

Land-terminating glaciers are retreating globally, resulting in the expansion of the ice-free glacier forelands (GFs). These GFs act as a natural laboratory to study microbial community succession, soil formation, and ecosystem development. Here, we have employed gene-centric and genome-resolved metagenomic approaches to disseminate microbial diversity, community structure, and their associated biogeochemical processes involved in the carbon, nitrogen, and sulfur cycling across three GF ecosystems. Here, we present a compendium of draft Metagenome Assembled Genomes (MAGs) belonging to bacterial (n = 899) and archaeal (n = 4) domains. These MAGs were reconstructed using a total of 27 shotgun metagenomic datasets obtained from three different GFs, including Midtre Lovénbreen glacier (Svalbard), Russell glacier (Greenland), and Storglaciaren (Sweden). The taxonomic classification revealed that 98% of MAGs remained unclassified at species levels, suggesting the presence of novel microbial lineages. The abundance of metabolic genes associated with carbon, nitrogen, and sulfur cycling pathways varied between and within the samples collected across the three GF ecosystems. Our findings indicate that MAGs from different GFs share close phylogenetic relationships but exhibit significant differences in abundance, distribution patterns, and metabolic functions. This compendium of novel MAGs, encompassing autotrophic, phototrophic, and chemolithoautotrophic microbial groups reconstructed from GF ecosystems, represents a valuable resource for further studies.

Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems.

The Gemmatimonadota phylum has been widely detected in diverse natural environments, yet their specific ecological roles in many habitats remain poorly investigated. Similarly, the Candidatus ARS69 phylum has been identified only in a few habitats, and literature on their metabolic functions is relatively scarce. In the present study, we investigated the ecological significance of phyla Ca. ARS69 and Gemmatimonadota in the Arctic glacier foreland (GF) ecosystems through genome-resolved metagenomics. We have reconstructed the first high-quality metagenome-assembled genome (MAG) belonging to Ca. ARS69 and 12 other MAGs belonging to phylum Gemmatimonadota from the three different Arctic GF samples. We further elucidated these two groups phylogenetic lineage and their metabolic function through phylogenomic and pangenomic analysis. The analysis showed that all the reconstructed MAGs potentially belonged to novel species. The MAGs belonged to Ca. ARS69 consist about 8296 gene clusters, of which only about 8% of single-copy core genes (n = 980) were shared among them. The study also revealed the potential ecological role of Ca. ARS69 is associated with carbon fixation, denitrification, sulfite oxidation, and reduction biochemical processes in the GF ecosystems. Similarly, the study demonstrates the widespread distribution of different classes of Gemmatimonadota across wide ranges of ecosystems and their metabolic functions, including in the polar region. KEY POINTS: • Glacier foreland ecosystems act as a natural laboratory to study microbial community structure. • We have reconstructed 13 metagenome-assembled genomes from the soil samples. • All the reconstructed MAGs belonged to novel species with different metabolic processes. • Ca. ARS69 and Gemmatimonadota MAGs were found to participate in carbon fixation and denitrification processes.

Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.

Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.

Water Mass Controlled Vertical Stratification of Bacterial and Archaeal Communities in the Western Arctic Ocean During Summer Sea-Ice Melting.

The environmental variations and their interactions with the biosphere are vital in the Arctic Ocean during the summer sea-ice melting period in the current scenario of climate change. Hence, we analysed the vertical distribution of bacterial and archaeal communities in the western Arctic Ocean from sea surface melt-ponds to deep water up to a 3040 m depth. The distribution of microbial communities showed a clear stratification with significant differences among different water depths, and the water masses in the Arctic Ocean - surface mixed layer, Atlantic water mass and deep Arctic water - appeared as a major factor explaining their distribution in the water column. A total of 34 bacterial phyla were detected in the seawater and 10 bacterial phyla in melt-ponds. Proteobacteria was the dominant phyla in the seawater irrespective of depth, whereas Bacteroidota was the dominant phyla in the melt-ponds. A fast expectation-maximization microbial source tracking analysis revealed that only limited dispersion of the bacterial community was possible across the stratified water column. The surface water mass contributed 21% of the microbial community to the deep chlorophyll maximum (DCM), while the DCM waters contributed only 3% of the microbial communities to the deeper water masses. Atlantic water mass contributed 37% to the microbial community of the deep Arctic water. Oligotrophic heterotrophic bacteria were dominant in the melt-ponds and surface waters, whereas chemoautotrophic and mixotrophic bacterial and archaeal communities were abundant in deeper waters. Chlorophyll and ammonium were the major environmental factors that determined the surface microbial communities, whereas inorganic nutrient concentrations controlled the deep-water communities.

Salinity-controlled distribution of prokaryotic communities in the Arctic sea-ice melt ponds.

The thawing of snow and sea ice produces distinctive melt ponds on the surface of the Arctic sea ice, which covers a significant portion of the surface sea ice during summer. Melt-pond salinity impacts heat transfer to the ice below and the melting rate. It is widely known that melt ponds play a significant role in heat fluxes, ice-albedo feedback, and sea-ice energy balance. However, not much attention has been given to the fact that melt ponds also serve as a unique microbial ecosystem where microbial production begins as soon as they are formed. Here, we investigated the role of melt pond salinity in controlling the diversity and distribution of prokaryotic communities using culture-dependent and -independent approaches. The 16 S rRNA gene amplicon based next generation sequencing analysis retrieved a total of 14 bacterial phyla, consisting of 146 genera, in addition to two archaeal phyla. Further, the culture-dependent approaches of the study allowed for the isolation and identification of twenty-four bacterial genera in pure culture. Flavobacterium, Candidatus_Aquiluna, SAR11 clade, Polaribacter, Glaciecola, and Nonlabens were the dominant genera observed in the amplicon analysis. Whereas Actimicrobium, Rhodoglobus, Flavobacterium, and Pseudomonas were dominated in the culturable fraction. Our results also demonstrated that salinity, chlorophyll a, and dissolved organic carbon were the significant environmental variables controlling the prokaryotic community distribution in melt ponds. A significant community shift was observed in melt ponds when the salinity changed with the progression of melting and deepening of ponds. Different communities were found to be dominant in melt ponds with different salinity ranges. It was also observed that melt pond prokaryotic communities significantly differed from the surface ocean microbial community. Our observations suggest that complex prokaryotic communities develop in melt ponds immediately after its formation using dissolved organic carbon generated through primary production in the oligotrophic water.

Fjords of the western and northern regions of Svalbard harbour distinct bacterioplankton community structures.

Fjords are highly dynamic ecosystems that are known to be sentinels to climate change due to increased glaciomarine interactions. The convergence and mixing of warm Atlantic water (AtW) and cold Arctic water (ArW) is known to influence the hydrodynamics and ecology of the Arctic fjords. However, most past studies were limited to single-fjord ecosystems, determining the baseline knowledge of inter-fjord comparison on bacterioplankton diversity and distribution patterns. In the present study, we investigated the bacterial diversity and community composition across three Arctic fjords located in the western and northern regions of Svalbard. Our observations show that the bacterial community structure varied significantly among the fjords, while abundant Operational Taxonomic Units (OTUs) were widespread (n = 100) between all the samples and rare OTUs (n = 2221) mainly contributed to these differences. Phylogenetic classification revealed that Alpha (27.3-55%) and Gamma-proteobacteria (16-51.3%), followed by Bacteroidota (17-35.7%) were dominant in the St.Jonsfjorden and Magdalenefjorden, while Verrucomicrobiota (up to 84.19%) and Actinobacteriota (up to 76.5%) were predominant in the Raudfjorden. Temperature, dissolved inorganic phosphate (DIP) and depth were found to significantly influence the community composition of abundant bacterial groups, whereas the rare bacterial groups were affected by temperature, DIP, dissolved inorganic nitrate (DIN), ammonium and depth. A comparative meta-analysis along with Kongsfjorden and Krossfjorden also showed that each fjord had a significantly different bacterioplankton community structure.

Total nitrogen influence bacterial community structure of active layer permafrost across summer and winter seasons in Ny-Ålesund, Svalbard.

The permafrost in the polar regions is vital for maintaining the status quo of the earth's climate by limiting greenhouse gas emissions. The present study aims to investigate the seasonal variations and the influence of physicochemical parameters on the bacterial diversity and community structure of active layer permafrost (AL) around Ny-Ålesund, Svalbard. The AL soil samples were collected from four different geographical locations around Ny-Ålesund during the winter and summer seasons. The 16S rDNA amplicon sequencing was carried out to investigate the diversity and distribution profiles of bacterial communities among the collected AL samples. Physico-chemical parameters including soil pH, moisture content, total carbon (TC), total nitrogen (TN), and trace metals concentrations were measured. Bacterial phyla, Proteobacteria (15.4%-26%) and Chloroflexi (9.6%-22.5%) were predominantly distributed across both seasons. In the winter samples, Verrucomicrobiota (14.12%-23.39%) phylum, consisting of genera Chthoniobacter and Opitutus were highly abundant (Lefse, p < 0.05), whereas in summer bacterial genera belonging to Gemmatimonadota (3.3%-13.74%) and Acidobacteriota (18.02%-28.52%) phyla were highly abundant. The bacterial richness and diversity index were not significantly different between the winter and summer seasons. Principal coordinate analysis (PCoA) has revealed a distinct grouping between two seasons (PERMANOVA, p < 0.05). Bacterial community structure was significantly varied between winter and summer seasons, whereas the physico-chemical variable, TN, influenced the community structure. About 37.8% of the total operational taxonomic units (OTUs) were shared between seasons, whereas 25.4% and 36.8% of OTUs were unique to the summer and winter seasons. The present study revealed that the conditions prevailing during winter and summer has shaped bacterial community structure in AL samples albeit the stable diversity and most of the variation was explained by TN, indicating its critical role in oligotrophic permafrost.

Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal.

Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.

Microbial diversity and associated metabolic potential in the supraglacial habitat of a fast-retreating glacier: a case study of Patsio glacier, North-western Himalaya.

In the present study, we investigated the microbial community composition and their associated metabolic potentials using the 16S rRNA gene (V3-V4) and ITS (ITS1) amplicon sequencing approach in the Patsio glacier. The bacterial community composition was mainly dominated by Bacteroidota (18%-38% of total reads) and Cyanobacteria (9%-30%), along with a rare Candidate phylum Patescibacteria. Ferruginibacter (13%) and Polaromonas (8%) were the most dominant genera identified across the samples known to have potential ecological roles in colonization, driving the functioning of supraglacial habitats. The prevalence of metabolic genes associated with nitrogen, carbon and sulfur cycling processes was identified in the present study. The fungal diversity was dominated by members of unclassified phyla, followed by Ascomycota (up to 6%) and Basidiomycota (up to 4%), in terms of its relative abundance. The relative abundance of Fusarium and Didymella (8%-14%) was higher among the high altitude, cryoconite samples (P1-P5), while Rhodotorula (12%-29%) dominated in the glacial ice debris samples (P6-P8). Thus, our study provides significant insights into dynamics of microbial communities and its potential ecological roles in the changing climate.

Defunct gold mine tailings are natural reservoir for unique bacterial communities revealed by high-throughput sequencing analysis.

Mine tailing dumps are arguably one of the leading sources of environmental degradation with often both public health and ecologically consequences. The present study investigated the concentration of heavy metals in gold mine tailings, and used high throughput sequencing techniques to determine the microbial community diversity of these tailings using 16S rRNA gene based amplicon sequence analysis. The concentration of detected metals and metalloids followed the order Si > Al > Fe > K > Ca > Mg. The 16S rRNA gene based sequence analysis resulted in a total of 273,398 reads across the five samples, represented among 7 major phyla, 41 classes, 77 orders, 142 families and 247 major genera. Phylum Actinobacteria was the most dominant, followed by Proteobacteria, Firmicutes, Chloroflexi, Cyanobacteria, Bacteroidetes, Acidobacteria and Planctomycetes. Redundancy analysis (RDA) and pairwise correlation analysis positively correlated the distribution of Alphaproteobacteria and Gammaproteobacteria to Al and K; Actinobacteria to Cr and Chloroflexi to Si. Negative correlations were observed in the distribution of Bacteroidetes with respect to As concentrations, Actinobacteria to Al, and Alphaproteobacteria and Gammaproteobacteria to high As and Te content of the soils. Predictive functional analysis showed the presence of putative biosynthetic and degradative pathways across the five sample sites. The study concludes that mine tailing sites harbour diverse and unique microbial assemblages with potentially biotechnologically important genes for biosynthesis and biodegradation.

Distribution, Interaction and Functional Profiles of Epiphytic Bacterial Communities from the Rocky Intertidal Seaweeds, South Africa.

Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.

A pivotal role for ocean eddies in the distribution of microbial communities across the Antarctic Circumpolar Current.

Mesoscale variability and associated eddy fluxes play crucial roles in ocean circulation dynamics and the ecology of the upper ocean. In doing so, these features are biologically important, providing a mechanism for the mixing and exchange of nutrients and biota within the ocean. Transient mesoscale eddies in the Southern Ocean are known to relocate zooplankton communities across the Antarctic Circumpolar Current (ACC) and are important foraging grounds for marine top predators. In this study we investigated the role of cyclonic and anti-cyclonic eddies formed at the South-West Indian Ridge on the spatial variability and diversity of microbial communities. We focused on two contrasting adjacent eddies within the Antarctic Polar Frontal Zone to determine how these features may influence the microbial communities within this region. The water masses and microbiota of the two eddies, representative of a cyclonic cold core from the Antarctic zone and an anti-cyclonic warm-core from the Subantarctic zone, were compared. The data reveal that the two eddies entrain distinct microbial communities from their points of origin that are maintained for up to ten months. Our findings highlight the ecological impact that changes, brought by the translocation of eddies across the ACC, have on microbial diversity.

Nanomaterials in the Pharmaceuticals: Occurrence, Behaviour and Applications.

Nanoparticles are an emerging class of multi-functional materials defined by size-dependent properties. The ever-growing interest in nanotechnology research has been attributed to the significant properties and parameters of the nanoparticles that make them more versatile than their bulk counter parts that are expected to have large spectrum impact on existing technologies such as drug delivery, biomedical, therapeutics, healthcare and pharmaceutical. The main objectives of this review are to study the impact, occurrence and behaviour of nanomaterials and their applications in pharmaceuticals. Nano-approaches are being explored globally to enhance bioavailability of drugs and diagnostics. This is due to the extremely small size and large specific surface areas of the nanoparticles that may interact directly with cellular system. Biomacromolecule surface recognition by nanoparticles acts as artificial receptors, which provide a potential tool for controlling cellular and extracellular processes for numerous biological applications such as diagnostics, therapy, drug delivery and biosensing. This review article is expected to broaden our understanding towards the development of nanoparticles based diagnostics, combination therapies in treating different diseases and other pharmaceutical applications.

Beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra.

Microorganisms in the rhizosphere mediate the cycling of nutrients, their enhanced mobilisation and facilitate their uptake, leading to increased root growth, biomass and yield of plants. We examined the promise of beneficial cyanobacteria and eubacteria as microbial inoculants, applied singly or in combination as consortia or biofilms, to improve growth and yields of okra. Interrelationships among the microbial activities and the micro/macro nutrient dynamics in soils and okra yield characteristics were assessed along with the changes in the soil microbiome. A significant effect of microbial inoculation on alkaline phosphatase activity was recorded both at the mid-crop and harvest stages. Microbial biomass carbon values were highest due to the Anabaena sp. - Providencia sp. (CR1 + PR3) application. The yield of okra ranged from 444.6-478.4 g(-1) plant and a positive correlation (0.69) recorded between yield and root weight. The application of Azotobacter led to the highest root weight and yield. The concentration of Zn at mid-crop stage was 60-70% higher in the Azotobacter sp. and Calothrix sp. inoculated soils, as compared to uninoculated control. Iron concentration in soil was more than 2-3 folds higher than control at the mid-crop stage, especially due to the application of Anabaena-Azotobacter biofilm and Azotobacter sp. Both at the mid-crop and harvest stages, the PCR-DGGE profiles of eubacterial communities were similar among the uninoculated control, the Anabaena sp. - Providencia sp. (CW1 + PW5) and the Anabaena-Azotobacter biofilm treatments. Although the profiles of the Azotobacter, Calothrix and CR1 + PR3 treatments were identical at these stages of growth, the profile of CR1 + PR3 was clearly distinguishable. The performance of the inoculants, particularly Calothrix (T6) and consortium of Anabaena and Providencia (CR1 + PR3; T5), in terms of microbiological and nutrient data, along with generation of distinct PCR-DGGE profiles suggested their superiority and emphasized the utility of combining microbiological and molecular tools in the selection of effective microbial inoculants.