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.

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.

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.

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.

Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard).

Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3+) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.

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.

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.

Roseitranquillus sediminis gen. nov., sp. nov. a novel genus and species of the family Rhodobacteraceae, isolated from sediment of an Arctic fjord.

A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain MCCB 386T was isolated from sediment samples collected from Kongsfjorden, an Arctic fjord. The strain MCCB 386T showed growth at 4-37 °C (optimum 27°C) in the presence of 1-8% NaCl (w/v, optimum 3.5%) and at pH 6.0-8.0 (optimum pH 7.0). The major fatty acids were C18:1ω7c (54.0%) and 11-methyl C18:1ω7c (22.6%). The dominant respiratory quinone was Q-10. The major polar lipids comprised of phosphatidylcholine (PC), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphoglycolipid (PGL), one unidentified aminolipid, two glycolipids and two unidentified lipids. The genomic G+C content of the strain MCCB 386T was 68.1 mol%. The 16 S rRNA gene sequences based phylogenetic analysis of MCCB 386T showed that Psychromarinibacter halotolerans YBW34T (95.88%) is the most closely related species. In addition, overall genome relatedness indices (OGRI) of MCCB 386T with closely related strains were lower than threshold level for species and genus delineation. The analysis of Biosynthetic Gene clusters (BGCs) revealed the potential of this strain for production of novel bioactive secondary metabolites. As per polyphasic taxonomic characterisation, strain MCCB 386T represents a novel species of a novel genus for which the name Roseitranquillus sediminis gen. nov., sp. nov. is suggested. The type strain of the species is MCCB 386T (= JCM 33,538T= KACC 21,531T).

Spatially resolved assembly, connectivity and structure of particle-associated and free-living bacterial communities in a high Arctic fjord.

The assembly processes that underlie the composition and connectivity of free-living (FL) and particle-associated (PA) bacterial communities from surface to deep waters remain little understood. Here, using phylogenetic null modeling, we quantify the relative influence of selective and stochastic mechanisms that assemble FL and PA bacterial communities throughout the water column in a high Arctic fjord. We demonstrate that assembly processes acting on FL and PA bacterial communities are similar in surface waters, but become increasingly distinct in deep waters. As depth increases, the relative influence of homogeneous selection increases for FL but decreases for PA communities. In addition, dispersal limitation and variable selection increase with depth for PA, but not for FL communities, indicating increased residence time of taxa on particles and less frequent decolonization. As a consequence, beta diversity of PA communities is greater in bottom than in surface waters. The limited connectivity between these communities with increasing depth leads to highly distinct FL and PA bacterial communities in bottom waters. Finally, depth-related trends for FL and PA beta diversity and connectivity in this study are consistent with previous observations in the open ocean, suggesting that assembly processes for FL and PA bacterial communities may also be distinct in other aquatic environments.

Marine Group-II archaea dominate particle-attached as well as free-living archaeal assemblages in the surface waters of Kongsfjorden, Svalbard, Arctic Ocean.

Marine archaea are a significant component of the global oceanic ecosystems, including the polar oceans. However, only a few attempts have been made to study archaea in the high Arctic fjords. Given the importance of Archaea in carbon and nitrogen cycling, it is imperative to explore their diversity and community composition in the high Arctic fjords, such as Kongsfjorden (Svalbard). In the present study, we evaluated archaeal diversity and community composition in the size-fractionated microbial population, viz-a-viz free-living (FL; 0.2-3 µm) and particle-attached (PA; > 3 µm) using archaeal V3-V4 16S rRNA gene amplicon sequencing. Our results indicate that the overall archaeal community in the surface water of Kongsfjorden was dominated by the members of the marine group-II (MGII) archaea, followed by the MGI group members, including Nitrosopumilaceae and Nitrososphaeraceae. Although a clear niche partitioning between PA and FL archaeal communities was not observed, 2 OTUs among 682 OTUs, and 3 ASVs out of 1932 ASVs were differentially abundant among the fractions. OTU001/ASV0002, classified as MGIIa, was differentially abundant in the PA fraction. OTU006/ASV0006/ASV0010 affiliated with MGIIb were differentially abundant in the FL fraction. Particulate organic nitrogen and C:N ratio were the most significant variables (P < 0.05) explaining the observed variation in the FL and PA archaeal communities, respectively. These results indicate an exchange between archaeal communities or a generalist lifestyle switching between FL and PA fractions. Besides, the particles' elemental composition (carbon and nitrogen) seems to play an essential role in shaping the PA archaeal communities in the surface waters of Kongsfjorden.

Pseudonocardia cytotoxica sp. nov., a novel actinomycete isolated from an Arctic fjord with potential to produce cytotoxic compound.

Herein we report the isolation of a novel actinomycete, strain MCCB 268T, from the sediment sample collected from a high Arctic fjord Kongsfjorden. MCCB 268T showed greater than 97% 16S rRNA gene sequence similarity with those of Pseudonocardia konjuensis LM 157T (98.06%), Pseudonocardia soli NW8-21 (97.22%) Pseudonocardia endophytica YIM 56035 (97.08%) and Pseudonocardia nantongensis KLBMP 1282 (97.34%) showing that the strain should be assigned to the genus Pseudonocardia. DNA-DNA hybridization with Pseudonocardia konjuensis LM 157T showed only 41.5% relatedness to strain MCCB 268T. The whole genome of the strain MCCB 268T was sequenced. Whole-genome average nucleotide identity, dDDH (%) and genome tree analysis demonstrated that strain significantly differed from other Pseudonocardia species. The G + C content was 70.5 mol%. MCCB 268T exhibited in vitro cytotoxicity and through bioassay guided fractionation followed by HPLC separation a cytotoxic compound (I) was isolated. The compound (I) was identified as 1-acetyl-ß-carboline through NMR spectra and high-resolution mass spectrometry. Compound (I) showed cytotoxicity against lung cancer cell line and mode of anticancer activity was found to be through the induction of apoptosis. Based on the genotypic and phenotypic features, MCCB 268T ought to be classified as a novel species under the genus Pseudonocardia for which the name Pseudonocardia cytotoxica sp. nov. is proposed (= CCUG72333T = JCM32718T).

Response of bacterial communities from Kongsfjorden (Svalbard, Arctic Ocean) to macroalgal polysaccharide amendments.

Macroalgae are abundant in coastal Arctic habitats and contain a large amount of polysaccharides. Increased macroalgal productivity due to warmer temperatures and reduced sea-ice cover contribute a significant amount of polysaccharide-rich detritus in the region. To study bacterial degradation of macroalgal polysaccharides and their potential impact on biogeochemical processes we studied the response of bacterial communities from Kongsfjorden, Svalbard (Arctic Ocean) to alginate (AL) and agarose (AG) amendments, using an ex-situ microcosm experiment. Our results show that bacterial communities responded to the increased availability of macroalgal polysaccharides and community shift was congruent with a significant decline in nutrient concentrations. Initially-rare bacterial taxa affiliated with Gammaproteobacteria and Bacteroidia responded to the polysaccharide addition. Each polysaccharide addition incited the growth of certain distinct bacteria taxa. Compared to the un-amended control microcosms (CM), Polaribacter, Colwellia, Pseudoalteromonas, and unclassified Gammaproteobacteria responded to AL addition, whereas Paraglaciecola, Lentimonas, Colwellia, unclassified Gammaproteobacteria, unclassified Alteromonadales, and unclassified Alteromonadaceae responded to the AG addition. These results suggest that polysaccharides shift bacterial community composition towards copiotrophic bacterial taxa, with implications for carbon and nutrient cycling in coastal Svalbard.

Diversity of retrievable heterotrophic bacteria in Kongsfjorden, an Arctic fjord

Abstract The diversity and abundance of retrievable pelagic heterotrophic bacteria in Kongsfjorden, an Arctic fjord, was studied during the summer of 2011 (June, August, and September). Retrievable bacterial load ranged from 103 to 107 CFU L−1 in June, while it was 104-106 CFU L−1 in August and September. Based on 16S rRNA gene sequence similarities, a higher number of phylotypes was observed during August (22 phylotypes) compared to that during June (6 phylotypes) and September (12 phylotypes). The groups were classified into four phyla: Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes. Bacteroidetes was represented only by a single member Leewenhoekiella aequorea during the three months and was dominant (40%) in June. However, this dominance changed in August to a well-known phytopathogenic species Rhodococcus fascians (32%), which could be a result of decrease in the phytoplankton biomass following the secondary bloom. It is the first report of Halomonas titanicae isolation from the Arctic waters. It showed an increase in its abundance with the intrusion of Atlantic water into Kongsfjorden. Increased abundance of Psychrobacter species in the late summer months coincided with the presence of cooler waters. Thus, the composition and function of heterotrophic bacterial community was fundamentally different in different months. This could be linked to the changes in the water masses and/or phytoplankton bloom dynamics occurring in Arctic summer.

Diversity of retrievable heterotrophic bacteria in Kongsfjorden, an Arctic fjord.

The diversity and abundance of retrievable pelagic heterotrophic bacteria in Kongsfjorden, an Arctic fjord, was studied during the summer of 2011 (June, August, and September). Retrievable bacterial load ranged from 103 to 107CFUL-1 in June, while it was 104-106CFUL-1 in August and September. Based on 16S rRNA gene sequence similarities, a higher number of phylotypes was observed during August (22 phylotypes) compared to that during June (6 phylotypes) and September (12 phylotypes). The groups were classified into four phyla: Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes. Bacteroidetes was represented only by a single member Leewenhoekiella aequorea during the three months and was dominant (40%) in June. However, this dominance changed in August to a well-known phytopathogenic species Rhodococcus fascians (32%), which could be a result of decrease in the phytoplankton biomass following the secondary bloom. It is the first report of Halomonas titanicae isolation from the Arctic waters. It showed an increase in its abundance with the intrusion of Atlantic water into Kongsfjorden. Increased abundance of Psychrobacter species in the late summer months coincided with the presence of cooler waters. Thus, the composition and function of heterotrophic bacterial community was fundamentally different in different months. This could be linked to the changes in the water masses and/or phytoplankton bloom dynamics occurring in Arctic summer.