Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach

Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage

BACKGROUND

The backbone of the eukaryotic tree of life contains taxa only found in molecular surveys, of which we still have a limited understanding. Such is the case of Picozoa, an enigmatic lineage of heterotrophic picoeukaryotes within the supergroup Archaeplastida, which has emerged as a significant component of marine microbial planktonic communities. To enhance our understanding of the diversity, distribution, and ecology of Picozoa, we conduct a comprehensive assessment at different levels, from assemblages to taxa, employing phylogenetic analysis, species distribution modeling, and ecological niche characterization.

RESULTS

Picozoa was among the ten most abundant eukaryotic groups, found almost exclusively in marine environments. The phylum was represented by 179 Picozoa's OTU (pOTUs) placed in five phylogenetic clades. Picozoa community structure had a clear latitudinal pattern, with polar assemblages tending to cluster separately from non-polar ones. Based on the abundance and occupancy pattern, the pOTUs were classified into four categories: Low-abundant, Widespread, Polar, and Non-polar. We calculated the ecological niche of each of these categories. Notably, pOTUs sharing similar ecological niches were not closely related species, indicating a phylogenetic overdispersion in Picozoa communities. This could be attributed to competitive exclusion and the strong influence of the seasonal amplitude of variations in environmental factors, such as temperature, shaping physiological and ecological traits.

CONCLUSIONS

Overall, this work advances our understanding of uncharted protists' evolutionary dynamics and ecological strategies. Our results highlight the importance of understanding the species-level ecology of marine heteroflagellates like Picozoa. The observed phylogenetic overdispersion challenges the concept of phylogenetic niche conservatism in protist communities, suggesting that closely related species do not necessarily share similar ecological niches. Video Abstract.

Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands

The Antarctic continent hosts exceptional niches, making it an ideal environment for studying polyextremophilic microorganisms. These organisms are uniquely shaped by the geographic niches and variations in soil types. Here we present, a culture-independent approach using DNA metabarcoding to assess the bacterial communities associated with accumulated snow and exposed sediments across different Antarctic islands situated in the Larsemann Hills, Antarctica. The exposed sediments (ES) were found to be more diverse than the accumulated snow (AS) sediments as represented by the alpha diversity metrics. Out of the total 303 amplicon sequence variants (ASVs) found at the genus level, 93 were unique to accumulated snow sediments and 97 were unique to exposed sediments. The bacterial community composition in accumulated snow was dominated by the phylum Actinobacteriota (24.7%). However, Pseudonocardia (11.9%), Crossiella (11%), and Rhodanobacter (9.1%) were the predominant genera. In contrast, in the exposed sediments, Bacteroidota (24.6%) was the most prevalent phylum, with Crossiella (17.1%), Rhodanobacter (11.1%), and Blastocatella (10%) as the most abundant genera. Metagenomic imputations revealed the abundance of gene families responsible for carbon metabolism, coping with environmental stresses through DNA repair mechanisms, and carbon fixation.

Autotrophy to Heterotrophy: Shift in Bacterial Functions During the Melt Season in Antarctic Cryoconite Holes

Microbes residing in cryoconite holes (debris, water, and nutrient-rich ecosystems) on the glacier surface actively participate in carbon and nutrient cycling. Not much is known about how these communities and their functions change during the summer melt-season when intense ablation and runoff alter the influx and outflux of nutrients and microbes. Here, we use high-throughput-amplicon sequencing, predictive metabolic tools and Phenotype MicroArray techniques to track changes in bacterial communities and functions in cryoconite holes in a coastal Antarctic site and the surrounding fjord, during the summer season. The bacterial diversity in cryoconite hole meltwater was predominantly composed of heterotrophs (Proteobacteria) throughout the season. The associated functional potentials were related to heterotrophic-assimilatory and -dissimilatory pathways. Autotrophic Cyanobacterial lineages dominated the debris community at the beginning and end of summer, while heterotrophic Bacteroidota- and Proteobacteria-related phyla increased during the peak melt period. Predictive functional analyses based on taxonomy show a shift from predominantly phototrophy-related functions to heterotrophic assimilatory pathways as the melt-season progressed. This shift from autotrophic to heterotrophic communities within cryoconite holes can affect carbon drawdown and nutrient liberation from the glacier surface during the summer. In addition, the flushing out and export of cryoconite hole communities to the fjord could influence the biogeochemical dynamics of the fjord ecosystem.

Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters

Metagenomic long-read sequencing is gaining popularity for various applications, including pathogen detection and microbiome studies. To analyze the large data created in those studies, software tools need to taxonomically classify the sequenced molecules and estimate the relative abundances of organisms in the sequenced sample. Because of the exponential growth of reference genome databases, the current taxonomic classification methods have large computational requirements. This issue motivated us to develop a new data structure for fast and memory-efficient querying of long reads. Here, we present Taxor as a new tool for long-read metagenomic classification using a hierarchical interleaved XOR filter data structure for indexing and querying large reference genome sets. Taxor implements several k-mer-based approaches, such as syncmers, for pseudoalignment to classify reads and an expectation-maximization algorithm for metagenomic profiling. Our results show that Taxor outperforms state-of-the-art tools regarding precision while having a similar recall for long-read taxonomic classification. Most notably, Taxor reduces the memory requirements and index size by >50% and is among the fastest tools regarding query times. This enables real-time metagenomics analysis with large reference databases on a small laptop in the field.

Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations

Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.

Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients

Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.

Biogeographic survey of soil bacterial communities across Antarctica

BACKGROUND

Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.

RESULTS

Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.

CONCLUSIONS

Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.

Microbial community composition of terrestrial habitats in East Antarctica with a focus on microphototrophs

The Antarctic terrestrial environment harbors a diverse community of microorganisms, which have adapted to the extreme conditions. The aim of this study was to describe the composition of microbial communities in a diverse range of terrestrial environments (various biocrusts and soils, sands from ephemeral wetlands, biofilms, endolithic and hypolithic communities) in East Antarctica using both molecular and morphological approaches. Amplicon sequencing of the 16S rRNA gene revealed the dominance of Chloroflexi, Cyanobacteria and Firmicutes, while sequencing of the 18S rRNA gene showed the prevalence of Alveolata, Chloroplastida, Metazoa, and Rhizaria. This study also provided a comprehensive assessment of the microphototrophic community revealing a diversity of cyanobacteria and eukaryotic microalgae in various Antarctic terrestrial samples. Filamentous cyanobacteria belonging to the orders Oscillatoriales and Pseudanabaenales dominated prokaryotic community, while members of Trebouxiophyceae were the most abundant representatives of eukaryotes. In addition, the co-occurrence analysis showed a prevalence of positive correlations with bacterial taxa frequently co-occurring together.

Microdiverse bacterial clades prevail across Antarctic wetlands

Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.

Structure and functions of a multireplicon genome of Antarctic Psychrobacter sp. ANT_H3: characterization of the genetic modules suitable for the construction of the plasmid-vectors for cold-active bacteria

Among Psychrobacter spp., there are several multireplicon strains, carrying more than two plasmids. Psychrobacter sp. ANT_H3 carries as many as 11 extrachromosomal replicons, which is the highest number in Psychrobacter spp. Plasmids of this strain were subjected to detailed genomic analysis, which enables an insight into the structure and functioning of this multireplicon genome. The replication and conjugal transfer modules of ANT_H3 plasmids were analyzed functionally to discover their potential for being used as building blocks for the construction of novel plasmid-vectors for cold-active bacteria. It was shown that two plasmids have a narrow host range as they were not able to replicate in species other than Psychrobacter, while remaining plasmids had a wider host range and were functional in various Alpha- and Gammaproteobacteria. Moreover, it was confirmed that mobilization modules of seven plasmids were functional, i.e., could be mobilized for conjugal transfer by the RK2 conjugation system. Auxiliary genes were also distinguished in ANT_H3 plasmids, including these encoding putative DNA-protecting protein DprA, multidrug efflux SMR transporter of EmrE family, glycine cleavage system T protein, MscS small-conductance mechanosensitive channel protein, and two type II restriction-modification systems. Finally, all genome-retrieved plasmids of Psychrobacter spp. were subjected to complex genome- and proteome-based comparative analyses showing that Antarctic replicons are significantly different from plasmids from other locations.

Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities

Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.

A Metagenomic Survey of Wood Decay Fungi in the Urban Trees of Singapore

Mature tropical urban trees are susceptible to root and trunk rot caused by pathogenic fungi. A metagenomic survey of such fungi was carried out on 210 soil and tissue samples collected from 134 trees of 14 common species in Singapore. Furthermore, 121 fruiting bodies were collected and barcoded. Out of the 22,067 OTUs (operational taxonomic units) identified, 10,646 OTUs had annotation information, and most were either ascomycetes (63.4%) or basidiomycetes (22.5%). Based on their detection in the diseased tissues and surrounding soils and/or the presence of fruiting bodies, fourteen basidiomycetes (nine Polyporales, four Hymenochaetales, one Boletales) and three ascomycetes (three species of Scytalidium) were strongly associated with the diseased trees. Fulvifomes siamensis affected the largest number of tree species surveyed. The association of three fungi was further supported by in vitro wood decay studies. Genetic heterogeneity was common in the diseased tissues and fruiting bodies (Ganoderma species especially). This survey identified the common pathogenic fungi of tropical urban trees and laid the foundation for early diagnosis and targeted mitigation efforts. It also illustrated the complexity of fungal ecology and pathogenicity.

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.

Antarctic fungi with antibiotic potential isolated from Fort William Point, Antarctica

The Antarctic continent is one of the most inhospitable places on earth, where living creatures, mostly represented by microorganisms, have specific physiological characteristics that allow them to adapt to the extreme environmental conditions. These physiological adaptations can result in the production of unique secondary metabolites with potential biotechnological applications. The current study presents a genetic and antibacterial characterization of four Antarctic fungi isolated from soil samples collected in Pedro Vicente Maldonado Scientific Station, at Fort William Point, Greenwich Island, Antarctica. Based on the sequences of the internal transcribed spacer (ITS) region, the fungi were identified as Antarctomyces sp., Thelebolus sp., Penicillium sp., and Cryptococcus gilvescens. The antibacterial activity was assessed against four clinical bacterial strains: Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, and Staphylococcus aureus, by a modified bacterial growth inhibition assay on agar plates. Results showed that C. gilvescens and Penicillium sp. have potential antibiotic activity against all bacterial strains. Interestingly, Thelebolus sp. showed potential antibiotic activity only against E. coli. In contrast, Antarctomyces sp. did not show antibiotic activity against any of the bacteria tested under our experimental conditions. This study highlights the importance of conservation of Antarctica as a source of metabolites with important biomedical applications.