Bacterial diversity of the rock-water interface in an East Antarctic freshwater ecosystem, Lake Tawani(P)†

Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base "St. Kliment Ohridski" on Livingston Island, Antarctica

As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.

Virome analysis in lakes of the South Shetland Islands, Antarctica - 2020

Polar freshwater ecosystems are characterized by a distinct microbiota. However, little is known about viral diversity and abundance, especially regarding the ecology of RNA viruses. We used shotgun metagenomic analysis on samples from Antarctic ecosystems, and report here the characterization of the virome fraction, from different lakes located in the South Shetland Islands (Penguin, Ardley, Deception and King George Island) in the Peninsula Antarctica, in the summer season 2020. DNA viruses (99.4 %) prevailed over RNA viruses (0.6 %) in the lake samples. Six viral orders were identified in the metagenomic libraries: Caudovirales (dsDNA), which was prevalent in most lakes; Picornavirales (ssRNA+); Sobelivirales (ssRNA+); Tolivirales (ssRNA+); Petitvirales (ssDNA) and Baphyvirales (ssDNA), including eight viral families (Herelleviridae, Siphoviridae, Myoviridae, Microviridae, Marnaviridae, Bacilladnaviridae, Barnaviridae and Tombusviridae) and several other, mainly non-classified ssRNA⁽⁺⁾ viruses in the lakes of Ardley Island. Bacteriophages (dsDNA) (Herelleviridae family) infecting the phylum Firmicutes and Siphoviridae were predominant in most lakes evaluated. Functional analysis demonstrated a prevalence of unknown proteins (68 %) in the virome. Our prospective study provides virome analysis data from different lakes in the South Shetland Islands, Antarctica, opening exploratory lines for future research related to the biodiversity and viral ecology in this extreme ecosystem.

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

Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.

Elasmobranch microbiomes: emerging patterns and implications for host health and ecology

Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has now begun to explore the role of body-associated microbiomes in shaping elasmobranch health. Here, we review the burgeoning efforts to understand elasmobranch microbiomes, highlighting microbiome variation among gastrointestinal, oral, skin, and blood-associated niches. We identify major bacterial lineages in the microbiome, challenges to the field, key unanswered questions, and avenues for future work. We argue for prioritizing research to determine how microbiomes interact mechanistically with the unique physiology of elasmobranchs, potentially identifying roles in host immunity, disease, nutrition, and waste processing. Understanding elasmobranch–microbiome interactions is critical for predicting how sharks and rays respond to a changing ocean and for managing healthy populations in managed care.

Understanding the Dependence of Micropollutant Biotransformation Rates on Short-Term Temperature Shifts

Temperature is a key factor that influences chemical biotransformation potential and rates, on which exposure and fate models rely to predict the environmental (micro)pollutant fate. Arrhenius-based models are currently implemented in environmental exposure assessment to adapt biotransformation rates to actual temperatures, assuming validity in the 0-30 °C range. However, evidence on how temperature shifts affect the physicochemical and microbial features in biological systems is scarce, questioning the validity of the existing modeling approaches. In this work, laboratory-scale batch assays were designed to investigate how a mixed microbial community responds to short-term temperature shifts, and how this impacts its ability to biotransform a range of structurally diverse micropollutants. Our results revealed three distinct kinetic responses at temperatures above 20 °C, mostly deviating from the classic Arrhenius-type behavior. Micropollutants with similar temperature responses appeared to undergo mostly similar initial biotransformation reactions, with substitution-type reactions maintaining Arrhenius-type behavior up to higher temperatures than oxidation-type reactions. Above 20 °C, the microbial community also showed marked shifts in both composition and activity, which mostly correlated with the observed deviations from Arrhenius-type behavior, with compositional changes becoming a more relevant factor in biotransformations catalyzed by more specific enzymes (e.g., oxidation reactions). Our findings underline the need to re-examine and further develop current environmental fate models by integrating biological aspects, to improve accuracy in predicting the environmental fate of micropollutants.

Diversity of Cultivable Microbes From Soil of the Fildes Peninsula, Antarctica, and Their Potential Application

To explore the diversity and application potential of Antarctic microorganisms, 1208 strains bacteria and fungi were isolated from 5 samples collected from the Fildes Peninsula during China’s 27th and 31st Antarctic expeditions. By using 16S and ITS sequence similarity alignment, 83 strains bacteria belonging to 20 genera and 30 strains fungi belonging to 7 genera were identified. Among them, 1 strains bacteria and 6 strains fungi showed low sequence similarity to the database, suggesting that they might be novel species. Physiological-biochemical characteristics showed that the identified bacteria could utilize many kinds of carbohydrates and that the identified fungi could produce several kinds of extracellular enzymes. The fungal strain MS-19, identified as Aspergillus sydowii, possesses the potential to produce antifungal activity agents based on an activity-guided approach. Further isolation yielded four polyketones: versicone A (1), versicone B (2), 4-methyl-5,6-dihydro-2H-pyran-2-one (3), and (R)-(+)-sydowic acid (4). It should be noted that 1 displayed strong activity against Candida albicans, with an MIC value of 3.91 μg/mL.

Prokaryotic Diversity and Composition of Sediments From Prydz Bay, the Antarctic Peninsula Region, and the Ross Sea, Southern Ocean

The V3–V4 hypervariable regions of the 16S ribosomal RNA gene were analyzed to assess prokaryotic diversity and community compositions within 19 surface sediment samples collected from three different regions (depth: 250–3,548 m) of Prydz Bay, the Antarctic Peninsula region, and the Ross Sea. In our results, we characterized 1,079,709 clean tag sequences representing 43,227 operational taxonomic units (OTUs, 97% similarity). The prokaryotic community distribution exhibited obvious geographical differences, and the sequences formed three distinct clusters according to the samples’ origins. In general, the biodiversity of Prydz Bay was higher than those of the Antarctic Peninsula region and the Ross Sea, and there were similar prokaryotic communities in different geographic locations. The most dominant clades in the prokaryotic communities were Proteobacteria, Bacteroidetes, Thaumarchaeota, Oxyphotobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, Fusobacteria, and Planctomycetes, but unique prokaryotic community compositions were found in each of the sampling regions. Our results also demonstrated that the prokaryotic diversity and community distribution were mainly influenced by geographical and physicochemical factors, such as Zn, V, Na, K, water depth, and especially geographical distance (longitude variation of sample location) and Ba ion content. Moreover, geochemical factors such as nutrient contents (TC, P, and Ca) also played important roles in prokaryotic diversity and community distribution. This represents the first report that Ba ion content has an obvious effect on prokaryotic diversity and community distribution in Southern Ocean sediments.

Source Environments of the Microbiome in Perennially Ice-Covered Lake Untersee, Antarctica

Ultra-oligotrophic Lake Untersee is among the largest and deepest surface lakes of Central Queen Maud Land in East Antarctica. It is dammed at its north end by the Anuchin Glacier and the ice-cover dynamics are controlled by sublimation - not melt - as the dominating ablation process and therefore surface melt during austral summer does not provide significant amounts of water for recharge compared to subsurface melt of the Anuchin Glacier. Several studies have already described the structure and function of the microbial communities within the water column and benthic environments of Lake Untersee, however, thus far there have been no studies that examine the linkages between the lake ecosystem with that of the surrounding soils or the Anuchin Glacier. The glacier may also play an important role as a major contributor of nutrients and biota into the lake ecosystem. Based on microbial 16S rRNA amplicon sequencing, we showed that the dominant bacterial signatures in Lake Untersee, the Anuchin Glacier and its surrounding soils were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Aerosol and local soil depositions on the glacier surface resulted in distinct microbial communities developing in glacier ice and cryoconite holes. Based on a source tracking algorithm, we found that cryoconite microbial assemblages were a potential source of organisms, explaining up to 36% of benthic microbial mat communities in the lake. However, the major biotic sources for the lake ecosystem are still unknown, illustrating the possible importance of englacial and subglacial zones. The Anuchin Glacier may be considered as a vector in a biological sense for the bacterial colonization of the perennially ice-covered Lake Untersee. However, despite a thick perennial ice cover, observed "lift-off" microbial mats escaping the lake make a bidirectional transfer of biota plausible. Hence, there is an exchange of biota between Lake Untersee and connective habitats possible despite the apparent sealing by a perennial ice cover and the absence of moat areas during austral summer.

Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains

A detailed understanding of microbial ecology in different supraglacial habitats is important due to the unprecedented speed of glacier retreat. Differences in bacterial diversity and community structure between glacial snow and glacial soil on the Chongce Ice Cap were assessed using 454 pyrosequencing. Based on rarefaction curves, Chao1, ACE, and Shannon indices, we found that bacterial diversity in glacial snow was lower than that in glacial soil. Principal coordinate analysis (PCoA) and heatmap analysis indicated that there were major differences in bacterial communities between glacial snow and glacial soil. Most bacteria were different between the two habitats; however, there were some common bacteria shared between glacial snow and glacial soil. Some rare or functional bacterial resources were also present in the Chongce Ice Cap. These findings provide a preliminary understanding of the shifts in bacterial diversity and communities from glacial snow to glacial soil after the melting and inflow of glacial snow into glacial soil.

Bacterial Community Structures in Freshwater Polar Environments of Svalbard

Two thirds of Svalbard archipelago islands in the High Arctic are permanently covered with glacial ice and snow. Polar bacterial communities in the southern part of Svalbard were characterized using an amplicon sequencing approach. A total of 52,928 pyrosequencing reads were analyzed in order to reveal bacterial community structures in stream and lake surface water samples from the Fuglebekken and Revvatnet basins of southern Svalbard. Depending on the samples examined, bacterial communities at a higher taxonomic level mainly consisted either of Bacteroidetes, Betaproteobacteria, and Microgenomates (OP11) or Planctomycetes, Betaproteobacteria, and Bacteroidetes members, whereas a population of Microgenomates was prominent in 2 samples. At the lower taxonomic level, bacterial communities mostly comprised Microgenomates, Comamonadaceae, Flavobacteriaceae, Legionellales, SM2F11, Parcubacteria (OD1), and TM7 members at different proportions in each sample. The abundance of OTUs shared in common among samples was greater than 70%, with the exception of samples in which the proliferation of Planctomycetaceae, Phycisphaeraceae, and Candidatus Methylacidiphilum spp. lowered their relative abundance. A multi-variable analysis indicated that As, Pb, and Sb were the main environmental factors influencing bacterial profiles. We concluded that the bacterial communities in the polar aquatic ecosystems examined mainly consisted of freshwater and marine microorganisms involved in detritus mineralization, with a high proportion of zooplankton-associated taxa also being identified.

Bacterial community composition in the water column of the deepest freshwater Lake Baikal as determined by next-generation sequencing

The composition of bacterial communities in Lake Baikal in different hydrological periods and at different depths (down to 1515 m) has been analyzed using pyrosequencing of the 16S rRNA gene V3 variable region. Most of the resulting 34 562 reads of the Bacteria domain have clustered into 1693 operational taxonomic units (OTUs) classified with the phyla Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, Acidobacteria and Cyanobacteria. It has been found that their composition at the family level and relative contributions to bacterial communities distributed over the water column vary depending on hydrological period. The number of OTUs and the parameters of taxonomic richness (ACE, Chao1 indices) and diversity (Shannon and inverse Simpson index) reach the highest values in water layers. The composition of bacterial communities in these layers remains relatively constant, whereas that in surface layers differs between hydrological seasons. The dynamics of physicochemical conditions over the water column and their relative constancy in deep layers are decisive factors in shaping the pattern of bacterial communities in Lake Baikal.