Dataset Information

Phages Actively Challenge Niche Communities in Antarctic Soils.

ABSTRACT: By modulating the structure, diversity, and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients, and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold deserts, relatively little is known regarding the precise ecological mechanisms. Here, we provide the first evidence of widespread antiphage innate immunity in Antarctic environments using metagenomic sequence data from hypolith communities as model systems. In particular, immunity systems such as DISARM and BREX are shown to be dominant systems in these communities. Additionally, we show a direct correlation between the CRISPR-Cas adaptive immunity and the metavirome of hypolith communities, suggesting the existence of dynamic host-phage interactions. In addition to providing the first exploration of immune systems in cold deserts, our results suggest that phages actively challenge niche communities in Antarctic polar deserts. We provide evidence suggesting that the regulatory role played by phages in this system is an important determinant of bacterial host interactions in this environment.IMPORTANCE In Antarctic environments, the combination of both abiotic and biotic stressors results in simple trophic levels dominated by microbiomes. Although the past two decades have revealed substantial insights regarding the diversity and structure of microbiomes, we lack mechanistic insights regarding community interactions and how phages may affect these. By providing the first evidence of widespread antiphage innate immunity, we shed light on phage-host dynamics in Antarctic niche communities. Our analyses reveal several antiphage defense systems, including DISARM and BREX, which appear to dominate in cold desert niche communities. In contrast, our analyses revealed that genes which encode antiphage adaptive immunity were underrepresented in these communities, suggesting lower infection frequencies in cold edaphic environments. We propose that by actively challenging niche communities, phages play crucial roles in the diversification of Antarctic communities.

SUBMITTER: Bezuidt OKI

PROVIDER: S-EPMC7205518 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Phages Actively Challenge Niche Communities in Antarctic Soils.

Bezuidt Oliver K I OKI Lebre Pedro Humberto PH Pierneef Rian R León-Sobrino Carlos C Adriaenssens Evelien M EM Cowan Don A DA Van de Peer Yves Y Makhalanyane Thulani P TP

mSystems 20200505 3

By modulating the structure, diversity, and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients, and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold deserts, relatively little is known regarding the precise ecological mechanisms. Here, we provide the first evidence of widespread antiphage innate im ...[more]

PMID: 32371471

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Project description:Ice-free areas represent less than 1% of the Antarctic surface. However, climate change models predict a significant increase in temperatures in the coming decades, triggering a relevant reduction of the ice-covered surface. Microorganisms, adapted to the extreme and fluctuating conditions, are the dominant biota. In this article we analyze the diversity and composition of soil bacterial communities in 52 soil samples on three scales: (i) fine scale, where we compare the differences in the microbial community between top-stratum soils (0-2 cm) and deeper-stratum soils (5-10 cm) at the same sampling point; (ii) medium scale, in which we compare the composition of the microbial community of top-stratum soils from different sampling points within the same sampling location; and (iii) coarse scale, where we compare communities between comparable ecosystems located hundreds of kilometers apart along the Antarctic Peninsula. The results suggest that in ice-free soils exposed for longer periods of time (millennia) microbial communities are significantly different along the soil profiles. However, in recently (decades) deglaciated soils the communities are not different along the soil profile. Furthermore, the microbial communities found in soils at the different sampling locations show a high degree of heterogeneity, with a relevant proportion of unique amplicon sequence variants (ASV) that appeared mainly in low abundance, and only at a single sampling location. The Core90 community, defined as the ASVs shared by 90% of the soils from the 4 sampling locations, was composed of 26 ASVs, representing a small percentage of the total sequences. Nevertheless, the taxonomic composition of the Core80 (ASVs shared by 80% of sampling points per location) of the different sampling locations, was very similar, as they were mostly defined by 20 common taxa, representing up to 75.7% of the sequences of the Core80 communities, suggesting a greater homogeneity of soil bacterial taxa among distant locations.

Project description:The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability. IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.

Dataset Information

Phages Actively Challenge Niche Communities in Antarctic Soils.

Publications

Phages Actively Challenge Niche Communities in Antarctic Soils.

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