High-throughput metabarcoding of SAR11 assemblages from the southwest Atlantic shelf and arid Patagonia: richness and associated rank abundance distributions

Abstract

Background: Massively parallel sequencing of environmental DNA allows microbiological studies to be performed in greater detail than was possible with first-generation sequencing. For example, it facilitates the use of approaches hitherto largely applied to flora and fauna, such as rank abundance distribution (RAD) analyses.

Methods: Here, we set out to advance the knowledge on Ca. Pelagibacterales (SAR11) communities from southern South America using environmental sequences from the open ocean in the Argentine sea, the uncharted Engaño Bay, as well as a river and an oligohaline shallow lake from the Patagonian Steppe ecoregion. The structures of the SAR11 assemblages present in these ecosystems were dissected by direct and rarefaction-based estimates of species richness, and evaluations of the corresponding abundance distributions (ADs), which was addressed by RAD analyses.

Results: Microbial community composition analyses revealed that the studied SAR11 assemblages coexist with 27 bacterial phyla. SAR11 richness was in general very high, but ADs turned out to be highly uneven. The results were compatible with prior knowledge, and similar to that derived from point estimates of diversity. However, our comprehensive dissection allowed for more detailed quantitative comparisons to be made between the environments surveyed, and revealed differences regarding both richness and the underlying ADs.

Conclusions: Despite SAR11 assemblages being extremely rich, their ADs are very uneven. Richness and ADs can vary, not only between fresh and salt water, but also between oceanic and coastal marine environments. The obtained results provide insights on general topics such as adaptation and the contrast between marine and freshwater radiations.

Author summary

The SAR11 clade is likely the most abundant microbial lineage on earth. Here, we provide detailed analyses of the group’s richness and AD in poorly studied Southern microbiomes. This requires whole community composition analyses to be performed, which are also provided in conjunction with the SAR11-specific studies. In this way, the work describes unknown aspects of the diversity of an outstanding bacterial lineage and novel data on remote and relatively little-studied microbial communities.

Graphical abstract

Keywords

SAR11 / richness / species abundance distribution / rank abundance distribution / Patagonia / Argentina

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/10.15302/J-QB-023-0329.

ACKNOWLEDGEMENTS

This work was supported by grants PIP 2021–2023 11220200102657CO (CONICET), PICT 2020 series A-03643 (FONCyT), and PI 1657 (UNPSJB). LRJ and JMM are members of CONICET. Continuous support from civil association ArGen (Argentina Genetics) is most appreciated.

COMPLIANCE WITH ETHICS GUIDELINES

Conflicts of interest The authors Leandro R. Jones and Julieta M. Manrique declare that they have no conflict of interests.

This article does not contain any studies with human or animal subjects performed by any of the authors.

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