Tropical South America Diatom Database: a tool for studying the macroecology of microorganisms

Abstract

Determining the mechanisms of community assembly forms the foundation of biogeography and community ecology. Studies of the biodiversity and distribution of Neotropical macro-organisms have revealed the roles of environmental, spatial, and historical factors in structuring communities at different spatial and temporal scales. The role of these factors for species and communities of microorganisms are still poorly understood. Diatoms are a very species-rich group of algae, widely distributed, and sensitive to environmental variation because of their position at the base of aquatic food webs. Here, we present the Tropical South American Diatom Database (TSADB), which contains geographical and ecological information on diatom species across lentic and lotic environments, including predictors that describe local (limnological) and regional (geo-climatic) factors. The open access database can be used to ask fundamental questions in macroecology, including testing foundational theories of metacommunity ecology and biogeography, and evaluating the sensitivity of species and communities to the rapid environmental changes characteristic of tropical regions. The TSADB includes diatom taxa from 437 samples from 326 sites distributed across 26 regions (0–5,070 m a.s.l, and between 8°N–35°S; 58–90°W). In addition, long-term, diatom-based paleolimnological records are presented as a complementary tool for identifying geographically well-covered regions with modern and palaeo-datasets. We describe the TSADB structure and functionality, together with the R codes for data manipulation and visualization. Each of the 26 study regions is represented by three data matrices: sampling site information, environmental variables (limnology, climate, and landscape), and diatom community data (relative abundance or presence/absence). Access to data and future additions is through publicly available repositories and a guide to contributors, respectively. Thus, it offers ample opportunities to complement existing databases on diatoms, allowing optimal usage of TSADB by scientists including diatomists, limnologists, and aquatic ecologists.

Keywords:

• diatoms
• database
• neotropics
• metacommunity
• paleolimnology
• biogeography

Acknowledgements

We thank two anonymous reviewers whose comments vastly improved the manuscript. We thank the Ministerio del Ambiente in Ecuador for permitting us to sample in its territory (151-2017-DPAA/MA and 008-ICDPACH-MAE-2017).We are enormously indebted to all the contributors of the South American diatom database including W. Gosling, M. McGlue, B. Valencia, M. Bush, F. Mayle, J. P. Bradbury, J. P. Smol and N. Michelutti.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

All diatom and environmental datasets, and R scripts to perform analyses and visualization of the TSADB are available from GitHub (https://github.com/xbenitogranell/diatoms-biogeography-southamerica). In addition, the TSADB has been stored in a zip folder at Dryad (https://do.org/10.5061/dryad.jm63xsjbs) and Zenodo (https://do.org/10.5281/zenodo.5415446). Note: GitHub repository represents the dynamic portal to access the TSADB, while Dryad and Zenodo are permanent repositories.

Supplemental data

Supplemental data for this article can be accessed here https://do.org/10.1080/0269249X.2022.2078429.

Additional information

Funding

XB has received funding from the postdoctoral fellowships programme Beatriu de Pinós, funded by the Secretary of Universities and Research (Government of Catalonia) and by the Horizon 2020 programme of research and innovation of the European Union under the Marie Sklodoska-Curie grant agreement No 801370. This study was partly funded by National Geographic 8672-09, NSF EAR-1338694, and NASA 15-BIODIV15-0013 grants SF.