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Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria

  • Microbiology of Aquatic Systems
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Abstract

Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism’s distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.

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Data Availability

The 16S rRNA amplicon results have been deposited in the NCBI repository under accession number PRJNA411849.

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Acknowledgments

We are grateful to Prof. Armando Vieira for providing the samples from the Biota-FAPESP project and to his lab team Cilene C. Mori, Fabrício S. Maeccheri, Guilherme P. de Moraes, Helena H. Vieira, Ingritt C. Moreira, Letícia P. Tessarolli, Lucas S. Tiberti, Luiz A. Joaquim, Naiara C. P. Archanjo, Rodrigo V. de Mello, and Thaís G. da Silva, who participated in the field sampling and performed physio-chemical analyses. We also thank the LMSeq Laboratory of UNESP for DNA sequencing. Adriano Caliman gratefully acknowledges continuous funding through Research Productivity Grants provided by CNPq.

Funding

This research was funded by the São Paulo Research Foundation - FAPESP (projects 2014/14139-3 and 2011/50054-4). EMB was funded by a CAPES scholarship (grant 001); HS was supported by CNPq (grant 309514/2017-7).

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Authors and Affiliations

  1. Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil

    Erick Mateus-Barros, Michaela L. de Melo & Hugo Sarmento

  2. Post Graduate Program in Ecology and Natural Resources (PPG-ERN), UFSCar, São Carlos, SP, 13565-905, Brazil

    Erick Mateus-Barros

  3. Département Des Sciences Biologiques, Université du Québec à Montréal, Montreal, Canada

    Michaela L. de Melo

  4. Department of Botany, Laboratory of Phycology, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil

    Inessa L. Bagatini

  5. Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-900, Brazil

    Adriano Caliman

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  1. Erick Mateus-Barros
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  2. Michaela L. de Melo
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  3. Inessa L. Bagatini
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Correspondence to Erick Mateus-Barros.

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The R scripts used in these analyses can be found at: https://github.com/LMPB/Occupancy-Frequency-Distribution

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Mateus-Barros, E., de Melo, M.L., Bagatini, I.L. et al. Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria. Microb Ecol 81, 26–35 (2021). https://doi.org/10.1007/s00248-020-01560-3

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