Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes

Phuongan Dam,Konstantinos T Konstantinidis,Chengwei Luo,Luis M Rodriguez-R,Janet Hatt,Despina Tsementzi,Eberhard O Voit

doi:10.1038/s41598-020-58769-y

Phuongan Dam, Konstantinos T Konstantinidis + Show 5 more

Open Access

https://doi.org/10.1038/s41598-020-58769-y

Copy DOI

Journal: Scientific Reports	Publication Date: Feb 12, 2020
Citations: 14	License type: open-access

Affiliation: Georgia Institute of Technology

Abstract

Lake Lanier (Georgia, USA) is home to more than 11,000 microbial Operational Taxonomic Units (OTUs), many of which exhibit clear annual abundance patterns. To assess the dynamics of this microbial community, we collected time series data of 16S and 18S rRNA gene sequences, recovered from 29 planktonic shotgun metagenomic datasets. Based on these data, we constructed a dynamic mathematical model of bacterial interactions in the lake and used it to analyze changes in the abundances of OTUs. The model accounts for interactions among 14 sub-communities (SCs), which are composed of OTUs blooming at the same time of the year, and three environmental factors. It captures the seasonal variations in abundances of the SCs quite well. Simulation results suggest that changes in water temperature affect the various SCs differentially and that the timing of perturbations is critical. We compared the model results with published results from Lake Mendota (Wisconsin, USA). These comparative analyses between lakes in two very different geographical locations revealed substantially more cooperation and less competition among species in the warmer Lake Lanier than in Lake Mendota.

Highlights

The health of our lakes is of utmost importance, especially if they serve directly or indirectly as reservoirs for our water and food supply
Adapting modeling strategies similar to those applied to the Lake Mendota data, we present here modeling results for Lake Lanier, including the effects of pairwise interactions between bacterial sub-communities and the effects of environmental factors on the seasonal abundances of each sub-community
Recent metagenomic sequencing technologies have advanced our understanding of the multiplicity and complexity of Operational Taxonomic Units (OTUs) in shared environments

Summary

Introduction

The health of our lakes is of utmost importance, especially if they serve directly or indirectly as reservoirs for our water and food supply. Lake Lanier is a large water reservoir that provides drinking water for about 5 Million people It contains in its surficial photic zone over 11,000 microbial Operational Taxonomic Units (OTUs). We measured the OTU abundances recurrently between 2010 and 2015, which resulted in a large dataset containing measurements at 29 time points that capture the bacterial community dynamics of the abundant species in Lake Lanier. Adapting modeling strategies similar to those applied to the Lake Mendota data, we present here modeling results for Lake Lanier, including the effects of pairwise interactions between bacterial sub-communities and the effects of environmental factors on the seasonal abundances of each sub-community. The proposed model provides a flexible framework for integrating available data into a single computational structure, identifying important environmental factors, characterizing dynamically changing, asymmetric, bi-directional species-species interactions of interest, and performing thought experiments regarding the effects of slight perturbations in the conditions affecting the lake. The comparison of results between lakes offers novel insights into the relationships between bacterial communities and environmental factors, as well as the prevalence of cooperation or competition among bacterial species

Methods

Results

Conclusion