Weitz
Joshua S.
Weitz
Joshua S.
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ArticleA primer for microbiome time-series analysis(Frontiers Media, 2020-04-21) Coenen, Ashley R. ; Hu, Sarah K. ; Luo, Elaine ; Muratore, Daniel ; Weitz, Joshua S.Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.
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ArticleDisentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre(Nature Research, 2024-03-07) Beckett, Stephen J. ; Demory, David ; Coenen, Ashley R. ; Casey, John R. ; Dugenne, Mathilde ; Follett, Christopher L. ; Connell, Paige ; Carlson, Michael C. G. ; Hu, Sarah K. ; Wilson, Samuel T. ; Muratore, Daniel ; Rodriguez-Gonzalez, Rogelio A. ; Peng, Shengyun ; Becker, Kevin W. ; Mende, Daniel R. ; Armbrust, E. Virginia ; Caron, David A. ; Lindell, Debbie ; White, Angelicque E. ; Ribalet, Francois ; Weitz, Joshua S.Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. We find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics.