Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 1-21-2020 Top-Down and Bottom-Up Controls on Microeukaryotic Diversity (i.e., Amplicon Analyses of SAR Lineages) and Function (i.e., Metatranscriptome Analyses) Assessed in Microcosm Experiments Jean David Grattepanche Smith College Laura A. Katz Smith College, [email protected] Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Grattepanche, Jean David and Katz, Laura A., "Top-Down and Bottom-Up Controls on Microeukaryotic Diversity (i.e., Amplicon Analyses of SAR Lineages) and Function (i.e., Metatranscriptome Analyses) Assessed in Microcosm Experiments" (2020). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/78 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] fmars-06-00818 January 9, 2020 Time: 18:21 # 1 ORIGINAL RESEARCH published: 21 January 2020 doi: 10.3389/fmars.2019.00818 Top-Down and Bottom-Up Controls on Microeukaryotic Diversity (i.e., Amplicon Analyses of SAR Lineages) and Function (i.e., Metatranscriptome Analyses) Assessed in Microcosm Experiments Edited by: Iliana B. Baums, Jean-David Grattepanche1† and Laura A. Katz1,2* Pennsylvania State University (PSU), United States 1 Department of Biological Sciences, Smith College, Northampton, MA, United States, 2 Program in Organismic Reviewed by: and Evolutionary Biology, University of Massachusetts, Amherst, MA, United States Yongyu Zhang, Qingdao Institute of Bioenergy and Bioprocess Technology (CAS), The availability of high-throughput sequencing (HTS) has transformed our understanding China of the diversity of microbial eukaryotes (i.e., protists) across diverse habitats. Yet relating Adriana Lopes Dos Santos, this biodiversity to function remains a challenge, particularly in the context of microbial Nanyang Technological University, Singapore food webs. Here we perform a set of microcosm experiments to evaluate the impact *Correspondence: of changing predator and prey concentrations on a marine protist community, focusing Laura A. Katz on SAR (Stramenopila, Alveolata, and Rhizaria) lineages. We combine an estimate of [email protected] taxonomic diversity through analysis of SSU-rDNA amplicons with metatranscriptomics, †Present address: Jean-David Grattepanche, a proxy for function. We assess changes in a community sampled from New England Department of Biology, Temple waters with varying concentrations of predators (copepods) and prey (phytoplankton University, Philadelphia, PA, <15 mm in size). The greatest impact observed is on the diversity and function United States of the small plankton (2–10 mm, nanoplankton) community in the presence of high Specialty section: prey abundance (i.e., bloom conditions). Many SAR taxa in the nanosized fraction This article was submitted to decrease with increasing phytoplankton abundance, while ciliates (from both the Marine Molecular Biology and Ecology, nano- and microsized fractions) increase. A large number of transcripts and function a section of the journal estimates in the nanoplankton decreased during our simulated phytoplankton bloom. Frontiers in Marine Science We also find evidence of an interaction between increasing phytoplankton and copepod Received: 01 July 2019 Accepted: 18 December 2019 abundances on the microsized planktonic community, consistent with the hypothesis Published: 21 January 2020 that phytoplankton and copepods exert bottom-up control and top-down control on the Citation: microsized protists, respectively. Together our analyses suggest that community function Grattepanche J-D and Katz LA [i.e., diversity of gene families (GFs)] remains relatively stable, while the functions at the (2020) Top-Down and Bottom-Up Controls on Microeukaryotic Diversity species level (i.e., transcript diversity within GFs) show a substantial reduction of function (i.e., Amplicon Analyses of SAR under bloom conditions. Our study demonstrated that interactions within plankton food Lineages) and Function (i.e., Metatranscriptome Analyses) webs are complex, and that the relationships between diversity and function for marine Assessed in Microcosm Experiments. microeukaryotes remain poorly understood. Front. Mar. Sci. 6:818. doi: 10.3389/fmars.2019.00818 Keywords: protists, phytoplankton bloom, copepods, gene expression, nanoplankton, microplankton Frontiers in Marine Science| www.frontiersin.org 1 January 2020| Volume 6| Article 818 fmars-06-00818 January 9, 2020 Time: 18:21 # 2 Grattepanche and Katz Microeukaryotic Diversity and Function INTRODUCTION during bloom events (Rosetta and McManus, 2003; Grattepanche et al., 2011a; Monchy et al., 2012). Based on these analyses, Microbes dominate biodiversity and are responsible for key microheterotrophs are assumed to be the primary consumers ecosystem functions. They can function as heterotrophs, of phytoplankton of small size, with bacteria playing a autotrophs, or mixotrophs, and they can be free-living, parasitic negligible role (García-Martín et al., 2017). While still subject (detrimental for host), or mutualistic (beneficial for host). to debate, phytoplankton spring blooms have been assumed Thus, microbes have critical roles for other organisms including to be linked to an excess in nutrients at the end of humans (e.g., microbiome, including gut flora), other animals the winter (remineralization by bacteria and upwelling), (e.g., coral), and plants (e.g., mycorrhiza). While we know that combined with a lack of control by predators that include microbes are important, we still have only limited knowledge heterotrophic protists and higher trophic levels. On the other about eukaryotic microbes and their functions (e.g., what are the hand, microheterotrophs are efficient grazers when blooms main factors driving their diversity). This is in contrast to the start to decline (Laws et al., 1988; Archer et al., 2000). many tools that have been developed and used to explore the As such, questions remain concerning how the community diversity and function of bacteria. Here, we use some of these structure and functions change in relation to increasing tools, including metatranscriptomics, and amplicon analyses, phytoplankton abundance. to look at the marine planktonic food web and the roles of Metatranscriptomics has mainly been deployed to study eukaryotic microbes. bacterial functions such as the microbiomes of organisms as In marine food webs, the importance of microbes for diverse as humans (Franzosa et al., 2014) and termites (Tartar transfer of energy from bacteria to higher trophic levels is well- et al., 2009), or in marine systems (Gifford et al., 2011) established [reviewed in Azam et al.(1983), Fenchel(1988), and in response to environmental changes such as oil spills Worden et al.(2015), Edgcomb(2016), and Menden-Deuer (Mason et al., 2012; Rivers et al., 2013). The studies looking and Kiørboe(2016)]. Several studies have characterized the at eukaryotic metatranscriptomes are rare. One reason for this marine plankton diversity on a large scale (e.g., Tara Ocean lack of studies is the paucity of databases of eukaryotic gene for plankton in the photic zone, Malaspina for the aphotic functions. Current databases contain mainly bacterial functions zone and others; Irigoien et al., 2004; de Vargas et al., 2015; or functions related to diseases, which result in the majority of Pernice et al., 2016) and show a geographical distribution the environmental eukaryotic transcripts not being annotated of the plankton related to oceanic basins. Other studies (sometimes >80% of the transcripts cannot be annotated; Damon have looked at patterns on a smaller scale (from meters to et al., 2012; Lesniewski et al., 2012; Cooper et al., 2014). kilometers; e.g., Grattepanche et al., 2014, 2016a,b; Mousing To study eukaryotic metatranscriptomes, given the paucity in et al., 2016) and find that distance alone does not explain available microbial eukaryote genomes (reviewed in del Campo the patterns of diversity. One of the likely reasons for the et al., 2014), authors have focused on clades with reference mismatch is that these studies assess different processes: studies genomes such as diatoms (Alexander et al., 2015) and fungi at smaller scales tend to be more directly impacted by species- (Bailly et al., 2007). specific interactions and functions expressed by each member Here, we use a microcosm approach and high-throughput of the community, while the larger scale studies are designed molecular tools, combining amplicon and metatranscriptomic to look at overall ecosystem processes such as the impact analyses, to assess the impact of phytoplankton (prey) and of climate change. copepods (predators) on the rest of the planktonic community. Other studies have looked at species-specific relationships To study protist diversity, we use primers designed to amplify between prey and predators, such as between microzooplankton the SAR (Stramenopila, Alveolata, Rhizaria; Grattepanche et al., and phytoplankton or between copepods and microzooplankton. 2018; Sisson et al., 2018) community as this includes many These studies show that microzooplankton such as ciliates and major marine clades such as dinoflagellates, diatoms, and ciliates. dinoflagellates are efficient grazers of phytoplankton of small We added phytoplankton (i.e., prey)