Exploring bacteria–diatom associations using single-cell whole genome amplification

Abstract

Diatoms are responsible for a large fraction of oceanic and freshwater biomass production and are critically important for sequestration of carbon to the deep ocean. As with most surfaces present in aquatic systems, bacteria colonize the exterior of diatom cells, and they interact with the diatom and each other. The ecology of diatoms may be better explained by conceptualizing them as composite organisms consisting of the host cell and its bacterial associates. Such associations could have collective properties that are not predictable from the properties of the host cell alone. Past studies of these associations have employed culture-based, whole-population methods. In contrast, we examined the composition and variability of bacterial assemblages attached to individual diatoms. Samples were collected in an oligotrophic system (Station ALOHA, 22°45' N, 158°00' W) at the deep chlorophyll maximum. Forty eukaryotic host cells were isolated by flow cytometry followed by multiple displacement amplification, including 26 Thalassiosira spp., other diatoms, dinoflagellates, coccolithophorids, and flagellates. Bacteria were identified by amplifying, cloning, and sequencing 16S rDNA using primers that select against chloroplast 16S rDNA. Bacterial sequences were recovered from 32 of 40 host cells, and from parallel samples of the free-living and particle-associated bacteria. Bacterial assemblages varied substantially even among closely related host cells. Host cells and the free-living and particle-associated samples can be placed into distinct groups based on the phylogenetic relatedness of their associated bacteria, rather than the identity of the host cell. As yet, the functional implications of these groups are unknown.KEY WORDS: Bacterioplankton diversity · Marine diatoms · Algal-bacterial interaction · Micro environment · Multiple displacement amplification · Single-cell Resale or republication not permitted without written consent of the publisher

Response of diatom‐associated bacteria to host growth state, nutrient concentrations, and viral host infection in a model system

“…In contrast to our previous work on the attached bacteria of field-collected single diatom cells (Baker and Kemp, 2014), the two major phylotypes associated with Chaetoceros sp. KBDT20 were Alteromonas and Marinobacter, two genera previously reported to be associated with algal hosts including diatoms (Amin et al, 2012a, b).…”

“…with recurrence and relative abundance of each phylotype. In our previous work, we found a maximum of 61 bacterial cells attached to a single field‐collected diatom cell (mean of 24 bacterial cells per diatom), but a maximum of 11 different bacterial OTUs co‐occurring on one diatom (Baker and Kemp, ). This may indicate that some free‐living bacteria were carried over during the original isolation.…”

Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible

“…Notably, studies addressing bacterial community assembly resulting from interactions between two microscopic players (i.e., phytoplankton and seawater bacteria) are challenging due to the microscopic scale at which they occur. The only studies to date, comparing bacterial assemblages on individual cells of congeneric diatoms obtained from natural waters, found that recovered bacterial phylotypes were extremely diverse and rarely shared across individual diatom cells [27,28], potentially supporting a lottery assembly model.…”

A fluorescence‐activated cell sorting subsystem for the Imaging FlowCytobot

“…Cell sorters typically divert cells within a defined flow cytometric parameter space (i.e., defined by fluorescence and/or light scattering measurements) into a holding container; the cells within the holding container can then be analyzed further (Chisholm et al 1988a). Cell sorting has been used in combination with a variety of chemical analyses to better understand biogeochemical cycling (Fawcett et al 2011;Lomas et al 2011), to delve into interactions between bacteria and phytoplankton (Thompson et al 2012;Baker and Kemp 2014), and to investigate intra-species genetic variability (Kashtan et al 2014). With advances in single-cell genomics, transcriptomics, and cell sorting technologies, it is now possible to conduct analyses of individual sorted cells that have been isolated from cultures or environmental samples (Baker and Kemp 2014;Kashtan et al 2014;Luo et al 2014;Thrash et al 2014).…”