Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations.

Klervi Crenn,Christian Jeanthon,Delphine Duffieux

doi:10.3389/fmicb.2018.02879

Abstract

Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community-level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and collection cultures, regarded here as short- and long-term associations, respectively. Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning-sequencing of 16S rRNA genes obtained from whole-genome amplification products. The prevalence of epibiotic bacteria was higher in cultures and dependent of the host species. Culture approaches demonstrated that both diatoms carry distinct bacterial communities in short- and long-term associations. Bacterial epibonts, commonly associated with phytoplankton, were repeatedly isolated from cells of diatom collection cultures but were not recovered from environmental cells. Our results suggest that in controlled laboratory culture conditions bacterial–diatom and bacterial–bacterial interactions select for a simplified, but specific, epibiotic microbiota shaped and adapted for long-term associations.

Highlights

Bacteria eukaryotic microalgae are the major components of the plankton in the upper and ocean layers and their metabolism largely controls pelagic energy flow and nutrient cycling (Falkowski et al, 2008)
Both culture-based and molecular approaches yielded generally nearly identical proportions of Chaetoceros cells colonized by bacteria. Both methods yielded different epibiont proportions in Thalassiosira. This was somewhat surprising because (i) the observed epibiont proportions were remarkably stable in the different Thalassiosira Roscoff Culture Collection (RCC) 2560 cultures used for epibiont isolation whatever the approach used and (ii) the high epibiont prevalences observed using the culture-based approach were consistent with that measured by scanning electron microsopy (Supplementary Table 1)
This may explain the differential proportions of diatom cells colonized by bacteria we found in cultures and in natural samples

Summary

Introduction

Bacteria eukaryotic microalgae are the major components of the plankton in the upper and ocean layers and their metabolism largely controls pelagic energy flow and nutrient cycling (Falkowski et al, 2008). The use of rRNA gene sequencing and barcoding approaches allowed establishing links between phytoplankton and bacterial community dynamics in natural communities (Rooney-Varga et al, 2005; Teeling et al, 2012) and culture collections (Schäfer et al, 2002; Jasti et al, 2005; Sapp et al, 2007). These partners often co-occur which lead to beneficial, neutral or parasitic interactions (Amin et al, 2012; Cooper and Smith, 2015; Seymour et al, 2017)

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