Microbial diversity within the Trichodesmium holobiont

Abstract

Nitrogen-fixing cyanobacteria in the genus Trichodesmium play a critical role in the productivity of the tropical and subtropical oligotrophic oceans. The ecological success of these populations is likely associated with the diverse microbial interactions occurring within the Trichodesmium holobiont, especially between Trichodesmium and heterotrophic bacterial epibionts. Yet, the composition of the Trichodesmium holobiont and the processes governing microbial assemblage are not well documented. Here, we used high-resolution 16S rDNA amplicon sequencing to examine the diversity of Trichodesmium and associated epibionts across different ocean regions and colony morphologies (puffs and rafts). Trichodesmium Clade I (i.e., T. thiebautii-like) dominated the colonies in all ocean basins regardless of morphology, although the Trichodesmium community structure significantly varied between morphologies in some regions. On average, Alphaproteobacteria (i.e., Thalassobius), Gammaproteobacteria (i.e., Pseudoalteromonas), Sphingobacteria (i.e., Microscilla and Vibrio) and Flavobacteria dominated the epibiont communities, but community composition and structure significantly differed between regions. Epibionts from the two colony morphologies were taxonomically and functionally distinct in the North Atlantic and North Pacific. These findings suggest that the colony types might define two distinct niches and that epibiont assemblage might be driven in part by selective processes, where epibionts are selected according to their influence on colony metabolism.

<i>Trichodesmium</i> physiological ecology and phosphate reduction in the western Tropical South Pacific

“…Trichodesmium samples were obtained with six hauls of a 130 µm mesh size net towed through surface sea water. Colonies were skimmed with a Pasteur pipette from the 15 surface layer of net towed samples and then washed two times with 0.2 µm sterile-filtered surface seawater on 5 µm, 47 mm polycarbonate filters with gentle vacuuming to remove non-tightly associated microorganisms. All colony samples were cleaned and processed within 15 minutes of collection.…”

“…1) using the MoBio Power Plant Pro DNA Isolation Kit (MoBio Laboratories, Inc., Carlsbad, CA, USA) following the manufacturer instructions. Genomic DNA extracts were sequenced at the Argonne 15 National Lab (Lemont, IL, USA) following a Trichodesmium consortium protocol previously described (Frischkorn et al, 2017 and functionally annotated after clustering into genome bins using MaxBin 2.0 with default parameters (Wu et al, 2015). Taxonomic partitioning of binned scaffolds was carried out after translation of each Suzek et al, 2007) with an e-10 value cut-off of 1x10 -3 .…”

“…Prokaryotic RNA was extracted and sequenced from samples obtained from SD2, SD6 and SD9 as well 15 as three samples from LDB ( Fig. 1) following a protocol described previously (Frischkorn et al, 2018).…”

“…4). In particular, the co-limitation marker genes and iron 15 responsive genes have relatively high expression. The metE (co-limitation) and isiA (iron limitation) markers have the 3 rd and 5 th highest average expression overall, following behind a gene encoding a photosynthetic reaction centre protein and an uncharacterized gene (Fig.…”

“…Trichodesmium, as well as the 2,982 OGs generated from the T. erythraeum IMS101 protein coding genes (Frischkorn et al, 2017 Trichodesmium does not exist in isolation, as filaments and colonies are associated with an assemblage of epibiotic microorganisms that co-occur ubiquitously in the environment (Lee et al, 2017;Rouco et al, 2016) and contribute a large amount of metabolic potential that could underpin success in oligotrophic, low nutrient environments (Frischkorn et al, 2017). Here, as in the western North Atlantic (Frischkorn et al, 2017), the large amount of unique, microbiome-only OGs (65,740), the low amount strategies where co-limitation patterns of expression are distinct from either iron or phosphate limitation individually.…”