Introduction
Marine protists encompass a large and heterogeneous community
representing the majority of the eukaryotic diversity in the oceans
(Worden et al. 2015). They include primary producers
(autotrophs), heterotrophs (phagotrophs and parasitic), and a
substantial collection of lineages exhibiting varying degrees of
mixotrophic strategies (Mitra et al. 2016). These groups occupy
distinct niches in the marine food web, playing essential roles in
biogeochemical cycles (Mitra et al. 2014; Worden et al.2015). They are responsible for ~50% of annual
planktonic photosynthetic primary productivity (PP), of which they
consume ~66%, plus an additional 10% of bacterial PP
(Calbet & Landry 2004; Steinberg & Landry 2017). Recent applications
of molecular tools such as metabarcoding (Choi et al. 2020; de
Vargas et al. 2015), metagenomics and single cell genomics
(Latorre et al. 2021), have significantly sharpened our
understanding of protist diversity, distributions, and functionality,
from basic trophic modes to complex metabolic pathways, and emphasized
their importance in channeling marine productivity to upper trophic
levels. The available observational data is rich in horizontal spatial
and temporal coverage, yet lacks vertical resolution, particularly below
the photic zone (Ollison et al. 2021). There, a large and diverse
community of heterotrophic protists thrives on sinking particulate
matter, preys upon the prokaryotic populations (Ollison et al.2021; Rocke et al. 2015) and removes a similar percentage of the
prokaryotic standing stock compared to the epipelagic realm (Rockeet al. 2015). This trophic transfer may represent a critical
mechanism sustaining the upper levels of mesopelagic trophic webs.
The warm oligotrophic subtropical gyres of the major ocean basins are
the largest biome in the planet, and these nutrient-poor regions are
expanding in size (Irwin & Oliver 2009). To predict future conditions,
it is essential to characterize their present state (Agusti et
al. 2019). In these regions, PP is dominated by the prokaryotic and
eukaryotic picophytoplankton (Agusti et al. 2019; Cotti-Rauschet al. 2020; Orsi et al. 2018; Riemann et al.2011). Much of the PP of the larger size fractions depends on
mixotrophic strategies, combining autotrophy with phagotrophy on the
smaller primary producers (Mitra et al. 2016). The Bermuda
Atlantic Time-series Study (BATS) is located in the western limits of
the North Atlantic subtropical gyre (Lomas et al. 2013). The
hydrography at BATS responds to a locally large seasonal cycle in
atmospheric forcing, reflected in winter mixing that extends below the
photic layer and contrasts sharply with a stratified summertime photic
zone that is progressively mixed away during the fall. These
characteristics drive nutrient availability, primary production and
community composition (Church et al. 2013). Particle fluxes
(Conte et al. 2001) and zooplankton community composition
(Blanco-Bercial 2020) show a seasonal signal. Likewise, metazooplankton
exhibit signals that reflect seasonal timescales, and it is expected
that the protist community also exhibit seasonality, at least in the
epipelagic layers.
A significant hurdle to studying the marine protist community is the
complex and tedious procedure needed to characterize these organisms.
Historically, this was achieved by microscopy, and required expert
personnel for sample preparation, analyses and taxonomic identification.
Microscopy or image-based methods have the advantage of being
quantitative, providing an estimate of cell sizes, and enabling biomass
proxies. These methods are limited, as any other morphology-based
analyses, by the presence of cryptic species, and the natural complexity
of the diversity of protists. In the oligotrophic ocean, a large
proportion of the protist community falls within the 2-20 µm size class,
many of them naked, which makes the identification very complicated when
using automated optical instruments (e.g. FlowCam, IFCB), or even with
classical methods after fixation. Molecular techniques as metabarcoding
(Ollison et al. 2021) and metagenomics (Sunagawa et al.2015) allow for direct characterization of planktonic communities (Notet al. 2007; Treusch et al. 2012; Treusch et al.2009) and its potential functionality. These methods provide a better
understanding of the diversity of the protist community in the oceans
(Caron & Hu 2019) and the associated trophic relationships, including
the large presence of symbionts (Ollison et al. 2021).
The present study applies DNA metabarcoding to samples collected over
three years in conjunction with the BATS time-series to assess marine
protist communities in the epipelagic and mesopelagic zones. Its purpose
is to describe the vertical and temporal distributions of community
composition, their evolution and transitions over the annual cycle, and
relationships to hydrographic structure. We aimed to characterize the
distinct communities with depth and detail how their boundaries evolve
and transition, as a response to the hydrographic features throughout
the year. In lieu of traditional approaches that bin data in depth
layers, and seasons by calendar months, we employ a physical framework
defined by four seasons and 11 vertical layers that delineate dynamical
zones shaped by locally varying ocean mixing, stratification, and light
penetration in the Sargasso Sea (Table 1; Curry et al., in prep)