@phdthesis{01J6EYQ7EMACEYZ5XQ75AY5GPF,
  abstract     = {{Intertidal coastal ecosystems, lying at the interface of the terrestrial and marine realms, are
hugely important from an ecological and economic viewpoint. In temperate climate zones,
intertidal sediment ecosystems (sand- and mudflats) are often characterized by the presence
of phototrophic microphytobenthic (MPB) biofilms dominated by diatoms. These underlie the
high primary production in these coastal systems, drive nutrient and biogeochemical cycles,
support benthic (and pelagic) food webs, and stabilize sediments. The biodiversity and
functioning of these biofilms have traditionally mainly been studied using microscopy-based
and physiological approaches. In this thesis, we combined a multi-omics approach, both in situ
and in controlled lab experiments, with traditional approaches to obtain a more in-depth
understanding of the diversity and functioning of these microbial biofilms in the dynamic and
heterogeneous intertidal environment.
Community composition, functioning, and carbon flows within diatom-dominated microbial
biofilms were compared between contrasting intertidal sediment types (mud vs sand) in
Bourgneuf Bay (France), using an in situ 13C-bicarbonate labeling approach in combination
with metabarcoding, pigment and fatty acid analyses, and CO2 flux measurements. Despite
pronounced differences in community composition and MPB biomass, both the muddy and
sandy sites demonstrated high primary production. Carbon turnover was faster in the sandy
sediment, with more transient carbon cycling, and low retention of stable isotope signal in the
organic carbon pool as opposed to the muddy sediment, where about 23% of the signal was
still present after five days. Under conditions indicative of nitrogen limitation, in both
sediment types substantial incorporation of carbon into bound, high-molecular-weight
extracellular polymeric substances (EPS) was observed. Bound EPS turnover was rapid (hours),
indicating a high potential for the degradation of complex EPS by the heterotrophic bacterial
communities. Alongside the fast degradation of colloidal (low-molecular-weight) EPS, this
facilitated rapid carbon transfer from MPB to bacteria and subsequently to meio- and
macrofauna. Free-living MPB in mud responded to high irradiance by vertical downward
migration but also used physiological photoprotection mechanisms. Species-specific
differences in vertical micromigration dynamics during tidal emersion ensured high gross
primary production (GPP) throughout the whole tidal emersion period.
Meta-omics (metabarcoding, metatranscriptomics, and metabolomics), pigment and fatty
acid analyses, and CO2 flux measurements were carried out to profile functional responses of
an MPB biofilm community to daytime and nighttime tidal emersion at a mudflat in the
Westerschelde estuary (The Netherlands). Despite highly fluctuating environmental
conditions and sedimentary processes, overall microbial functionality remained high. We
observed significant diurnal shifts in the metatranscriptomic activity of primary producers,
particularly of diatoms, showing increased expression related to photosynthesis during
daylight. Diatoms predominantly relied on repair systems as their main photoprotection
mechanism during daytime emersion. In contrast, within the bacterial community,
cyanobacteria was the main group with increased transcriptional activity during the day,
primarily due to photosynthesis. Despite the rhythmic signals emitted by MPB, the
1-3
heterotrophic bacterial community did not strongly respond to the influx of
photosynthetically fixed carbon during peak photosynthesis. This minimal effect is attributed
to the organic matter-rich environment of the Biezelingse Ham mudflat, suggesting that the
presence of abundant organic material may diminish the impact of new photosynthate on
heterotrophic bacterial activity.
In a final study, we exposed a marine benthic diatom to its native (marine biofilm) and a
foreign (forest soil) bacterial inoculum and taxonomically and functionally characterized the
established associations using metabarcoding, metatranscriptomics, and 13C-bicarbonate
labeling. The established foreign microbiome displayed a stochastic assembly pattern, as
opposed to a more deterministic assembly in the native microbiome. The core transcriptional
response of both the diatom and the bacteria was comparable in both treatments, but a much
more diverse array of transcripts was upregulated in the native one, including transcripts
related to diatom and bacterial signaling pathways, secreted extracellular proteins, and
nutrient recycling. Nutrient utilization and carbon transfer were also more efficient in the
treatment with the native microbiome. Our results suggest that while diatoms can coexist and
interact with foreign bacteria, the complexity, and specificity of these associations were less
pronounced than in the native microbiome.
Taken together, the three research chapters underscore the importance of microbial
biodiversity and microbial interactions for the functioning of intertidal soft sediment
ecosystems. Species-specific adaptations to the highly dynamic intertidal environment and
highly specific interactions between bacteria and microalgae are essential for sustaining
carbon and nutrient cycles and productivity in intertidal ecosystems. The majority of the
bacterial community displayed a stable profile, both in terms of community structure and
gene expression, throughout the tidal and diurnal cycle, suggesting an overall high metabolic
resilience to diurnal and tidal environmental changes. Co-evolution fostered close and
species-specific associations and interactions between biofilm-forming diatoms and their
microbiome, which are essential for efficient nutrient utilization and carbon transfer in these
host-microbiome associations, and the intertidal ecosystem as a whole.}},
  author       = {{Bogorad, Margarita}},
  language     = {{eng}},
  pages        = {{var. p.}},
  publisher    = {{Ghent University. Faculty of Sciences}},
  school       = {{Ghent University}},
  title        = {{Omics-based insights into the biodiversity and functioning of microbial biofilms in intertidal sediments}},
  year         = {{2024}},
}