Particle-Associated Bacterioplankton Communities Across the Red Sea

Abstract

Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.

Keywords: bacteria; environmental genomics; microbial communities; microbial ecology.

FIGURE 1

Locations of water column samples taken during the Red Sea Decade Expedition. (a) Overview map of the Red Sea with sampling locations (n = 108) (b) Composition of the 209 samples taken and their attribution to the five geographical regions (Gulf of Aqaba, Northern Red Sea, Northern Central Red Sea, Southern Central Red Sea, Southern Red Sea) and water column layers (Epipelagic, Mesopelagic, Bathypelagic). GPS coordinates and environmental parameters can be found in File S1.

FIGURE 2

Environmental parameters characterising the epipelagic, mesopelagic and bathypelagic layers within geographical regions of the Red Sea. (a) Minima dissolved oxygen (μmol L⁻¹) (b) Maxima dissolved oxygen (μmol L⁻¹) (c) Minima temperature (°C), (d) Median salinity (psu), (e) Minima beam attenuation (1/m), (f) Median fluorescence (mg m⁻³), (g) Minima fluorescence (mg m⁻³), and (h) Maxima fluorescence (mg m⁻³). Tukey's boxplots depict the distribution of values, with raw data overlaid for clarity. Minima and maxima values have been calculated based on all measured values within one layer.

FIGURE 3

Tukey boxplots of alpha diversity measures of all geographical regions within the Red Sea along all water column layers. Geographical region abbreviations as follows: SRS, Southern Red Sea; SCRS, Southern Central Red Sea; NCRS, Northern Central Red Sea; NRS, Northern Red Sea; AQB, Gulf of Aqaba. For panels (a–c), layers are combined, as they have no significant effect on alpha diversity measures (File S7), whereas Layer × Location are depicted for panels (d) and (e). Statistical comparison and significance values for all measures can be found in File S7.

FIGURE 4

Venn diagrams with numbers of shared and unique ASVs per each Layer (a) and geographical region (b). Geographical region abbreviations as follows: Southern Red Sea (SRS), Southern Central Red Sea (SCRS), Northern Central Red Sea (NCRS), Northern Red Sea (NRS), and the Gulf of Aqaba (AQB).

FIGURE 5

Relative read abundance by taxonomic assignment separated by geographical region. (a) Phylum‐level assignment displaying the 10 most abundant phyla in all water layers with low abundance phyla summarised in ‘Other’. (b) Class‐level assignments displaying the 15 most abundant classes in all water layers with low abundance classes summarised in ‘Other’. Geographical region abbreviations as follows: Southern Red Sea (SRS), Southern Central Red Sea (SCRS), Northern Central Red Sea (NCRS), Northern Red Sea (NRS), and the Gulf of Aqaba (AQB).

FIGURE 6

Bacterial community structure in the different water column layers of the Red Sea. (a–c) Nonmetric multidimensional ordinations based on Bray‐Curtis distance of bacterial communities from the (a) epipelagic, (b) mesopelagic and (c) bathypelagic water layer displaying distribution between the five geographical regions of the Red Sea distinguished by colour. Length of arrows indicates strength of correlation. Results of environmental fitting can be found in File S8. For increased readability, arrows stemming from the same variable (e.g., Temperature‐mean and Temperature‐median) pointing in the same direction were merged into a shared arrow. If only one variation of a parameter had significant values, it was noted in the figure (e.g., ‘Oxygen min.’). Only significantly correlating parameters are shown. (d–h) NMDS ordination of bacterial communities from (d) Gulf of Aqaba, (e) Northern Red Sea, (f) Northern Central Red Sea, (g) Southern Central Red Sea and (h) Southern Red Sea with shapes indicating different water column layers. (i) Ordination of the whole dataset with colours showcasing geographical region and shape defines water column layer.