Biodiversity patterns of plankton assemblages at the extremes of the Red Sea

Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula

The Arabian Peninsula accounts for approximately 6% of the world's coral reefs. Some thrive in extreme environments of temperature and salinity. Using 51 Autonomous Reef Monitoring Structure (ARMS), a standardized non-destructive monitoring device, we investigated the spatial patterns of coral reef cryptobenthic diversity in four ecoregions around the Arabian Peninsula and analyzed how geographical and/or environmental drivers shape those patterns. The mitochondrial cytochrome c oxidase subunit I (COI) gene was used to identify Amplicon Sequence Variants and assign taxonomy of the cryptobenthic organisms collected from the sessile and mobile fractions of each ARMS. Cryptobenthic communities sampled from the two ecoregions in the Red Sea showed to be more diverse than those inhabiting the Arabian (Persian) Gulf and the Gulf of Oman. Geographic distance revealed a stronger relationship with beta diversity in the Mantel partial correlation than environmental distance. However, the two mobile fractions (106-500 µm and 500-2000 µm) also had a significant correlation between environmental distance and beta diversity. In our study, dispersal limitations explained the beta diversity patterns in the selected reefs, supporting the neutral theory of ecology. Still, increasing differences in environmental variables (environmental filtering) also had an effect on the distribution patterns of assemblages inhabiting reefs within short geographic distances. The influence of geographical distance in the cryptofauna assemblages makes these relevant, yet usually ignored, communities in reef functioning vulnerable to large scale coastal development and should be considered in ecosystem management of such projects.

Increased prokaryotic diversity in the Red Sea deep scattering layer

BACKGROUND

The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450-600 m.

RESULTS

Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer.

CONCLUSIONS

We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200 m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.

Comparative metagenomics of phytoplankton blooms after nutrient enrichment of oligotrophic marine waters

Increasing anthropogenic pressures on the coastal marine environments impact these ecosystems via a variety of mechanisms including nutrient loading, leading to eutrophication and increases in algal blooms. Here, we use a metagenomics approach to assess the taxonomic and functional changes of the microbial community throughout a nutrient enriched mesocosm phytoplankton bloom. We tested four different nutrient treatments consisting of either nitrate and phosphate or nitrate, phosphate and silicate, administered on the first day or continuously for the first two weeks of the experiment. Our results show a shift in the taxonomic composition of the community over time that is dependent on the nutrient addition regime. Significant differences in the functional potential of the communities were detected, with an interaction between bloom period (pre-bloom, bloom and post-bloom) and nutrient treatment (p = 0.004). A sharp drop in functional similarity was observed in the first week in all treatments and after 20 days had not returned to pre-bloom levels. Changes within energy metabolism pathways showed a remarkable enrichment of the dissimilatory nitrate reduction pathway in the post-bloom period. Eukaryotic oxidative phosphorylation and photosynthetic antenna proteins were more abundant during the bloom, especially in the continuous treatment with silicate. Our results suggest that continuous (i.e. chronic) nutrient enrichment has a larger effect on the functioning of marine systems compared to a single (i.e acute) addition. A deep understanding of the functional and taxonomic shifts in the community during blooms is essential to reverse or mitigate human impacts on coastal environments.

A Conceptual Approach to Partitioning a Vertical Profile of Phytoplankton Biomass Into Contributions From Two Communities

We describe an approach to partition a vertical profile of chlorophyll-a concentration into contributions from two communities of phytoplankton: one (community 1) that resides principally in the turbulent mixed-layer of the upper ocean and is observable through satellite visible radiometry; the other (community 2) residing below the mixed-layer, in a stably stratified environment, hidden from the eyes of the satellite. The approach is tuned to a time-series of profiles from a Biogeochemical-Argo float in the northern Red Sea, selected as its location transitions from a deep mixed layer in winter (characteristic of vertically well-mixed systems) to a shallow mixed layer in the summer with a deep chlorophyll-a maximum (characteristic of vertically stratified systems). The approach is extended to reproduce profiles of particle backscattering, by deriving the chlorophyll-specific backscattering coefficients of the two communities and a background coefficient assumed to be dominated by non-algal particles in the region. Analysis of the float data reveals contrasting phenology of the two communities, with community 1 blooming in winter and 2 in summer, community 1 negatively correlated with epipelagic stratification, and 2 positively correlated. We observe a dynamic chlorophyll-specific backscattering coefficient for community 1 (stable for community 2), positively correlated with light in the mixed-layer, suggesting seasonal changes in photoacclimation and/or taxonomic composition within community 1. The approach has the potential for monitoring vertical changes in epipelagic biogeography and for combining satellite and ocean robotic data to yield a three-dimensional view of phytoplankton distribution.

Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species

The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.

Eukaryotic communities in coastal water from Shenzhen in South China

Eukaryotic microorganisms are ubiquitous in the marine environment, and have a wide variety of ecosystem functions. Shenzhen is one of the most developed cities in South China, but the eukaryotic communities in the water along its coastlines remain poorly understood. The study applied 18S rRNA gene ITS (internal transcribed spacer) sequencing to identify the eukaryotic community from twenty sites of Shenzhen coast water. The alpha-diversity of the samples between these sites were significantly different, and the seawater of eastern coast had higher alpha-diversity compared to that of the western coast. The abundance of Chlorophyta was notably higher in the seawater of western coast, but Picozoa was relatively depleted. Specifically, Cryptocaryon, Pseudovorticella, and Cyclotella were significantly higher in the water of western coast, while Guinardia, Minutocellus, and Amoebophrya were increased in eastern samples. The spatially variations of eukaryotic microorganism community in the seawater of Shenzhen coast were associated with the water quality. The results have important significance for the understanding of coastal eukaryotic community, their interaction network, and build a foundation for future management and protection of coastal water quality.

Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain

Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24-34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94-1.38 d-1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38-24.4 d-1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.

Links between Phenology of Large Phytoplankton and Fisheries in the Northern and Central Red Sea

Phytoplankton phenology and size structure are key ecological indicators that influence the survival and recruitment of higher trophic levels, marine food web structure, and biogeochemical cycling. For example, the presence of larger phytoplankton cells supports food chains that ultimately contribute to fisheries resources. Monitoring these indicators can thus provide important information to help understand the response of marine ecosystems to environmental change. In this study, we apply the phytoplankton size model of Gittings et al. (2019b) to 20-years of satellite-derived ocean colour observations in the northern and central Red Sea, and investigate interannual variability in phenology metrics for large phytoplankton (>2 µm in cell diameter). Large phytoplankton consistently bloom in the winter. However, the timing of bloom initiation and termination (in autumn and spring, respectively) varies between years. In the autumn/winter of 2002/2003, we detected a phytoplankton bloom, which initiated ~8 weeks earlier and lasted ~11 weeks longer than average. The event was linked with an eddy dipole in the central Red Sea, which increased nutrient availability and enhanced the growth of large phytoplankton. The earlier timing of food availability directly impacted the recruitment success of higher trophic levels, as represented by the maximum catch of two commercially important fisheries (Sardinella spp. and Teuthida) in the following year. The results of our analysis are essential for understanding trophic linkages between phytoplankton and fisheries and for marine management strategies in the Red Sea.

Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems

The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture

Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between "distance" from the farm and "kit" in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.

Long-term exposure to increasing temperature can offset predicted losses in marine food quality (fatty acids) caused by ocean warming

Marine phytoplankton produce essential fatty acids (FA), which are key component of a healthy diet in humans and marine food webs. Increased temperatures can reduce lipid and FA content in phytoplankton; thus, ocean warming poses a risk for the global production of these essential FA. However, responses to warming may differ between phytoplankton species especially after long-term exposure because phenotypic plasticity, de novo mutations, or genetic evolution may occur. Here, we examine the content of FA and lipids in phytoplankton following long-term selection (~2 years) to warming conditions (+4°C), and we observe that FA and lipids content were partly or entirely recovered following long-term exposure to warming conditions. Furthermore, this observed long-term response also offset the predicted losses of some essential polyunsaturated fatty acids (PUFA) in three of the four species tested. Our study suggests that long-term exposure of phytoplankton to warming may help to maintain marine food quality in a moderately warming ocean. The responses of FA to increasing temperatures may vary among species, and the level of this idiosyncrasy remains to be further studied.

Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS)

Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to describe eukaryotic cryptic reef fauna. Conversely, bacterial communities, which are critical components of coral reef ecosystem functioning, remain largely overlooked. Here we deployed 56 ARMS across the 2,000-km spread of the Red Sea to assay biodiversity, composition and inferred underlying functions of coral reef-associated bacterial communities via 16S rRNA gene sequencing. We found that bacterial community structure and diversity aligned with environmental differences. Indeed, sea surface temperature and macroalgae cover were key in explaining bacterial relative abundance. Importantly, taxonomic and functional alpha diversity decreased under more extreme environmental conditions (e.g., higher temperatures) in the southern Red Sea. This may imply a link between bacterial community diversity and functional capabilities, with implications for conservation management. Our study demonstrates the utility of ARMS to investigate the response of coral reef-associated bacterial communities to environmental change.

Free-living dinoflagellates of the central Red Sea, Saudi Arabia: Variability, new records and potentially harmful species

The diversity of free-living dinoflagellates in the coastal areas of the central Red Sea, Saudi Arabia, was studied from April 2016 to March 2017. A total of 106 dinoflagellates belonging to 36 genera, 20 families and 7 orders were identified and characterized using light microscopy. Of these, 47 taxa were potentially harmful, and 60 taxa were recorded for the first time from the Red Sea. The unexpectedly high species diversity, including new records, was due to the benthic species. The monthly variability of planktonic species records exhibited negative correlations with temperature and salinity, although in most cases, the links between them were insignificant. Subsequently, the dinoflagellates checklist for the entire Red Sea was updated and showed that there were currently 395 taxa and 66 genera. The results of this study provide a solid foundation for future studies of dinoflagellate biodiversity in the Red Sea, particularly for benthic and harmful species.

Fast adaptation of tropical diatoms to increased warming with trade-offs

Ocean warming with climate change is forcing marine organisms to shift their distributions polewards and phenology. In warm tropical seas, evolutionary adaptation by local species to warming will be crucial to avoid predicted desertification and reduction in diversity. However, little is known about the adaptation of phytoplankton in warm seas. Across the ocean, diatomic microalgae are the main primary producers in cold waters; they also contribute to tropical communities where they play a necessary role in the biological pump. Here we show that four species of diatoms isolated from the tropical Red Sea adapted to warming conditions (30 °C) after 200–600 generations by using various thermal strategies. Two of the warming adapted species increased their optimal growth temperature (T_opt) and maximum growth rate. The other two diatoms did not increase T_opt and growth, but shifted from specialist to generalist increasing their maximum critical thermal limit. Our data show that tropical diatoms can adapt to warming, although trade offs on photosynthetic efficiency, high irradiance stress, and lower growth rate could alter their competitive fitness. Our findings suggest that adaptive responses to warming among phytoplankton could help to arrest the sharp decline in diversity resulting from climate change that is predicted for tropical waters.

Plankton community assessment in anthropogenic-impacted oligotrophic coastal regions

Microbial planktonic communities are critical components of marine biogeochemical pathways. Despite this, there is still limited knowledge on the dynamics of this group in warm and oligotrophic waters. We used high-throughput sequencing to characterise the bacterial (16S rRNA) and eukaryotic (18S rRNA) microbial plankton communities in two regions under the influence of anthropogenic impacts (a port and sewage outflow) and a coastal region with no direct anthropogenic disturbances in the central Red Sea. Overall, bacterial and eukaryotic components responded in a similar way to the environmental conditions. Community composition and structure were more sensitive than alpha diversity measures to environmental impacts. With the exception of eukaryotes, for which the number of OTU differed significantly between sampling periods in all the regions, environmental changes associated with anthropogenic pressures seem to be better reflected by variations in the relative dominance of microbial groups. For example, elevated proportional abundances of nitrifying and sewage-/faecal-related bacteria at the impacted sites were observed compared with the coastal region. The recently developed microgAMBI also appeared to correlate well with the level of anthropogenic impact the regions experienced, showing the potential to be applied in oligotrophic waters.

Water chemistry reveals a significant decline in coral calcification rates in the southern Red Sea

Experimental and field evidence support the assumption that global warming and ocean acidification is decreasing rates of calcification in the oceans. Local measurements of coral growth rates in reefs from various locations have suggested a decline of ~6–10% per decade since the late 1990's. Here, by measuring open water strontium-to-alkalinity ratios along the Red Sea, we show that the net contribution of hermatypic corals to the CaCO₃ budget of the southern and central Red Sea declined by ~100% between 1998 and 2015 and remained low between 2015 and 2018. Measured differences in total alkalinity of the Red Sea surface water indicate a 26 ± 16% decline in total CaCO₃ deposition rates along the basin. These findings suggest that coral reefs of the southern Red Sea are under severe stress and demonstrate the strength of geochemical measurements as cost-effective indicators for calcification trends on regional scales.

Ocean acidification and warming threaten coral reefs globally. Here, the authors show that the net contribution of corals to the CaCO₃ budget of the tropical Red Sea declined dramatically between 1998 and 2015 and remained low between 2015 and 2018.

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence

The semi-enclosed nature of the Red Sea (20.2°N-38.5°N) makes it a natural laboratory to study the influence of environmental gradients on microbial communities. This study investigates the composition and structure of microbial prokaryotes and eukaryotes using molecular methods, targeting ribosomal RNA genes across different regions and seasons. The interaction between spatial and temporal scales results in different scenarios of turbulence and nutrient conditions allowing for testing of ecological theory that categorizes the response of the plankton community to these variations. The prokaryotic reads are mainly comprised of Cyanobacteria and Proteobacteria (Alpha and Gamma), with eukaryotic reads dominated by Dinophyceae and Syndiniophyceae. Periodic increases in the proportion of Mamiellophyceae and Bacillariophyceae reads were associated with alterations in the physical oceanography leading to nutrient increases either through the influx of Gulf of Aden Intermediate Water (south in the fall) or through water column mixing processes (north in the spring). We observed that in general dissimilarity amongst microbial communities increased when nutrient concentrations were higher, whereas richness (observed OTUs) was higher in scenarios of higher turbulence. Maximum abundance models showed the differential responses of dominant taxa to temperature giving an indication how taxa will respond as waters become warmer and more oligotrophic.

Please mind the gap - Visual census and cryptic biodiversity assessment at central Red Sea coral reefs

Coral reefs harbor the most diverse assemblages in the ocean, however, a large proportion of the diversity is cryptic and, therefore, undetected by standard visual census techniques. Cryptic and exposed communities differ considerably in species composition and ecological function. This study compares three different coral reef assessment protocols: i) visual benthic reef surveys: ii) visual census of Autonomous Reef Monitoring Structures (ARMS) plates; and iii) metabarcoding techniques of the ARMS (including sessile, 106-500 μm and 500-2000 μm size fractions), that target the cryptic and exposed communities of three reefs in the central Red Sea. Visual census showed a dominance of Cnidaria (Anthozoa) and Rhodophyta on the reef substrate, while Porifera, Bryozoa and Rhodophyta were the most abundant groups on the ARMS plates. Metabarcoding, targeting the 18S rRNA gene, significantly increased estimates of the species diversity (p < 0.001); revealing that Annelida were generally the dominant phyla (in terms of reads) of all fractions and reefs. Furthermore, metabarcoding detected microbial eukaryotic groups such as Syndiniophyceae, Mamiellophyceae and Bacillariophyceae as relevant components of the sessile fraction. ANOSIM analysis showed that the three reef sites showed no differences based on the visual census data. Metabarcoding showed a higher sensitivity for identifying differences between reef communities at smaller geographic scales than standard visual census techniques as significant differences in the assemblages were observed amongst the reefs. Comparison of the techniques showed no similar patterns for the visual techniques while the metabarcoding of the ARMS showed similar patterns amongst fractions. Establishing ARMS as a standard tool in reef monitoring will not only advance our understanding of local processes and ecological community response to environmental changes, as different faunal components will provide complementary information but also improve the estimates of biodiversity in coral reef benthic communities. This study lays the foundations for further studies looking at integrating traditional reef survey methodologies with complementary approaches, such as metabarcoding, which investigate other components of the reef community.