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Abstract 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.

Abstract Two gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and ‘other microalgae’. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.

Abstract Man‐made environments such as ports and marinas are gateways for many marine non‐indigenous species (mNIS) transported via shipping worldwide. These habitats are often the focus of biosecurity programs for the surveillance of mNIS, but there have been few studies investigating the distribution of biofouling communities in natural habitats and nearby artificial habitats. Here, following a DNA metabarcoding approach, we tested for differences in spatio‐temporal trends of biological pioneer communities established after one‐week colonization between a port, a marina, and coral reefs using two different matrices (PVC panels and water samples) in the central Red Sea. In addition, we aimed to investigate differences in the prevalence of mNIS between man‐made and natural habitats during the summer and winter seasons, and whether the number and patterns of mNIS differed between the port (an active historic port subjected to intense shipping traffic) and the marina (a small recently developed marina utilized by small and medium research vessels). The community structure from samples collected at the two coral reefs showed greater similarity to each other compared to that obtained from the port and the marina. A total of 29 mNIS were detected across all sites, of which 16 were reported in the Red Sea for the first time, with Jeddah port hosting 28 mNIS. By applying standardized methodological approaches, this study provides comparable data regarding the monitoring of introduced and invasive species, particularly within the data‐poor Red Sea, a major shipping corridor. This study serves as the foundation for implementing a robust and rapid baseline monitoring system to assess native biodiversity and facilitate the early detection of NIS.

Introduced trout can induce trophic cascades, however, a lack of pre-introduction data limits knowledge on their impact in many lakes. Traditional paleolimnological approaches have been used to study historic species changes, but until recently these have been restricted to taxa with preservable body-parts. To explore the ecosystem effects of Salmo trutta (brown trout) introduction on an oligotrophic lake in Aotearoa-New Zealand, we used a multi-marker sedimentary environmental DNA (sedDNA) approach coupled with pigments to detect changes across multiple trophic levels. DNA was extracted from core depths capturing approximately 100 years before and after the expected arrival of S. trutta, and metabarcoding was undertaken with four primer sets targeting the 12S rRNA (fish), 18S rRNA (eukaryotes) and cytochrome c oxidase (COI; eukaryotes) genes. The earliest detection of S. trutta eDNA was 1906 (1892–1919 CE with 95% high probability density function) suggesting their introduction was shortly before this. Native fish diversity (12S and 18S rRNA) decreased after the detection of S. trutta, albeit the data was patchy. A shift in overall eukaryotic and algal communities (18S rRNA and COI) was observed around 1856 (1841–1871 CE) to 1891 (1877–1904 CE), which aligns with the expected S. trutta introduction. However, taxonomy could not be assigned to many of the 18S rRNA and COI sequences. Pigment concentrations did not change markedly after S. trutta introduction. SedDNA provides a new tool for understanding the impact of disturbances such as the introduction of non-native species; however, there are still several methodological challenges to overcome.

Understanding how biological communities are assembled is central to many ecological studies. The semi-confined nature of the Red Sea, with limited exchange of waters with other seas and strong environmental gradients, is an ideal ecosystem to investigate assembly processes of biological communities. Sampling through the water column (surface, deep chlorophyll maximum (DCM), oxygen minimum zone (OMZ), and bottom) along the latitudinal axis of the Red Sea was undertaken during cruises in 2015/2016. The composition and assembly of eukaryotic communities were assessed using high-throughput sequencing of the 18S rRNA gene. Distinct differences were noted in the composition of the eukaryotic community across the different depth layers. Dinophyceae were more prevalent in the euphotic zone (surface = 35.3%; DCM = 18.1%), while Syndiniales had the highest relative abundances in the OMZ (45.9%) and the bottom waters (52.6%). We showed that the assembly of eukaryotic communities through the water column was primarily determined by deterministic processes, especially variable selection due to different environmental conditions. The exception was between the OMZ and the bottom, where deterministic and stochastic processes were balanced with homogeneous selection and homogenizing dispersal dominating, indicating similar environmental conditions and high levels of dispersal between the layers. Across the latitudinal gradient, environmental variable selection was predominant in the euphotic zone, most likely driven by the strong environmental gradients present in the Red Sea. In the aphotic zones, homogenizing dispersal was more prevalent, especially in the OMZ. Our study highlights the contrasting assembly mechanisms governing the distribution of eukaryotic planktonic communities through the water column.

Abstract The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.

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.

Molecular-based techniques offer considerable potential to provide new insights into the impact of anthropogenic stressors on lake ecosystems. Microbial communities are involved in many geochemical cycling processes in lakes and a greater understanding of their functions could assist in guiding more targeted remedial actions. Recent advances in metagenomics now make it possible to determine the functional potential of entire microbial communities. The present study investigated microbial communities and their functional potential in surface sediments collected from three lakes with differing trophic states and characteristics. Surface sediments were analysed for their nutrient and elemental contents and metagenomics and metabarcoding analysis undertaken. The nutrients content of the surface sediments did not show as distinct a gradient as water chemistry monitoring data, likely reflecting effects of other lake characteristics, in particular, depth. Metabarcoding and metagenomics revealed differing bacterial community composition and functional potential amongst lakes. Amongst the differentially abundant metabolic pathways, the most prominent were clusters in the energy and xenobiotics pathways. Differences in the energy metabolism paths of photosynthesis and oxidative phosphorylation were observed. These were most likely related to changes in the community composition and especially the presence of cyanobacteria in two of the three lakes. Xenobiotic pathways, such as those involving polycyclic aromatic hydrocarbons, were highest in the lakes with the greatest agricultural land-use in their catchment. These results highlight how microbial metagenomics can be used to gain insights into the causes of differences in trophic status amongst lakes.

Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.

Abstract Undertaking environmental assessments on non‐wadeable rivers is challenging due to their size, depth, and water velocity. The cotton strip assay (CSA) is a functional indicator used in assessing the ecological health of non‐wadeable rivers by measuring cellulose decomposition potential. Enhancing knowledge on the microbial communities responsible for decomposition would assist in developing a microbial‐based biotic index that could complement the CSA. The aims of this study were to explore the temporal and spatial variability of bacterial communities on cotton strips, identify environmental drivers of differences, and detect potential indicator taxa. Cotton strips were deployed at 12 sites, spanning a range of water quality and catchment land uses in three separate months. Each site was placed into an ecological health category (EHC) from A (healthy) to D (poor). Metabarcoding (16S rRNA) was used to characterize bacterial communities. There was a significant interaction between month and site and between month and EHC. Higher temperatures and pH were identified as key drivers of differences in bacterial communities in February (summer) and higher levels of ammoniacal nitrogen, nitrate/nitrite nitrogen, and turbidity in August (winter). After removal of amplicon sequence variants (ASVs) in low abundance, 27 taxa indicative of EHCs were identified. ASVs associated with EHC‐A were generally negatively correlated with modified land use and nitrate/nitrite nitrogen. In contrast, ASVs associated with EHC‐D were positively correlated to modified land use and temperature. With further validation, a molecular microbial index could be developed to aid in assessing the health of non‐wadeable rivers.

Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.

Abstract Globalization has increased connectivity between countries enhancing the spread of marine nonindigenous species (NIS). The establishment of marine NIS shows substantial negative effects on the structure and functioning of the natural ecosystems by competing for habitats and resources. Ports are often hubs for the spread of NIS via commercial and recreational vessels. Prevention, detection, and mitigation efforts are required to avoid and manage the establishment of NIS in new ecosystems. In this study, metabarcoding approaches targeting the nuclear small‐subunit ribosomal RNA (18S rRNA) gene and mitochondrial cytochrome c oxidase I (COI) gene were used to investigate planktonic and sessile (i.e., biofouling) communities and NIS at four locations in Tahiti, including two marinas and one port with varying anthropogenic impacts, and a relatively pristine site (Manava) used as a control. ASV richness values showed significant differences (18S rRNA gene: p = .023; COI: p

Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.

Picocyanobacteria (Pcy) are important yet understudied components of lake foodwebs. While phylogenetic studies of isolated strains reveal a high diversity of freshwater genotypes, little is known about abiotic drivers associated with Pcy in different lakes. Due to methodological limitations, most previous studies assess potential drivers using total cell abundances as a response, with often conflicting and inconsistent results. In the present study, we explored how picocyanobacterial communities respond to environmental change using a combination of epifluorescence microscopy and community data determined using 16S rRNA gene metabarcoding. Temporal shifts in picocyanobacterial abundance, diversity and community dynamics were assessed in relation to potential environmental drivers in five contrasting lakes over 1year. Cell abundances alone were not consistently related to environmental variables across lakes. However, the addition of metabarcoding data revealed diverse picocyanobacterial communities that differed significantly between lakes, driven by environmental variables related to trophic state. Within each lake, communities were temporally dynamic and certain amplicon sequence variants (ASVs) were strongly associated with specific environmental drivers. Rapid shifts in community structure and composition were often related to environmental changes, indicating that lacustrine Pcy can persist at high abundances through collective community adaptation. These results demonstrate that a combination of microscopy and metabarcoding enables an in-depth characterisation of picocyanobacterial communities and reveals strain-specific drivers. We recommend that future studies cease referring to picocyanobacterial as one functional group and take strain specific variability into consideration.

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.

Tetrodotoxin (TTX) is one of the most potent naturally occurring compounds and is responsible for many human intoxications worldwide. Paphies australis are endemic clams to New Zealand which contain varying concentrations of TTX. Research suggests that P. australis accumulate the toxin exogenously, but the source remains uncertain. The aim of this study was to identify potential bacterial TTX-producers by exploring differences in bacterial communities in two organs of P. australis: the siphon and digestive gland. Samples from the digestive glands of a non-toxic bivalve Austrovenus stutchburyi that lives amongst toxic P. australis populations were also analyzed. Bacterial communities were characterized using 16S ribosomal RNA gene metabarcoding in P. australis sourced monthly from the Hokianga Harbor, a site known to have TTX-bearing clams, for 1 year, from ten sites with varying TTX concentrations around New Zealand, and in A. stutchburyi from the Hokianga Harbor. Tetrodotoxin was detected in P. australis from sites all around New Zealand and in all P. australis collected monthly from the Hokianga Harbor. The toxin averaged 150 μg kg–1 over the year of sampling in the Hokianga Harbor but no TTX was detected in the A. stutchburyi samples from the same site. Bacterial species diversity differed amongst sites (p < 0.001, F = 5.9) and the diversity in siphon samples was significantly higher than in digestive glands (p < 0.001, F = 65.8). Spirochaetaceae (4–60%) and Mycoplasmataceae (16–78%) were the most abundant families in the siphons and the digestive glands, respectively. The bacterial communities were compared between sites with the lowest TTX concentrations and the Hokianga Harbor (site with the highest TTX concentrations), and the core bacterial communities from TTX-bearing individuals were analyzed. The results from both spatial and temporal studies corroborate with previous hypotheses that Vibrio and Bacillus could be responsible for the source of TTX in bivalves. The results from this study also indicate that marine cyanobacteria, in particular picocyanobacteria (e.g., Cyanobium, Synechococcus, Pleurocapsa, and Prochlorococcus), should be investigated further as potential TTX producers.

Prochlorococcus and Synechococcus are pico-sized cyanobacteria that play a fundamental role in oceanic primary production, being particularly important in warm, nutrient-poor waters. Their potential response to nutrient enrichment is expected to be contrasting and to differ from larger phytoplankton species. Here, we used a metagenomic approach to characterize the responses to nutrient enrichment in the community of picocyanobacteria and to analyze the cyanophage response during a mesocosms experiment in the oligotrophic Red Sea. Natural picoplankton community was dominated by Synechococcus clade II, with marginal presence of Prochlorococcus (0.3% bacterial reads). Increased nutrient input triggered a fast Synechococcus bloom, with clade II being the dominant, with no response of Prochlorococcus growth. The largest bloom developed in the mesocosms receiving a single initial input of nutrients, instead of daily additions. The relative abundances of cyanophage sequences in cellular metagenomes increased during the experiment from 12.6% of total virus reads up to 40% in the treatment with the largest Synechococcus bloom. The subsequent collapse of the bloom pointed to a cyanophage infection on Synechococcus that reduced its competitive capacity, and was then followed by a diatom bloom. The cyanophage attack appears to have preferentially affected the most abundant Synechococcus clade II, increasing the evenness within the host population. Our results highlight the relevance of host-phage interactions on determining population dynamics and diversity of Synechococcus populations.

Abstract 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.

Very little is known about the composition and the annual cycle of zooplankton assemblages in the Red Sea, a confined water body characterized by a high biodiversity and endemism but at the same time one of the most understudied areas in the world in terms of marine biodiversity. This high diversity together with the lack of references for several of the groups poses a problem in obtaining basic information on zooplankton seasonal patterns. In the present work, we used high throughput sequencing to examine the temporal and spatial distribution of the zooplankton communities inhabiting the epipelagic zone in the central Red Sea. The analysis of zooplankton assemblages collected at two sites—coastal and offshore—twice a month at several depth strata by using MANTA, Bongo and WP2 nets provides baseline information of the seasonal patterns of the zooplankton community over 1 year. We show that the seasonal fluctuation of zooplankton communities living in the upper 100 m of the water column is driven mainly by the annual changes in seawater temperature. The 18S rRNA gene was used for metabarcoding of zooplankton assemblages revealing 630 metazoan OTUs (97% similarity) in five phyla, highlighting the richness of the Red Sea community. During colder months, communities were characterized by lower richness and higher biomass than communities found during the hot season. Throughout the year the zooplankton communities were dominated by the class Maxillopoda, mainly represented by copepods and class Hydrozoa. The rise in the water temperature favors the appearance of classes Malacostraca, Cephalopoda, Gastropoda, and Saggitoidea. The present study provides essential baseline information for future monitoring and improves our knowledge of the marine ecosystem in the Red Sea while reporting the main environmental variable structuring zooplankton assemblages in this region.

An essential component of the coral reef animal diversity is the species hidden in crevices within the reef matrix, referred to as the cryptobiome. These organisms play an important role in nutrient cycling and provide an abundant food source for higher trophic levels, yet they have been largely overlooked. Here, we analyzed the distribution patterns of the mobile cryptobiome (>2000 μm) along the latitudinal gradient of the Saudi Arabian coast of the Red Sea. Analysis was conducted based on 54 Autonomous Reef Monitoring Structures. We retrieved a total of 5273 organisms, from which 2583 DNA sequences from the mitochondrially encoded cytochrome c oxidase I were generated through sanger sequencing. We found that the cryptobiome community is variable over short geographical distances within the basin. Regression tree models identified sea surface temperature (SST), percentage cover of hard coral and turf algae as determinant for the number of operational taxonomic units present per Autonomous Reef Monitoring Structures (ARMS). Our results also show that the community structure of the cryptobiome is associated with the energy available (measured as photosynthetic active radiation), sea surface temperature, and nearby reef habitat characteristics (namely hard corals, turf and macroalgae). Given that temperature and reef benthic characteristics affect the cryptobiome, current scenarios of intensive climate change are likely to modify this fundamental biological component of coral reef functioning. However, the trajectory of change is unknow and can be site specific, as for example, diversity is expected to increase above SST of 28.5°C, and with decreasing hard coral and turf cover. This study provides a baseline of the cryptobenthic community prior to major coastal developments in the Red Sea to be used for future biodiversity studies and monitoring projects. It can also contribute to better understand patterns of reef biodiversity in a period where Marine Protected Areas are being discussed in the region.

Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.

An important aspect of population dynamics for coral reef fishes is the input of new individuals from the pelagic larval pool. However, the high biodiversity and the difficulty of identifying larvae of closely related species represent obstacles to more fully understanding these populations. In this study, we combined morphology and genetic barcoding (Cytochrome Oxidase I gene) to characterize the seasonal patterns of the larval fish community at two sites in close proximity to coral reefs in the central-north Red Sea: one shallower inshore location (50 m depth) and a nearby site located in deeper and more offshore waters (~ 500 m depth). Fish larvae were collected using oblique tows of a 60 cm-bongo net (500 μm mesh size) every month for one year (2013). During the warmer period of the year (June-November), the larval fish stock was comparable between sampling sites. However, during the colder months, abundances were higher in the inshore than in the offshore waters. Taxonomic composition and temporal variation of community structure differed notably between sites, potentially reflecting habitat differences, reproductive patterns of adults, and/or advective processes in the area. Eleven out of a total of 62 recorded families comprised 69-94% of the fish larval community, depending on sampling site and month. Richness of taxa was notably higher in the inshore station compared to the offshore, particularly during the colder period of the year and especially for the gobiids and apogonids. Two mesopelagic taxa (Vinciguerria sp. and Benthosema spp.) comprised an important component of the larval community at the deeper site with only a small and sporadic occurrence in the shallower inshore waters. Our data provide an important baseline reference for the larval fish communities of the central Red Sea, representing the first such study from Saudi Arabian waters.

The composition of zooplankton in the water column has received limited attention in the main body of the Red Sea and this study investigates the change in the community both spatially and temporally across 11 stations in the central Red Sea. Using molecular methods to target the v9 region of the 18S rRNA gene a total of approximately 11.5 million reads were sequenced resulting in 2528 operational taxonomic units (OTUs) at 97% similarity. The phylum Arthropoda dominated in terms of reads accounting for on average 86.2% and 65.3% for neuston nets and vertical multinets respectively. A reduction in the number of OTUs was noticed with depth for both total metazoa and Maxillopoda whilst there was also a significant change in the composition of the Maxillopoda community. The genus Corycaeus had a higher proportion of reads in the epipelagic zone with Pleuromamma becoming increasingly dominant with depth. No significant difference was observed in the community between night and day sampling however there was a significant difference in the zooplankton community between two sampling periods separated by 10 days.