Summary: This study is an initial description and discussion of the kidney and liver microbial communities of five common fish species sampled from four sites along the Eastern Mediterranean Sea shoreline. The goals of the present study were to establish a baseline dataset of microbial communities associated with the tissues of wild marine fish, in order to examine species‐specific microbial characteristics and to screen for candidate pathogens. This issue is especially relevant due to the development of mariculture farms and the possible transmission of pathogens from wild to farmed fish and vice versa. Although fish were apparently healthy, 16S rRNA NGS screening identified three potential fish bacterial pathogens: Photobacterium damselae, Vibrio harveyi and Streptococcus iniae . Based on the distribution patterns and relative abundance, 16 samples were classified as potential pathogenic bacteria‐infected samples (PPBIS). Hence, PPBIS prevalence was significantly higher in kidneys than in liver samples and variation was found between the fish species. Significant differences were observed between fish species, organs and sites, indicating the importance of the environmental conditions on the fish microbiome. We applied a consistent sampling and analytical method for monitoring in long‐term surveys which may be incorporated within other marine fish pathogens surveys around the world.

The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship—coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphyllia paradivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of “symbiosis differentially expressed genes” and “coral heat-stress genes” in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E. paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge.

Analysis of data, curated over 3 years of sediment sampling, improves our understanding of microbiota assembly in marine sediment. Furthermore, we demonstrate the importance of cross-kingdom integration of information in the study of microbial community ecology. Finally, the urgent need to propose an applicable approach for environmental health monitoring is addressed here by establishment of sediment microbiota as a robust and sensitive model.

Sharks, as apex predators, play an essential ecological role in shaping the marine food web and maintaining healthy and balanced marine ecosystems. Sharks are sensitive to environmental changes and anthropogenic pressure and demonstrate a clear and rapid response. This designates them a “keystone” or “sentinel” group that may describe the structure and function of the ecosystem. As a meta-organism, sharks offer selective niches (organs) for microorganisms that can provide benefits for their hosts. However, changes in the microbiota (due to physiological or environmental changes) can turn the symbiosis into a dysbiosis and may affect the physiology, immunity and ecology of the host. Although the importance of sharks within the ecosystem is well known, relatively few studies have focused on the microbiome aspect, especially with long-term sampling. Our study was conducted at a site of coastal development in Israel where a mixed-species shark aggregation (November–May) is observed. The aggregation includes two shark species, the dusky (Carcharhinus obscurus) and sandbar (Carcharhinus plumbeus) which segregate by sex (females and males, respectively). In order to characterize the bacterial profile and examine the physiological and ecological aspects, microbiome samples were collected from different organs (gills, skin, and cloaca) from both shark species over 3 years (sampling seasons: 2019, 2020, and 2021). The bacterial composition was significantly different between the shark individuals and the surrounding seawater and between the shark species. Additionally, differences were apparent between all the organs and the seawater, and between the skin and gills. The most dominant groups for both shark species were Flavobacteriaceae, Moraxellaceae, and Rhodobacteraceae. However, specific microbial biomarkers were also identified for each shark. An unexpected difference in the microbiome profile and diversity between the 2019–2020 and 2021 sampling seasons, revealed an increase in the potential pathogen Streptococcus. The fluctuations in the relative abundance of Streptococcus between the months of the third sampling season were also reflected in the seawater. Our study provides initial information on shark microbiome in the Eastern Mediterranean Sea. In addition, we demonstrated that these methods were also able to describe environmental episodes and the microbiome is a robust measure for long-term ecological research.

The recognition of the microbiota complexity and their role in the evolution of their host is leading to the popularization of the holobiont concept. However, the coral holobiont (host and its microbiota) is still enigmatic and unclear. Here, we explore the complex relations between different holobiont members of a mesophotic coral Euphyllia paradivisa. We subjected two lines of the coral—with photosymbionts, and without photosymbionts (apo-symbiotic)—to increasing temperatures and to antibiotics. The different symbiotic states were characterized using transcriptomics, microbiology and physiology techniques. The bacterial community’s composition is dominated by bacteroidetes, alphaproteobacteria, and gammaproteobacteria, but is dependent upon the symbiont state, colony, temperature treatment, and antibiotic exposure. Overall, the most important parameter determining the response was whether the coral was a symbiont/apo-symbiotic, while the colony and bacterial composition were secondary factors. Enrichment Gene Ontology analysis of coral host’s differentially expressed genes demonstrated the cellular differences between symbiotic and apo-symbiotic samples. Our results demonstrate the significance of each component of the holobiont consortium and imply a coherent link between them, which dramatically impacts the molecular and cellular processes of the coral host, which possibly affect its fitness, particularly under environmental stress.

Accelerated anthropogenic changes in the Eastern Mediterranean Sea (EMS) have facilitated the introduction, spread and establishment of invasive copepod species in this region. Here, we report the introduction of two non-native cyclopoid copepods Dioithona oculata and Oithona davisae for the first time in the Israeli coastal waters and describe their temporal variability. The species were identified by morphological characteristics, DNA barcoding and phylogenetic inference. Molecular identification and phylogenetic analysis supported the taxonomical identification, nevertheless, showed cryptic speciation within D. oculata, separating the Western Pacific and EMS clades. In the Israeli coastal waters, D. oculata presented a temporally restricted occurrence, appearing from September 2019 to December 2019 (30.0±0.7 – 21.0±1.1 °C) and October 2020 (28.0±0.7 °C). The highest abundances of D. oculata occurred in the autumn (October 2019 and 2020), when the water temperature reached 28.0 °C (7 and 10 ind. m-3, respectively). The lowest abundance occurred in December 2019 (0.35 ind. m-3), when the water temperature decreased to 21.0 °C, indicating that the thermal affinity of D. oculata for warm-temperate conditions, for reproduction and the maintenance of viable populations, has persisted in the introduced range. In contrast, O. davisae appeared almost all year around (17.0±0.5 – 28.0±0.7 °C). This species demonstrated peaks in abundance both in October 2019 and October 2020, when the water temperature reached 28.0 °C (406 and 92 ind. m-3), as well as when the temperature decreased to 17.0 °C (31 ind. m-3, February 2020), confirming its wide eurythermal tolerance. Based on our findings and previous observations, we suggest that D. oculata may have invaded the EMS through the Suez Canal and is now at the onset of its spread in the Mediterranean Sea, whereas O. davisae has been introduced via shipping, likely from the Northeast Atlantic, widely spreading and successfully establishing viable populations across the entire Mediterranean Sea, until the coastal Levantine Sea.