Summary The Red Sea harbours approximately 25 deep‐sea anoxic brine pools. They constitute extremely unique and complex habitats with the conjugation of several extreme physicochemical parameters rendering them some of the most inhospitable environments on Earth. After 50 years of research mostly driven by chemists, geophysicists and geologists, the microbiology of the brines has been receiving increased interest in the last decade. Recent molecular and cultivation‐based studies have provided us with a first glimpse on the enormous biodiversity of the local microbial communities, the identification of several new taxonomic groups, and the isolation of novel extremophiles that thrive in these environments. This review presents a general overview of these unusual biotopes and compares them with other similar environments in the Mediterranean Sea and the Gulf of Mexico, with a focus on their microbial ecology.

The Red Sea is a unique marine ecosystem with contrasting gradients of temperature and salinity along its north-to-south axis. It is an extremely oligotrophic environment that is characterized by perpetual year-round water column stratification, high annual solar irradiation, and negligible riverine and precipitation inputs. In this study, we investigated whether the contemporary environmental conditions shape community assemblages by pyrosequencing 16S rRNA genes of bacteria in surface water samples collected from the northeastern half of this water body. A combined total of 1855 operational taxonomic units (OTUs) were recovered from the 'small-cell' and 'large-cell' fractions. Here, a few major OTUs affiliated with Cyanobacteria and Proteobacteria accounted for ∼93% of all sequences, whereas a tail of 'rare' OTUs represented most of the diversity. OTUs allied to Surface 1a/b SAR11 clades and Prochlorococcus related to the high-light-adapted (HL2) ecotype were the most widespread and predominant sequence types. Interestingly, the frequency of taxa that are typically found in the upper mesopelagic zone was significantly elevated in the northern transects compared with those in the central, presumably as a direct effect of deep convective mixing in the Gulf of Aqaba and water exchange with the northern Red Sea. Although temperature was the best predictor of species richness across all major lineages, both spatial and environmental distances correlated strongly with phylogenetic distances. Our results suggest that the bacterial diversity of the Red Sea is as high as in other tropical seas and provide evidence for fundamental differences in the biogeography of pelagic communities between the northern and central regions.

Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.

BackgroundThe next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.ResultsWe developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. ConclusionsWe developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus ). An emended description of the genus Halorhabdus is also proposed.An ever increasing diversity of extremely halophilic archaea is being uncovered from practically every type of hypersaline biotope, but no strain has ever been described from a deep-sea, hypersaline, anoxic basin. These deep-sea brines are unusual athalassohaline environments created by the evaporation, and subsequent exposure and flooding, of ancient seas, and are relatively stable as a result of their higher density (DasSarma & Arora, 2001). All of the known deep-sea brines are associated with tectonic activity, though found in regions around the world that represent entirely different geodynamic environments, namely divergent and convergent plate boundary settings (Red Sea and Mediterranean Sea, respectively) and the salt tectonics of the Gulf of Mexico (Degens & Ross, 1969; Scientific Staff of Cruise Bannock 1984-12, 1985Wiesenburg et al., 1985).The first deep-sea brines to be discovered were in the Red Sea, but only a few microbiological studies have been performed on these brines and, consequently, only a few micro-organisms (all of which are bacteria) have been isolated from these unusual biotopes (Antunes et al., , 2007Eder et al., 2001;Fiala et al., 1990; Trüper, 1969). Nonetheless, data from phylogenetic and biochemical studies have shown that a diverse archaeal population exists in these deep-sea brines (Eder et al., 1999(Eder et al., , 2001(Eder et al., , 2002Michaelis et al., 1990).New samples for microbiological studies were retrieved from the northern-most brine-filled depths of the Red Sea during Cruise 52/3 of RV Meteor in 2002(Antunes, 2003. Strain SARL4BT was isolated from the brine-sediment interface of the Shaban Deep as the result of a subsequent microbial diversity assessment study that relied on phylogenetic targeting of members of the Archaea. A phylogenetic analysis based on 16S rRNA gene sequencing revealed a close relationship between strain SARL4BT and Halorhabdus utahensis, the sole recognized species of the genus Halorhabdus. We propose that, on the basis of The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SARL4BT is EF127229.Polar lipid profiles of Halorhabdus utahensis and strain SARL4B T , separated by mono-dimensional TLC, are shown in a supplementary figure available with the online version of this paper.

The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools - water bodies characterized by a unique combination of extreme conditions. The ‘polyextremophiles’ that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.

A novel, moderately halophilic bacterium was isolated from the brine-seawater interface of the Shaban Deep, northern Red Sea. A polyphasic approach was used for the taxonomic characterization of this isolate, with the phenotypic and phylogenetic data clearly showing the distinctiveness of this bacterium. Cells of isolate E1L3A were Gram-negative, monotrichous cocci that showed a remarkable physiological flexibility, as could be seen by the quite broad growth ranges for oxygen, temperature, NaCl, and, to a smaller degree, pH. In addition, it was able to grow from atmospheric pressure up to 15 MPa, making it a piezotolerant bacterium. Phylogenetically, strain E1L3A represents a new, deeply branching lineage within the gamma-Proteobacteria, as determined by 16S rRNA gene sequence analysis. No close relatives are known so far, with sequence similarity to other cultivated members of the gamma-Proteobacteria being lower than 88%. The creation of the new genus Salinisphaera and the new species Salinisphaera shabanensis (DSM 14853; JCM 11575) for this new and highly versatile microorganism is therefore proposed.

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares B54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.