Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea.

The candidate Division MSBL1 (Mediterranean Sea Brine Lakes 1) comprises a monophyletic group of uncultured archaea found in different hypersaline environments. Previous studies propose methanogenesis as the main metabolism. Here, we describe a metabolic reconstruction of MSBL1 based on 32 single-cell amplified genomes from Brine Pools of the Red Sea (Atlantis II, Discovery, Nereus, Erba and Kebrit). Phylogeny based on rRNA genes as well as conserved single copy genes delineates the group as a putative novel lineage of archaea. Our analysis shows that MSBL1 may ferment glucose via the Embden-Meyerhof-Parnas pathway. However, in the absence of organic carbon, carbon dioxide may be fixed via the ribulose bisphosphate carboxylase, Wood-Ljungdahl pathway or reductive TCA cycle. Therefore, based on the occurrence of genes for glycolysis, absence of the core genes found in genomes of all sequenced methanogens and the phylogenetic position, we hypothesize that the MSBL1 are not methanogens, but probably sugar-fermenting organisms capable of autotrophic growth. Such a mixotrophic lifestyle would confer survival advantage (or possibly provide a unique narrow niche) when glucose and other fermentable sugars are not available.

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea.

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 ∼54% 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.

Benzoic acid-degrading bacteria from the intestinal tract of Macrotermes michaelseni Sjöstedt.

The intestinal tracts of termites host a wide variety of microbial symbionts, which have been implicated in degradative processes. In this study, a fungus-cultivating termite, Macrotermes michaelseni was found to harbor 2.2 x 10(6) bacterial cells per ml of gut homogenates capable of degrading benzoic acid. Two benzoic acid degrading bacteria were isolated from the highest dilution of gut homogenates in oxic media with benzoic acid as the sole carbon source. Isolate CBC was related to Stenotrophomonas maltophila LMG 958(T), Xanthomonas campestris DSM 3586(T) and Stenotrophomonas acidaminophila DSM 13117(T) with a sequence similarity of 98.3%, 94.7% and 94.2%, respectively. Isolate CBW was related to Enterobacter aerogenes JCM 1235(T) and Raoultella ornithinolytica ATCC 31898(T) with sequence similarity of 98.4% and 97.8%, respectively. In addition to growing on benzoic acid (up to 9 mM) aerobically, isolate CBW also degraded benzoic acid under anoxic conditions with nitrate as electron acceptor. Isolate CBC did not degrade bezoic acid with nitrate but could degraded resorcinol under oxic conditions.