Summary
Life at high salt concentrations is energetically expensive. The upper salt concentration limit at which different dissimilatory processes occur in nature appears to be determined to a large ...extent by bioenergetic constraints. The main factors that determine whether a certain type of microorganism can make a living at high salt are the amount of energy generated during its dissimilatory metabolism and the mode of osmotic adaptation used. I here review new data, both from field observations and from the characterization of cultures of new types of prokaryotes growing at high salt concentrations, to evaluate to what extent the theories formulated 12 years ago are still valid, need to be refined, or should be refuted on the basis of the novel information collected. Most data agree well with the earlier theories. Some new observations, however, are not easily explained: the properties of Natranaerobius and other haloalkaliphilic thermophilic fermentative anaerobes, growth of the sulfate‐reducing Desulfosalsimonas propionicica with complete oxidation of propionate and Desulfovermiculus halophilus with complete oxidation of butyrate, growth of lactate‐oxidizing sulfate reducers related to Desulfonatronovibrio at 346 g l−1 salts at pH 9.8, and occurrence of methane oxidation in the anaerobic layers of Big Soda Lake and Mono Lake.
Several groups of Archaea, all
Euryarchaeota
, develop in hypersaline environments (from >10 % salt up to saturation). The cultured diversity of halophilic Archaea includes the family
...Halobacteriaceae
of aerobic or facultative anaerobic, generally red-pigmented species (47 genera and 165 species as of February 2014) and seven representatives of four genera of methanogens, most of which obtain energy from methylated amines under anaerobic conditions. Metagenomic studies have identified an additional deep lineage of Archaea in salt lakes and ponds with brines approaching NaCl saturation. Genomic information is now available for representatives of these ‘Nanohaloarchaea’, but no members of this lineage have yet been cultured. Multilocus sequence analysis is becoming increasingly popular in taxonomic studies of the
Halobacteriaceae
, and such studies have demonstrated that recombination of genetic traits occurs at an extremely high frequency at least in some genera. Metagenomic studies in an Antarctic lake showed that large identical regions of up to 35 kb in length can be shared by members of different genera living together in the same environment. Such observations have important implications not only for the taxonomy of the
Halobacteriaceae
, but also for species concepts and questions on taxonomy and classification for prokaryotic microorganisms in general.
The halophilic Archaea of the family Halobacteriaceae (36 genera with 129 species with standing in nomenclature as of November 2011) provide an excellent example of how changing concepts on ...prokaryote taxonomy and the development of new methods have influenced the way in which the taxonomy of a single group of prokaryotes is treated. This review gives an overview of the taxonomy of the family Halobacteriaceae, showing the impact that methods of phenotypic characterization, numerical taxonomy, chemotaxonomy and especially polar lipid analysis, 16S rRNA gene sequence comparisons, multilocus type analysis and comparative genomics have had on their classification.
Extremely halophilic microorganisms that accumulate KCl for osmotic balance (the Halobacteriaceae, Salinibacter) have a large excess of acidic amino acids in their proteins. This minireview explores ...the occurrence of acidic proteomes in halophiles of different physiology and phylogenetic affiliation. For fermentative bacteria of the order Halanaerobiales, known to accumulate KCl, an acidic proteome was predicted. However, this is not confirmed by genome analysis. The reported excess of acidic amino acids is due to a high content of Gln and Asn, which yield Glu and Asp upon acid hydrolysis. The closely related Halorhodospira halophila and Halorhodospira halochloris use different strategies to cope with high salt. The first has an acidic proteome and accumulates high KCl concentrations at high salt concentrations; the second does not accumulate KCl and lacks an acidic proteome. Acidic proteomes can be predicted from the genomes of some moderately halophilic aerobes that accumulate organic osmotic solutes (Halomonas elongata, Chromohalobacter salexigens) and some marine bacteria. Based on the information on cultured species it is possible to understand the pI profiles predicted from metagenomic data from hypersaline environments.
Halophilic representatives of the genus Dunaliella, notably D. salina and D. viridis, are found worldwide in salt lakes and saltern evaporation and crystallizer ponds at salt concentrations up to ...NaCl saturation. Thanks to the biotechnological exploitation of D. salina for β-carotene production we have a profound knowledge of the physiology and biochemistry of the alga. However, relatively little is known about the ecology of the members of the genus Dunaliella in hypersaline environments, in spite of the fact that Dunaliella is often the main or even the sole primary producer present, so that the entire ecosystem depends on carbon fixed by this alga. This review paper summarizes our knowledge about the occurrence and the activities of different Dunaliella species in natural salt lakes (Great Salt Lake, the Dead Sea and others), in saltern ponds and in other salty habitats where members of the genus have been found.
The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes. In view of inconsistencies in the use of names of many prokaryotic taxa and ...confusion caused by recent nomenclature changes, this essay presents an overview of how to use correct names of taxa. It includes information on validly published names of prokaryotic phyla, the way to deal with names of species that were transferred to newly created genera, and the nomenclature of uncultivated Candidatus taxa. It also provides recommendations for databases that provide reliable nomenclature information.
The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented ...availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and ...reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.
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