MicrobiologyBytes

Microorganisms from the bacterial and archaeal domains of the tree of life comprise the greatest breadth of biodiversity on earth. Yet the essential evolutionary process of speciation (through which biodiversity is generated) is poorly understood in microbes. At issue is the fundamental question of whether gene flow among individuals of clonally reproducing microorganisms is rapid enough to provide coherence within – and prevent speciation between – coexisting lineages.

Researchers used complete sequencing of microbial genomes to observe speciation in action. They looked at Archaea called Sulfolobus islandicus gathered from a geothermal hot spring from the Mutnovsky Volcano in Kamchatka, Russia, whose physical isolation allows us to pinpoint evolutionary processes to one location. Contrary to the theoretical predictions for microbes, they were able to provide evidence that two novel lineages are in the process of becoming ecologically distinct and evolutionarily independent despite the fact that they recombine. The divergence is not happening uniformly across the genome because certain genomic regions are more prone to become differentiated between species than others. This genomic view of the process of speciation occurring within a single natural microbial population contributes to our understanding of the generation of biodiversity in Archaea and furthers our understanding of speciation across the tree of life.

Patterns of Gene Flow Define Species of Thermophilic Archaea. (2012) PLoS Biol 10(2): e1001265. doi:10.1371/journal.pbio.1001265
Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic ”continents,” indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.

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The Archaea possess unique metabolic pathways, distinct from those in Bacteria and Eukarya. Based on the genome sequences of the Archaea, there are many cases in which a particular metabolic pathway seems to be absent or incomplete. The search for these ‘missing’ pathways or enzymes has been an exciting field of research in the Archaea. A representative example was the CO₂-fixing mechanisms in autotrophic Crenarchaeota. Although many autotrophic Crenarchaeota had been isolated, homologs of previously recognized CO₂-fixing pathways could not be identified on their genomes. Genes responsible for the degradation and biosynthesis of various sugars had also been unidentified. This paper describes recent findings in archaeal metabolism, including sugar metabolism, CO₂ fixation and a wide range of biosynthetic pathways. The predicted distributions of these pathways, based on genome sequence analyses, in the Archaea are also discussed. These investigations will help understand how microorganisms use and interact with the many natural and man-made compounds they encounter in their environments and also provide the foundation for many biotechnology developments.

Novel metabolic pathways in Archaea, Curr Opin Microbiol. May 23 2011 doi:10.1016/j.mib.2011.04.014
The Archaea harbor many metabolic pathways that differ to previously recognized classical pathways. Glycolysis is carried out by modified versions of the Embden-Meyerhof and Entner-Doudoroff pathways. Thermophilic archaea have recently been found to harbor a bi-functional fructose-1,6-bisphosphate aldolase/phosphatase for gluconeogenesis. A number of novel pentose-degrading pathways have also been recently identified. In terms of anabolic metabolism, a pathway for acetate assimilation, the methylaspartate cycle, and two CO(₂)-fixing pathways, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, have been elucidated. As for biosynthetic pathways, recent studies have clarified the enzymes responsible for several steps involved in the biosynthesis of inositol phospholipids, polyamine, coenzyme A, flavin adeninedinucleotide and heme. By examining the presence/absence of homologs of these enzymes on genome sequences, we have found that the majority of these enzymes and pathways are specific to the Archaea.

Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. This paper proposes that the scarcity of disease-causing Archaea is due, in part, to mutually-exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association of bacterial virulence factors with phages or mobile elements. The ability of bacterial phages to infect Bacteria and then use them as a vehicle to infect eukaryotes may be difficult for archaeal viruses to evolve independently. Differences in extracellular structures between Bacteria and Archaea would make adsorption of bacterial phage particles onto Archaea (i.e. horizontal transfer of virulence) exceedingly hard. If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control.

The proportional lack of archaeal pathogens: Do viruses/phages hold the key? (2011) BioEssays 1521-1878 doi: 10.1002/bies.201000091

Related:

• Archaea – timeline of the third domain
• Archaea – a microbial cockatrice?

The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea – their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This review charts the ‘archaea movement’, from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.

Archaea — timeline of the third domain. (2011) Nature Reviews Microbiology 9: 51-61 doi:10.1038/nrmicro2482

Related:

• Unique cell division machinery in the Archaea
• Archaea – a microbial cockatrice?

A cockatrice was a flamboyant sight at medieval banquets, featuring a roasted chimera of rooster fused to a suckling pig. In this article in Microbiology Today (pdf) Ed Bolt and Stephane Delmas suggest that there are similarities with archaea, ancient micro-organisms that have features of both bacteria and eukaryotes within their genomes:

Archaea and bacteria are micro-organisms that are similar, yet different. Archaea are evolutionarily ancient organisms that have soaked up diverse ecosystems for at least 2.5 billion years. They are, like bacteria, unencumbered by various complex sub-cellular structures (e.g. mitochondria, a membrane-bound nucleus) and as such have been for most of their long existence, or at least from when microbiologists started looking at them, considered to be bacteria that had evolved to thrive in extreme environments (e.g. at high temperature or salinity). For this reason they were often called archeabacteria. However, DNA sequencing experiments in the 1970s drove a wedge through the bacteria, splitting it into two separate domains of cellular life: the Bacteria and the Archaea. The genetic distinction between bacteria and archaea is now generally accepted since its original proposal in 1977, but has its evolutionary root much earlier, probably pre-dating the emergence of oxygen 2.5 billion years ago. Therefore, the classification of cellular organisms is now usually represented in a tree of life consisting of three domains, Bacteria, Archaea and Eukarya.

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Related:

• Unique cell division machinery in the Archaea

The Archaea form a separate domain of life that has evolved in parallel with Bacteria and Eukarya. While aspects of archaeal biology appear to be unique, certain traits resemble those in eukaryotes, including the machineries that govern information storage, maintenance, and processing. Several features of archaeal cell cycle progression have been elucidated in considerable detail including the overall organization of the cell cycle in certain species, and regulatory and mechanistic aspects of the replication process. Conversely, the genome segregation machinery remains essentially uncharacterized in this domain.

A unique cell division machinery in the Archaea. PNAS USA November 5, 2008
In contrast to the cell division machineries of bacteria, euryarchaea, and eukaryotes, no division components have been identified in the second main archaeal phylum, Crenarchaeota. Here, we demonstrate that a three-gene operon, cdv, in the crenarchaeon Sulfolobus acidocaldarius, forms part of a unique cell division machinery. The operon is induced at the onset of genome segregation and division, and the Cdv proteins then polymerize between segregating nucleoids and persist throughout cell division, forming a successively smaller structure during constriction. The cdv operon is dramatically down-regulated after UV irradiation, indicating division inhibition in response to DNA damage, reminiscent of eukaryotic checkpoint systems. The cdv genes exhibit a complementary phylogenetic range relative to FtsZ-based archaeal division systems such that, in most archaeal lineages, either one or the other system is present. Two of the Cdv proteins, CdvB and CdvC, display homology to components of the eukaryotic ESCRT-III sorting complex involved in budding of luminal vesicles and HIV-1 virion release, suggesting mechanistic similarities and a common evolutionary origin.

Related:

• Yeast shows what drives cells to divide