Archaea | Biology and Biochemistry for MCAT PDF Download

Archaea Etymology

Archaea is a modern Latin word derived from the Greek word “arkhaios” meaning ‘primitive’. The singular of archaea is archaeon. Archaea is the plural form of “archaeon“.

Domain Archaea and other Classification Systems

When biological sciences are studied, a variety of different organisms come into the picture. Understanding one organism in relation to the other is very difficult due to the vast diversity. For ease of studying, classification systems are proposed. In the history of life science, several such methods have been proposed. Look at the table below for a brief summary of the different classification systems over the course of time.

Table 1: Summary of the Different Classification Systems

Notice the introduction of archaea in 1990 by Carl R. Woese. It was at this time that nucleotide sequences of the small subunit of rRNA (16S ribosomal RNA) were compared from all the cellular life forms from common ancestors. Since this molecule is conserved in all other life forms that are cellular in nature, the genome phylogeny (phylogenetic structures derived from phylogenetic trees upon phylogenetic analyses) derived from this work turned out revolutionary. What was earlier believed to be just “monera” was now split into “bacteria and archaea”. This global phylogeny overturned the existing notions of purely prokaryotic and eukaryotic cell dichotomy. An understanding of the prokaryotic domain deepened from this point.

Archaea Versus Archaebacteria

Since they were earlier placed under the monera kingdom up till the 5-kingdom classification (1969), they are called archaebacteria then. But after the introduction of the 3-domain system (1990) and the identification of the major differences between archaea and bacteria, the term “archaebacteria” has fallen out of use in the scientific community.

Difficulties with Studies of Archaea Group

• Although the discovery of this group from the studies of Carl R. Woese and group ignited interest in the subject, there were some legit problems associated with it. Most of the archaeal cells haven’t been discovered or isolated in the lab. They have only been detected in some environmental samples with the aid of gene sequencing.
• This has made their classification into different phyla relatively difficult. In recent years, a lot of evolutionary biology-related work has been undertaken to better understand evolutionary relationships between different archaeal species.
• Evolutionary relationships and evolutionary history can bring a lot of clarity to the table. Evolutionary histories help in clearly deciphering the origin, evolution, and directions of further changes at molecular levels (molecular evolution). Molecular biology tools help in such work.

Eukarya group is in red, the bacteria group is in blue and the archaea group is in green. Notice the close affinity of archaea with eukarya rather than with bacteria.

Differences Between Archaea and Bacteria

Look at the table of comparison below to learn about the major differences between these 2 domains of life; archaea vs bacteria. Both of these domains have been found to be evolutionarily distinct as per 16S rRNA phylogeny.
Table 2: Summary of the Differences between Archaea and Bacteria

Notice the differences in the structure of RNAP (RNA polymerase) required for the transcription process. Archaeal lineage RNAP shares similarities with eukaryotic RNAP II, while the RNAP of bacteria is different from both groups.

Archaeal membrane is formed by lipids containing ether links. Contrastingly, bacterial membranes are formed by lipids containing ester links.

Habitats of the Archaea

Archaea were first identified from extreme environments like volcanoes, hydrothermal vents, etc. But as the sequencing technology became more widely available, the archaeal presence was found to be ubiquitous. Now they are known to inhabit a vast range of natural environments and habitats. Besides constituting a major part of the ecosystem, they play an instrumental role in its functioning, too. They inhabit both terrestrial and aquatic ecosystems.
Where do archaebacteria live? To answer that, here’s the list of some of their major habitats:

• Deeps seas and oceans (archaea form nearly 20% of microbial diversity of the oceans)
• Geysers
• Hot water springs
• Hydrothermal vents
• Volcanoes
• Black smokers
• Mines and oil wells
• Very cold habitats like ice sheaths of tundra
• Highly saline lakes
• Highly acidic places
• Highly alkaline waters
• Swamps, wetlands, and marshlands
• Sewage
• Intestinal tracts of humans and animals
• Highly degraded soils, anoxic muds (archaea in soil)

Archaeal Groups Inhabiting Different Extreme Habitats

Since archaea inhabit extreme habitats, they are called extremophiles. Within extremophiles, there are different physiological categories or types of archaea like:

• Halophiles (live in extreme salt conditions like salt lakes, and brackish waters)
  Example: Halobacterium spp.
• Thermophiles (live in extremely high temperatures like hot springs and vents)
  Example: Methanopyrus kandleri
• Alkaliphiles (live in extreme alkaline conditions like marine hydrothermal systems)
  Example: Thermococcus alcaliphilus is a marine archaea.
• Acidophiles (live in extremely acidic conditions like dry hot soil and volcanic sites)
  Example: Picrophilus torridus

An archaeon doesn’t necessarily come under only one of these categories. In fact, many archaea are a combination of two or more of these features.
The Great Salt Lake of Utah in the United States is home to halophilic archaea species. They inhabit the salt crust (shown in [a]). Figure [b] shows them growing in lab conditions on salt agar. Figure [c] shows the pinkish tinge that these halophilic archaea impart to the Utah lake.

Picrophilus torridus is an acidophilic archaeon whose membrane integrity is disturbed at pH above 4.00. It was isolated for the 1st time from dry hot soil samples from Hokkaido in Japan.

Characteristics of the Archaea

So, read the archaea characteristics in this section and get an answer to what is special about archaea.

Energy sources used by archaea

• Relatively diverse group sources than eukaryotic organisms, like sugars, ammonia, metal ions, and hydrogen gas
• Based on their preference of source for deriving energy, they are divided into different nutritional groups. Some of them are:
• Phototrophic Archaea: Some species of archaea are known to utilize energy from the sun. Hence they are called phototrophic archaea. Although they can utilize sunlight like the plants, they can’t fix atmospheric carbon. So, the answer to the query “if archaea photosynthesize” is NO. They can be “PHOTOTROPHIC” and “NOT PHOTOSYNTHETIC”.
  Example: Haloarchaea or Halobacterium.

This is a picture of a lake in India, Lonar lake that recently turned color to pinkish red. A probe led by the scientists from CSIR-NEERI lab brought to light the presence of salt-tolerant Haloarchaea populations in the lake. The photo pigment (for phototropism) of these archaea organisms is called ‘bacteriorhodopsin’ which is opaque to long wavelengths (red) and imparts this color to the lake.

• Lithotrophic Archaea: Some species of archaea are known to utilize inorganic compounds (chemical energy) to take care of their energy needs like metal ions, hydrogen, ammonia, etc.
  Examples: Pyrolobus, Ferroglobus, Methanobacteria, ammonia oxidizing archaea, sulfate reducing archaea.

Ferroglobus placidus is a lithotrophic archaea. It is an extremophile and can grow at temperatures up to 113°C.

• Organotrophic Archaea: Some species of archaea are known to utilize organic compounds to take care of their energy needs like pyruvate, starch, maltose, etc.Examples: Methanosarcinales, Pyrococcus, Sulfolobus

Pyrococcus furiosus is an extreme thermophilic organotrophic archaeon that can grow at temperatures up to 100°C. The main metabolic pathway in this organism is anaerobic oxidation/ respiration as it’s an anaerobic archaeon. This metabolism makes it a suitable candidate for microbial fuel cell (MFC) development. MFCs are biological cells that can generate power at temperatures close to boiling point. As can be seen in the picture, the main source of energy is the organic compound “malt-short form of maltose”. 

• Extremophiles
  • Most of the members of the archaeal phylum are extremophilic in nature growing in vents, springs, salt lakes and ditches, volcanoes, marshlands, and deep surfaces of seas and oceans. In fact, archaea were first discovered in such habitats.
• Reproduction
  • Asexual reproduction is the only way for archaea. They reproduce asexually via binary fission, budding, or fragmentation. No archaeal member has been reported to undergo endospore formation.
• Roles in Earth’s biomes functioning
  • Archaea play a multitude of ecological roles ranging from that in the nitrogen cycle to the maintenance of microbial symbiotic communities. Most of the known archaea either build mutualistic or commensalistic relationships. Their pathogenic or parasitic representatives haven’t been observed yet.
• Example of mutualistic archaea: Methanogenic archaea inhabiting the GIT of humans and other organisms like ruminating animals like cows, buffalo, etc. Archaea in the gut help in the facilitation of digestion.
  A number of examples of the archaea inhabiting the human gastrointestinal tracts (archaea in humans).

Archaea in biogas production 

Because of their methanogenic and extremophilic activity, archaea are extensively used in the commercial production of biogas and also in sewage treatment plants. Biotechnological advancements enable the exploitation of archaeal enzymes from these extremophilic species. Since processes including high temperatures, pressures, and usage of organic solvents are mainstream in biogas production and sewage treatment; these hydrogenotrophic species widen the scope.

Structure, Composition Development, and Operation

Archaea, although different from bacteria, share many common features with bacteria too. Both of them being prokaryotic life forms lack nuclei and membrane-bound cell organelles.

• Size range: 0.1-15 micrometers
• Shape range: Spherical, rod-like, spiral, plates, irregularly shaped, lobed, needle-like filamentous, rectangular rods, flat square shape.

Structure of archaeal cells 

Cell wall and archaella (archaeal flagella)

The cell wall is present in most archaea except Thermoplasma and Ferroplasma. The surface-layer proteins encoded constitute the cell wall or S-layer. The role of the S-layer or cell wall in archaea is for physical and chemical protection. While bacterial cell walls are made up of peptidoglycan, archaea cell walls lack it. They rather possess pseudo-peptidoglycan like in Methanobacteriales. Pseudopeptidoglycan is similar to bacterial peptidoglycan (morphologically, functionally) but is chemically distinct (no D-amino acids & N-acetylmuramic acid). Rather, they have N-Acetyltalosaminuronic acid. The name for archaeal flagella is archaella. It functions similar to bacterial flagella.
Notice the presence of pseudopeptidoglycan in the archaeal cell walls

Membranes

• While bacterial and eukarya cell membranes have ester-linked lipids, archaea cell membranes have ether-linked lipids. Bacterial and eukarya cells have D-glycerols in their membranes but archaeal membranes have L-glycerols.
• The bacterial and eukarya backbone is built on “sn-glycerol-3-phosphate” whereas the archaeal phospholipid backbone is built on “sn-glycerol-1-phosphate”.
• The enzymes used by archaea for their membrane synthesis are different from those used by bacteria and eukarya.
• Archaeal membrane lipid tails possess multiple side branches whereas the bacterial and eukarya membranes lipid tails are devoid of side branches or rings.
• Isoprenoids find their distinct usage in the archaeal membrane phospholipids. Other microbes/organisms have isoprenoids in their bodies but not in membrane phospholipids.
• Archaea also have archaeols, a type of core membrane lipids. These are often used as “archaeal biomarkers” associated with methanogens.

Notice the presence of archaeol, ether-links and branched isoprene chains in the archaeal membrane. Contrastingly, bacterial membranes lack archaeol and possess unbranched fatty acids with ester links. Archaea cell structure is distinct in a number of ways. 

Archaeols are unique core membrane lipids synthesized by the archaea group. The process of archaeol synthesis is carried out via an ‘alternate MVA pathway’. For the synthesis of the isoprenoid chains constituting archaeol, a total of 3 unique steps have been identified.

Metabolism

Archaeal metabolism displays a range of biochemical reactions. Some of these are common to all archaeal species; others are specific to certain taxa.

Chemical structure of methanofuran, a unique coenzyme possessed by methanogenic archaea

• As discussed in previous sections, there are 3 major nutritional groups namely phototrophic, lithotrophic and organotrophic. Lithotrophic and organotrophic are sometimes placed under a broader category called chemotrophic. They, as chemotrophs, play vivid roles like:
  • Nitrifiers
  • Methanogens
  • Anaerobic methane oxidizers (main inhabitants of anaerobic environments)
• Phototrophic archaea carry out the chemiosmosis process without fixing atmospheric carbon.
• Archaea also carry out aerobic and anaerobic respiration. The process of glycolysis occurring in the archaea is a modified form of the one happening in eukarya and bacteria.
• Archaea carry out citric cycles; complete or partial.
• Archaea residing in anaerobic conditions are often methanogenic (produce methane). Studies have found that this metabolic reaction would have evolved very early on, probably signaling the methanogenic nature of the 1st free-living organisms on this planet.
• Archaea are in possession of a unique set of coenzymes for methanogenesis activity. Example: Methanofuran and coenzyme M.

Genetics

Let’s briefly discuss archaeal genomes and genetic material.

• Number and nature of chromosome: 1 and circular
• The largest known genome for archaea: Methanosarcina acetivorans (5,751,492 bp)
• The smallest known genome for archaea: Nanoarchaeum equitans (490,885 bp)
• The presence of plasmids is also noted in archaea just like in bacteria. And their inter-cell transfer is also similar via conjugation-like processes. Both archaea and bacterial conjugation aid plasmid transfer.
• Genetically quite different from bacteria and eukarya.
• Transcription: Close resemblance to eukaryotic transcription (archaeal RNAP is also similar to that of eukaryotes RNAP II).
• Some of the archaeal transcription factors (TFs) have a resemblance with those of bacteria.
• Post-transcriptional modification (PTMs): Closely resemble those of eukaryotes.

Gene Transfer and Genetic Exchange

Gene transfer, exchange, and horizontal gene transfer/ lateral gene transfer happen via inter-cell cytoplasmic bridges.
The illustration shows the “cytoplasmic bridge” formation between 2 Haloferax volcanii cells. These are extreme halophilic archaeal species. 

Cellular aggregations are also known for genetic exchange and recombinations in archaeal species. These aggregations are induced by physical agents (UV, pH, temperature) or chemical agents (mitomycin C, bleomycin). These homologous recombinations serve as the repair mechanisms for the DNA damage caused due to different agents. Some scientists have also speculated this as an alternative type of sexual reproduction in primitive archaeal species.
“Cellular aggregation” has been studied in hyperthermophilic archaeal species Sulfolobus solfataricus.
Pic A: Cellular aggregation after different UV doses.
Pic B: Light micrographs of Sulfolobus solfataricus cell aggregates at different UV doses.
Pic C: A cell aggregate at 75 J/m2 UV dose.

Archaeal viruses

A number of viruses target archaea; some are archaea-specific while some are cosmopolitan. In contrast to bacterial viruses which either conduct lytic or lysogenic pathways or display a mixed version of both, archaeal viruses usually maintain stable, lysogenic-like pathways.

Archaea Reproduction

Archaea reproduction strategies encompass:

• Binary fission
• Multiple fission
• Fragmentation
• Budding