Genes Confirm Archaea's Uniqueness

Biologist Carl Woese of the University of Illinois upended the microbial world in 1997, when he argued that a newly discovered group of primitive-looking microorganisms weren't really bacteria-but were so different genetically that they belonged in a new domain which he labeled Archaea. Later that year, genome sequencing gave Woese's judgement a hearty second. The ringing endorsement came from The Institute for Genomic Research (TIGR) in Gaithersburg, Maryland, where researchers sequenced the genome of Methanococcus jannaschii, a member of the Archaea family that lives near undersea hot vents. This unusual organism thrives at near-boiling temperatures (around 100^o C), replicates using only inorganic compounds, and emits methane as a byproduct.

Carol Bult, leader of the research team, announced on 30 January, 1997, that her group had decoded all 1.7 million base pairs in the M. jannaschii genome, and the great majority of the genes have no equivalent in other organisms whose genes have been deposited in public databases. She made the announcement at a meeting in Santa Fe hosted by the Department of Energy. "This is a wonderful development," said microbiologist Norman Pace of Indiana University, Bloomington. "It defines the Archaea as a unique phylogenetic domain, and it raises the hope that genetic analyses will soon define a progenitor organism for both bacteria and Archaea. Declares Woese: "We're opening doors to a whole new world" of primitive life.




Table 1. Representative soil organisms in the Universal Tree.

Domain	Kingdoms	Representative Soil Organisms
Procarya	Eubacteria	True bacteria, green and purple sulfur bacteria, actinomycetes, sporogenic bacilli, cyanobacteria
Archaea	Euryarcheota	Extreme halophiles, methanogens
	Crenarcheota	Extreme thermophiles, sulfur reducers
Eucarya	Protozoa	Ciliates, zooflagellates, amoebae, slime molds
	Chromista	Oomycetes, Algae
	Mycota	Zygomycetes, the fungi
	Animalia	Nematodes, mites, millipedes, centipedes, annelid worms, collembolans, winged insects
	Planta	Higher Plants

1. The Eubacteria

• No true nucleus.
• Organelles are not membrane-bound.
• Cell wall contains peptidoglycan of varying amounts (more in Gram positive, less in Gram negative).

Table 2. Major features of some representative soil bacteria (true bacteria).

Genus	Cell shape	Spores	Motility	Oxygen requirement	Other features
Eubacteriales--Gram negative
Azotobacter	Rods or yeast-like cells	cysts	+ or -; peritrichous flagella	Aerobic	Fix atmospheric nitrogen and grow best on nitrogen deficient media.
Nitrosomonas	Rods	No	+ or -; polar flagella	Aerobic	Autotrophic. Oxidise ammonia to nitrite.
Pseudomonas	Rods	No	+ or -;peritrichous or polar flagella	Aerobic	Oxidative metabolism. Often produce fluorescent pigments.
Rhizobium	Rods	No	+ or -;peritrichous or polar flagella	Aerobic	Glucose utilised without much acid formulation. Form nodules with legumes and fix nitrogen.
Thiobacillus	Rod	No	+; polar flagella	Strictly aerobic	Most species are acidophilic, some can denitrify, some oxidize iron. Autotrophic, with sulfate oxidized to sulfur or sulfide.
Eubacteriales--Gram positive
Arthrobacter	Rods, later forming cocci	No	No	Aerobic	Form cystites. Little reaction in many of the usual biochemical tests.
Bacillus	Rods	Yes	+ or -; peritrichous flagella	Aerobic	Fermentative metabolism. Usually proteolytic. Rarely pigmented.
Clostridium	Rods	Yes	+; peritrichous flagella	Anaerobic	Fermentative metabolism. Often proteolytic. Some fix nitrogen.
Micrococcus	Cocci	No	No	Aerobic or microaerophilic	Fermentative metabolism. Often tolerate high osmotic pressure. Often yellow pigmented.
Mycobacterium	Rods or filaments	No	No	Obligately aerobic	Not readily stainable, lipid content of cell walls is very high. Growth is usually slow, pigments are rare, mycelial-like structures are common.

2. The Actinomycetes

Table 3. Subgrouping of the 39 genera of Actinomycetes described in Bergey's Manual.

Group designation	Brief characterization of one genus in each group
Nocardioforms--11 genera	Nocardia. Filaments unstable, fragmenting easily; 0.5-1.2 micro-meters in diameter. Chains of conidia on aerial or both aerial and substrate hyphae. No sporangia produced. Aerobic and mesophilic. Mycobacterium, Corynebacterium, and Arthrobacter are now classified in this group of Actinomycetes.
Multiloculars--3 genera	Frankia. Filaments 0.5-2.0 micrometers in diameter; no aerial mycelium. Multilocular sporangia formed by hyphal septation in three planes; sporangiospores nonmotile. Mutualistic or symbiotic diazotrophs, forming root nosules on nonleguminous plants.
Actinoplanetes--5 genera	Micromonospora. Branched septate mycelium. 0.5 micrometers in diameter. Aerial mycelium absent. Spores formed singly on substrate mycelium. Growth between 20o and 40o, not above 50oC.
Streptomycetes--4 genera	Streptomyces. Filaments 0.5-2.0 micrometers in diameter; extensively branched. Chains of three to many spores, usually aerial. Optimal growth 25o-35oC. Production of pigments or antibiotics or both.
Maduromycetes--7 genera	Streptosporangium. Stable, branched mycelium producing globose sporangia on aerial hyphae. Sporangiospores formed on a coiled, unbranched hypha. Hyphal hydrolysates contain madurose, a methylated galactose.
Thermomonosporas--4 genera	Thermonospora. Branched, nonfragmenting filaments forming leathery colonies. Spores formed in clusters at tips of branched sporophores. Optimal growth 40o-48oC. Common in manures, composts, and rotting hay.
Thermoactinomycetes--1 genus	Thermoactinomycetes. Substrate mycelium well developed, branched, septate; 0.4-0.8 micrometers in diameter. Forms endospores, suggesting classification should be with the Bacillaceae rather than with the Actinomycetales. Optimal growth 35o-58oC. Common in composts.
Others--4 genera	Glycomyces. Branching vegetative hyphae, 0.4 micrometers in diameter. Forms short chains of aerial, square-ended conidia. Mycelium contains no nitrogenous phospholipids and no mycolic acid, but does contain glycolipids.

3. The Cyanobateria (Blue-Green Algae)

Table 4. Characteristics of the five recognized orders of Cyanobacteria

Order	Characteristics	Generic Names
Chroococcales	Unicellular, or forming nonfilamentous aggregates;cell aggregate form dependent on planes of division and presence or absence of extracellular slimes or sheaths. Coccoids and rods 0.5-3.0 micrometers in diameter.	Chamaesiphon, Gloeothece, Gloeobacter, Cyanothece, Gloeocapsa, Synechococcus, Synechocystis
Pleurocapsales	Unicellular or nonfilamentous aggregates; reproduction by internal multiple fission to form daughter cells (baeocytes) smaller or much smaller than the parent; also binary fission.	Dermocarpa, Xenococcus, Chroococcidiopsis, Dermocarpella, Pleurocapsa, Myxosarcina
Oscillatoriales	Filamentous forms with cells not differentiating into heterocysts and akinetes. Binary fission in a single plane. Trichome (a chain of cells) diameters from 0.4 to (rarely) 100 micrometers. Trichomes flexible or rigid; may be wound into loose or tight spirals. Gliding motility.	Spirulina, Lyngbya, Oscillatoria, Arthrospira, Thrichodesmium, Pseudanabaena, Microcoleus.
Nostocales	Filamentous forms dividing in one plane only. Produce heterocysts when the concentration of combined N is low. Akinetes sometimes produced. False branching in some genera.	Nostoc, Cylindrospermum, Anabaena, Scytonema, Nodularia, Calothrix, Aphanizomenon.
Stigonematales	High degree of morphological complexity and differentiation. Longitudinal and oblique divisions in addition to transverse. True branching occurs; also two or more cell rows in trichomes. Heterocysts both intercalary and terminal in trichomes. Hormogonia formed in most genera; akinetes and pore channels between cells in some.	Stigonema, Fischerella, Haplosiphon, Westiella, Mastigocoleus, Loriella, Nostochopsis, Geitleria, Chlorogloeopsis.

4. Anoxygenic Phototrophic Bacteria (also known as the Green and Purple Sulfur Bacteria)

These bacteria are thought to have appeared very early in microbial evolution. Cells are spherical, spiral, or rod- or vibriod-shaped and are 0.3-0.6 micrometers in diameter. They occur singly or in regular or irregular aggregates; unicellular or uniseriately multicellular filamentous forms also occur. Gram negative. In most cases, multiplication is by binary fission; some species multiply by budding. With or without gas vacuoles. Motile or nonmotile; motility is by flagella or by gliding. Flagella are either monotrichous or multitrichous. There are six recognized subgroups, but only three have been well characterized (subgroups 1, 3, and 5). Photosynthetic pigments are located in the cytoplasmic membrane (Subgroup 4), in various types of intracytoplasmic membrane systems (Subgroups 1-3), or in chlorosomes (Subgroups 5 and 6). Colors of cell suspensions are purple-violet to purple-red, rose-red, yellowish-brown, brown, and green. Common to all species is the presence of bacteriochlorophylls (see Table 5A) and of carotenoid pigments (see Table 5B).

Photoautotrophic or photoorganotrophic under anaerobic or microaerobic conditions. In contrast to oxygenic photosynthesis of cyanobacteria, anoxygenic photosynthesis is dependent on external electron donors, such as reduced sulfur compounds, molecular hydrogen, or organic compounds. During sulfude oxidation, highly refractile globules of sulfur are transiently stored either inside the cells (Subgroup 1) or outside the cells (Subgroups 2 and 5). Storage materials are polysaccharides, poly-°-hydroxybutyrate, and polyphosphate. Carbon dioxide is assimilated through the reductive pentose phosphate cycle or the reductive citric acid cycle (Subgroup 5). Ammonium salts are generally used as the nitrogen source. The fixation of dinitrogen has been demonstrated in most representatives of all subgroups except Subgroup 6. With the exception of Subgroup 5, many species are capable or growing as chemoautotrophs or chemoorganotrophs under aerobic or microaaerobic conditions. Fatty acids, organic acids, or alcohols serve as electron donors and carbon sources. Habitats are the anoxic parts of moist soils and aquatic environments including fresh water, brackish water, and marine and hypersaline environments.

Subgroup 1 (Purple Sulfur)

Cells are able to grow with sulfide and sulfur as the sole photosynthetic electron donor for CO₂ assimilation; grow well under photoautotrophic conditions. In the presence of both sulfide and light, globules of sulfur appear inside the cells and may be further oxidized to sulfate. Contain bacteriochlorophyll a or b and carotenoids of groups 1-4. Vitamin B₁₂ may be required for growth.

Genera of Subgroup 1 include Amoebobacter, Chromatium, Lamprobacter, Lamprocystis, Thiocapsa, Thiocystis, Thiodictyon, Thiopedia, and Thiospirillum. The most widely studied genus is Chromatium. Species within this genus are motile by polar flagella, do not produce gas vacuoles, cells are ovoid to rod-shaped, and cells do not always develop a slime capsules.

Subgroup 3 (Purple Nonsulfur)

Cells preferably grow via photoassimilation of simple organic substances; some species are capable of using sulfide or thiosulfate as the electron donor for CO₂ assimilation. In the presence of sulfide and light, globules of sulfur may appear only outside the cells, never inside. Sulfur is rarely oxidized further to sulfate. Most genera are able to grow as chemoheterotrophs under microaerobic or aerobic conditions. Ammonia or dinitrogen is used as the nitrogen source. Most genera depend on one or more growth factors; the most commonly required are biotin, thiamine, niacin, and p-aminobenzoic acid. Contain bacteriochlorophyll a or b and carotenoids of groups 1-4.

Genera of Subgroup 3 include Rhodobacter, Rhodocyclus, Rhodomicrobium, Rhodopila, Rhodopseudomonas, and Rhodospirillum. The most widely studied genera are probably Rhodopseudomonas and Rhodospirillum. Species within the genus Rhodospirillum are spiral or vibrioid-shaped, cell division is by binary bission, and internal membranes may or may not contain distinct vesicles. Lamellae may or may not be present and finger-like intrusions are not found. Motility is by polar flagella and exospores are not produced.

Subgroup 5 (Green Sulfur)

Cells are able to grow with sulfide or sulfur as the sole photosynthetic electron donor for CO₂ assimilation. In the presence of both sulfide and light, globules of sulfur appear outside the cells, never inside. All species are obligately anaerobic and phototrophic; they grow well under photoautotrophic conditions. Simple organic substrates are photoassimilated only in the presence of sulfide and bicarbonate. Vitamin B₁₂ may be required for growth. Cultures are green (bacteriochlorophyll c or d) or brown (bacteriochlorophyll e). Antenna shaped bacteriochlorophylls are located in chlorosomes that underlie and are attached to the cytoplasmic membrane. Contain bacteriochlorophyll c, d, or e and carotenoids of group 5.

Genera of Subgroup 5 include Ancalochloris, Chlorobium, Chloroherpeton, Pelodictyon, Prosthecochloris, and a poorly characterized consortia of symbiotic aggregates. The best studied genus is Chlorobium. Species within this genus are green or brown, without gas vacuoles, are generally non-motile, and cells are spherical, ovoid, or rod-shaped.

Archaea "Bacteria"

• Glycerol isopranyl ether lipids in the cell wall
• CO₂ not assimilated by the Calvin Cycle; Acetyl CO-A or Reductive TCA
• N₂ fixation demonstrated
• Similarities to Eucaryotes
  • "ribosomal" structures
  • Similar DNA and RNA polymerases

Table 6. Subdivision of the Archaea

Kingdoms and Groups	Representative genera
Kingdom euryarchaeota
Extreme halophiles	Halobacterium, Natronobacterium
Methanogens	Methanobacterium, Methanospirillum, Methanococcus
Extreme thermophiles	Archaeoglobus, Thermococcus, Thermoplasma
Kingdom crenarchaeota
Thermoacidophiles	Sulfolobus
Strictly anaerobic crenarchaeotes	Pyrodictium

Table 7. Optimal growth conditions for selected Archaea

	Temperature, oC	pH	NaCl	Aerobic	Anaerobic
Euryarchaeotes
Halobacterium halobium	40	7.3	4	+	-
Methanospirillum	34	7.0	0.01	-	+
Methanothermus fervidus	83	6.5	0.01	-	+
Thermoplasma acidophilum	60	1.5	tr	+	+
Archaeoglobus fulgidus	83	7.0	0.3	-	+
Pyrococcus furiosus	100	7.0	0.3	-	+
Crenarchaeotes
Sulfolobus acidocaldarius	73	1.5	tr	+	+
Pyrodictium occultum	105	6.5	0.03	-	+
Thermoproteus tenax	88	5.5	tr	-	+

1. Extremely Thermophilic and Hyperthermophilic S^o-Metabolizers

2. Extremely Halophilic, Aerobic Archaeobacteria (Halobacteria)

Aerobic; some are able to grow anaerobically in the presence of nitrate. Chemoheterotrophic. Carboydrates, alcohols, carboxylic acids, or amino acids serve as carbon and energy sources.

Require at least 1.5 M NaCl for growth, most growing optimally at 2-4M NaCl. Some members are alkaliphilic, growing only at pH >8.5. They occur in nature when the salt concentration is high (i.e. in salt lakes, soda lakes, salterns, and saline soils). One type occurs in proteinaceous products heavily salted with solar salt.

Current genera are largely defined by chemotaxonomic criteria, notable polar lipid composition. The lipids of all isolates to date contain diphytanyl or phytanyl sesterterpanyl derivatives of phosphatidyl glycerol and phosphatidyl glycerol phosphate.

3. Archaeal Sulfate Reducers

4. Cell Wall-less Archaeobacteria

Here is a link to an excellent overview of the ARCHAE and the sections on life history and ecology, systematics, and morphology are especially good.

Plants and Animals

• A true nucleus is present.
• Nucleus and organelles are membrane-bound.
• No peptidoglycan in cell walls (primarily carbohydrates instead).

Table 8. Subdivision and Classes of Fungi

Subdivision	Class
Mastigomycotina		Fungi with motile spores or gametes.
	Oomycetes	Zoospores biflagellate; one anterior and one posterior flagellum.
	Chytridiomycetes	Zoospores usually have one smooth posterior flagellum; none anterior.
Zygomycotina		Produce thick-walled zygospores by fusion of two gametangia.
	Trichomycetes	Obligate parasites of arthropods.
	Zygomycetes	Many are commonly occuring, rapidly growing saprotrophs; others are parasitic, predatory, or symbiotic in mycorrhizal associations.
Ascomycotina		Ascospores sexually produced, usually in asci borne on ascocarps; in yeasts, single cells may serve as a solitary ascus.
	No classes recognized	19 orders recognized, with more than 40,000 species. In many, asci develop high turgidity and forcefully eject spores. Among traditional classes have been those for the cup fungi, flask fungi, yeasts, and powdery mildews.
Basidiomycotina		Contains most of the large, conspicuous fungi seen in the field (mushrooms, shelf fungi, etc.). Basidiospores are produced externally, whereas ascospores are produced internally.
	Basidiomycetes	15 orders recognized; over 15,000 species. Many wood-rotting species.
	Ustomycetes	One order, the smuts. Infect plant fruit, seeds.
	Teliomycetes	One order, the rusts. Infect plant foliages.
Deuteromycotina		Fungi traditionally classified on the basis or lack of sexuality; often called the Fungi Imperfecti. Subdivision now becoming obsolete, with species being reassigned to Ascomycotina or Basidiomycotina. Retained here because of prominence in the literature.
	Coelomyces	Conidia commonly formed in a cavity within fungal tissue. Extremely common on dead foliage.
	Hyphomycetes	Conidia formed externally. An extremely large class, with many well-known genera such as Aspergillus, Fusarium, Penicillium, and Trichoderma.

Arbutoid Mycorrhizae
These are the mycorrhizae of desert plants (primarily shrubby species) in arid to semi-arid environments. The fungi are mainly basidiomycetes and form both a mantle and a net on host plants. Some of these mycorrhizae have been studied because of their water uptake efficiency.

Table 11. Approximate numbers of animals per square meter in a "typical"
grassland soil.

Organism	Thousands per Square Meter
Nematodes	120 x 106
Enchytraeid Worms (potworms)	20
Earthworms	2
Molluscs (slugs, snails)	8
Larger Myriapods (millipedes, centipedes)	2
Isopods (wood lice)	1
Ants	1.3
Beetles and larvae	1.5
Dipterous larvae (fly maggots)	2
Aracneidae (spiders)	1
Collembola (spring tails)	43
Acarina (mites)	124

Soil animals are usually described based on fresh weight per amount of soil, numbers (Table 11), or body size. Spiders and centipedes are wholly carnivorous, and ants predominately so; beetles, fly maggots, mites, and nematodes range widely in their diet according to species; the remaining groups feed largely on decaying organic matter, many collembola are closely associated with fungi and other microorganisms. Soil animals are very important in a food chain or food web that converts decaying organic matter into microbial (bacterial and fungal) biomass and then into animal biomass.