Phyla with few cultivated species

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There are several bacterial phlya that have only a few cultivated, well-known species. Several have been described in previous chapters, such as the Thermotogae, Aquificae, Cloroflexi, Chlorobi, &c, &c. The dividing lines between the classical 13 bacterial phyla and the phyla describes below are, of course, arbitrary and historical. In reality, some of these groups are apparently far more abundant in the environment and now have many more species known (although not as well known) as the groups already discussed.

Example phylum : Verrucomicrobia


This phylum contains a couple of appendaged Bacteria, Verrucomicrobium and Prosthecobacter. These were previously though to be related to the appendaged α-proteobacteria. The remaining cultivated members of this phylum are poorly-characterized. The uncultivated species in this group are apparently abundant in the soil and subsurface, making up significant fractions of the total number of sequences isolated. Fluorescent probes targeting EA25 (which appeared frequently in an analysis of soil) indicate that the organism it comes from can make up 1-10% of soil microbes; 107 - 108 per gram of soil. This phylum is probably related to the Chlamydiae.

Example species:


Verrucomicrobium spinosum is a mesophilic non-motile heterotrophic aerobe isolated from a small eutrophic lake (Lake Pluβsee). Unlike the appendaged α-proteobacteria, the appendages of V. spinosum have bundles of fimbriae at their tips (a bit like the stereotypical hairs from the nose warts of a witch). It is covered in many short (ca. 0.5μm long) appendages that appear conical under phase-contrast microscopy, often with a single large polar appendage.

Image : V. spinosum ; Dennis Kunkel Microscopy, Inc


Prosthecobacter fusiformis is a heterotrophic mesophile, obligate aerobe isolated from freshwater contact slides. Generally resemble Caulobacter, but are more fusiform, and dividing cells have a stalk on both cells. They do not have a dimorphic life cycle, and are non-motile throughout their life cycle.

Image : P. fusiformis : The Prokaryotes pp2165


Opitutus terrae is a heterotrophic, motile (monotrichous), obligately anaerobic coccus isolated from rice paddy soil. Cells are very small, only ca. 0.5μm in diameter; this organism and its relatives were previously informally known as Ultramicrobium. Pairs or longer chains of cells can be mistaken for rod-shaped cells.

Image : O.terrae : IJSEM 51:1965 2001

Example phylum : Acidobacteria


This group contains only 6 cultivated species, none of them well-known, but a large number of ssu-rRNA sequences from environmental samples, including mostly soils, but other from a wide variety of habitats, including a jet-fuel contaminated aquifer, a hot spring,a sponge symbiont, and freshwater and marine environments. Fluorescently-labeled oligonucleotide probes specific for one subgroup of this phylum (subgroup 6) hybridize to cells of all shapes & sizes, suggesting a broad phenotypic range to match the broad phylogenetic diversity of this group.

Example specie: Acidobacterium capsulatum

Acidobacterium capsulatum : Kishimoto, N. Curr. Microbiol. 22:1-7.

A. capsulatum is an acidophilic aerobic heterotroph isolated from acid mine drainage. It is heavily encapsulated and saccharolytic, rod-shaped and non-motile. Acidobacterium is related to a number of rRNA sequences isolated from acidic environments (e.g. peat bog, acid mine drainage), consistent with its acidophilic phenotype.

Example phylum : Nitrospira


This phylum contains only 5 cultivated species in 4 genera, all very different phenotypically and not well characterized. Nevertheless, members of this phylum are apparently common in acidic and nitrogen-cycling environments and anaerobic marine sediments.

Example species:

Nitrospira Nitrospira marina is, together with other species of this genus, the predominant nitrite oxidizer (to nitrate) in marine environments and aquariums. The species in this genus are poorly distinguished, and many of the original species have been lost. Nevertheless, mixtures of Nitrospira and Nitrobacter (another nitrite oxidizer) and Nitrosomonas (an ammonia oxidizer, produces nitrite) are sold commercially to help start a productive nitrogen cycle in aquariums.

Leptospirillum ferrooxidans is also a chemolithoautotroph, oxidizing Fe++ to Fe+++ in mine tailings and contributing to acid mine drainage, perhaps the pollution “worst case scenario”. The natural habitat for this organism is presumably the deep aquifers infusing iron-rich ores.

Image : Letospirillum : D. Barrie Johnson, Ph.D., University of Wales, Bangor


Magnetobacterium bavaricum is a magnetotactic organism, that swims North following the Earths magnetic field, directed by internal magnetite beads. These are anaerobic heterotrophs that live in aquatic sediments; in the Northern hemisphere, the magnetic field lines lead both North and down, toward their desired habitat. Other magnetotactic Bacteria (e.g. Magnetospirillum) are Proteobacteria, but few are cultivated.

Image " Magnetobacterium : Biomagnetism Group, University of Munich

Example phylum : Fusobacteria


Most of the few cultivated members of this group are animal symbionts, probably opportunistic rather than serious pathogens. By far the best studied genus of this Phylum is Fusobacterium. Some are also soil organisms, and environmental sequences have come primarily from oral samples (where Fusobacterium is common), fecal samples, soil and sediments.

Example specie : Fusobacterium nucleatum

Fusobacterium nucleatum : George Weinstock - Baylor College of Medicine

F. nucleatum is part of the normal flora of the oral cavity, and is particularly abundant in dental plaque, where it plays a central role in nucleating the accumulation of various types of Bacteria, including organisms such as Porphyromonas that can lead to periodontal disease. It is an anaerobic heterotroph, fermenting primarily sugars to butyric acid. F. nucleatum is spindle-shaped to filamentous with tapered ends, and so is easily mistaken for oral Bacteroids.

Other examples of Phyla with few cultivated species

  • Dehalococcoides - Dehalococcoides ethenogenes and relatives
  • Chrysiogenetes - Chrysiogenes arsenatis and relatives
  • Deferribacteres - Deferribacter and relatives
  • Fibrobacteres - Fibrobacter succiogenes, F. intestinales, and relatives
  • Dictyoglomi- Dictyoglomus thermophilum and relatives
  • Gemmatimonadetes - Gemmatimonas aurantiaca and relatives
  • Lentisphaerae - Lentisphaera araneosa, Victivallis vadensis, and relatives