Bacterial phyla with few or no cultivated species

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The 13 phyla of Bacteria described so far constitute the classical main phylogenetic groups, as defined by Carl Woese's 1987 review of bacterial diversity, with the more recent addition of Aquifex. As more sequences become available from cultivated species and from surveys of natural populations, it has become increasingly clear that the main radiation of bacterial phyla contains many more branches than originally thought; over a hundred contain at least two established sequences. Several of these groups contain only a few cultivated species, but in most cases contain none at all. These groups are known mainly or exclusively from ssu-rRNA sequences cloned from DNA extracted directly from environmental samples (see below).

This being said, don't forget that most of the cultivated, characterized Bacteria and most ssu-rRNA sequences from environmental samples fall into only 5 bacterial phyla: the Proteobacteria, the Gram-positive Bacteria (Firmicutes and Actinobacteria), the Bacteriodes and the Cyanobacteria. The other groups, the Aquificae, Thermotogae, Green sulfur and Green non-sulfur Bacteria, Planctomycetes, Chlamydiae, Deinococci, and even the Spirochaetes, qualify in some sense as “Phyla with few cultivated species”.

The observation that most cultivated species of Bacteria come from only a small number of phyla is similar to the situation in animals; the vast majority of animal diversity belongs to only 9 of the ca. 35 animal phyla: mollusks, sponges, cnidarians (coelenterates), flatworms, nematodes, annelids, arthropods, echinoderms, and chordates contain approximately 95% of animal species. The remaining 5%, most of animal diversity, are mostly obscure.

How do we know about these organisms?

The knowledge that these scattered species belong to novel bacterial phyla comes from their ssu-rRNA sequences. Some of these are species isolated long ago that have only recently had their ssu-rRNA sequences determined; both the ATCC (American Type Culture Collection) and DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, i.e. German Collection of Microorganisms and Cell Cultures) are involved in efforts to sequence ssu-rRNAs from their collections. Others are newly discovered organisms; obtaining ssu-rRNA sequence information is now one of the first steps in the characterization of new isolates.

However, most of the these odd phyla are best, or even entirely, represented by ssu-rRNA sequences extracted directly from environmental samples; so-called molecular phylogenetic surveys. In a typical molecular phylogenetic analysis, the ssu-rRNA sequence is obtained by PCR amplification from DNA isolated from a pure culture of the organisms of interest. The resulting sequence is used to determined the place of that organism in the 'big tree'. It is also possible, however, to start a molecular phylogenetic analysis with DNA extracted directly from an environmental sample instead of a pure culture. The collection of sequences obtained from such PCR amplification products (hopefully) represent the population of organisms in the original sample. This gives us phylogenetic information about organisms in an environment regardless of whether they can be cultivated or not. This approach is far superior to the traditional cultivation-based approaches, and we'll be going over it in detail later in this course.

Summary of molecular phylogenetic surveys

In a 1998 review (J. Bacteriol. 180:4765), Philip Hugenholtz, Brett Goebel and Norman Pace summarized the results of 86 ssu-rRNA molecular phylogenetic surveys of microbial populations from a wide range of environments: geothermal sites, soils, fresh and saltwater environments, wastewater, &c. The final distillation of these surveys was summarized in the following Table:

Table

(Note that in this table, the proteobacteria are so numerous that they are divided into their 5 sub-branches.)

They found that nearly 3000 bacterial sequences were reported, 90% of which fell into the proteobacteria, Gram-positive Bacteria (Firmicutes and Actinobaceria), or Cytophagales (Bacteroides). The remaining were widely scattered amongst the other groups and many were not related to any known cultivated specie. There were 9 groups of such sequences that did not fall into any of the standard bacterial groups. One of these groups (called OP11, from the first such sequence reported, originating from Obsidian Pool) seems to a a major constituent of subsurface environments and common in most other places, too.

Unfortunately, no more recent such compilation has been published, but this early work is probably representative of what would be found today in a compilation of the hundreds of thousands of environmental su-rRNA sequences now available from environmental surveys. However, the table below tabulates the numbers of ssu-rRNA sequences in release 10 of the Ribosomal database Project, divided into type strains, isolates with varying degrees of characterization, and sequences from uncultivated organisms. These numbers are largely consistent with those of the previous Table.

Phylum
Type strains
Other isolates
Uncultivated
Phylum
Type strains
Other isolates
Uncultivated
Aquificae
18
121
668
Acidobaceria
0
185
2566
Thermotogae
27
74
37
Bacteroides
355
5592
22959
Thermodesulfobacteria
4
8
67
Fusobacteria
34
172
513
Deinococcus/Thermus
40
400
189
Verrucomicrobia
10
96
2203
Chrisiogenetes
1
3
0
Dictyoglomi
1
5
3
Chloroflexi
9
62
1603
Gemmatimonads
1
4
323
Nitrospira
5
89
461
Lentisphaere
2
4
66
Deferribacteres
10
32
193
BRC1
0
0
27
Cyanobacteria
14
4353
1492
OP10
0
0
98
Chlorobi
9
154
58
OP11
0
0
43
Proteobacteria
1927
59028
38046
TM7
0
0
253
Firmicutes
2151
27635
54075
WS3
0
0
50
Actinobacteria
1286
22306
5310
Dehalococcoides
0
19
77
Planctomycetes
7
140
1674
SR1
0
0
2
Chlamydiae
4
192
43
OD1
0
0
32
Spirochaetes
54
1397
1367
unclassified
1
371
4985
Fibrobacteres
2
58
135
TOTALS
5,972
122,500
139,618