Skip to main content
. 1998 Dec;62(4):1353–1370. doi: 10.1128/mmbr.62.4.1353-1370.1998

TABLE 2.

“Species list” for the Octopus Spring cyanobacterial mat community

Phylogenetic typea Previously cultivated organism 16S rRNA sequence type Recently enriched or cultivated strain Physiological typeb Highest relative population densityc (%) GenBank accession no. Reference(s)
Cyanobacteria S. cf. lividusde S. cf. lividus C1 Oxygenic phototroph L35345, L35479-80 40, 62
A‴ Oxygenic phototroph U88530 37
A" Oxygenic phototroph U88069 41
A′ Oxygenic phototroph U42374 36
A Oxygenic phototroph X52544 159, 162
B′ S. cf. lividus P3 Oxygenic phototroph 12.5 U42375 36, 102, 111, 155
B S. cf. lividus P1,2 Oxygenic phototroph 12.5 M62776 102, 155, 159, 162
I Oxygenic phototroph L04709 162
J Oxygenic phototroph L04710 162
P S. cf. lividus B10 Oxygenic phototroph 4 L35331 40
S. cf. lividus C9 Oxygenic phototroph 0.4 L35481-3 40
Green nonsulfur bacteria and relatives C. aurantiacus Y-400-fle Anoxygenic phototroph; aerobic chemoorganotroph L04674 106, 162
Thermomicrobium roseume,f Aerobic chemoorganotroph M34115 60, 95, 176, 177
C M62775 159, 162
C′ U42421 36
C" U90433 41
OS-V-L-20 L04703 162
env.OS_ace3 Aerobic chemoorganotroph 0.3 L47199 121
env.OS_ace4 Aerobic chemoorganotroph 0.3 L47200 121
env.OS_ace5 Aerobic chemoorganotroph 0.3 L47201 121
Green sulfur bacterium-like E X52548 147
E′ U42419 36
E" U42420 36
M L04708 159
III-9 L04705 147
Planctomycetes I. pallidag Oligotrophic aerobic chemoorganotroph X64372 33, 52, 158
Thermus/Deinococcush T. aquaticus-like ac-1 Aerobic chemoorganotroph 0.000003 L37520 22, 87, 121
T. aquaticus-like ac-7 Aerobic chemoorganotroph 0.000004 L37522 22, 87
T. aquaticus-like ac-7′ Aerobic chemoorganotroph 0.0003 L47202i 121
T. ruber-like ac-2 Aerobic chemoorganotroph 0.3 L37521 87, 121
T. ruber-like ac-17 Aerobic chemoorganotroph 0.001 L37523 87
Thermus spp. Ramaley-4 Aerobic chemoorganotroph X58344 6
Proteobacteria
 α subdivision O L04706 147
env.OS_ace2 Aerobic chemoorganotroph 0.003 L47198 121
 β subdivision G X52550 159
R U46750 86
N Isolate ac-15 Aerobic chemoorganotroph 0.03 L04712, U46749 86
Enriched population N′ Aerobic chemoorganotroph 0.003 L47196 121
Isolate ac-16 Aerobic chemoorganotroph 0.001 U46748 86
 γ subdivision Isolate env.OS_ace7 Aerobic chemoorganotroph 0.0000003 L47204 86
 δ subdivision env.OS_ace8j Aerobic chemoorganotroph 0.3 L47205 121
Spirochetes H X52551 159
OS-V-L-7 L04704 162
Gram-positive bacteria Heliobacterium modesticaldum Anoxygenic phototroph U14559 63, 138
Thermoanaerobacter brockii HTD4k Fermenter L09165 8, 109, 175
Thermoanaerobacter ethanolicus JW200 and 39Ek Fermenter L09162, L09164 8, 109, 166, 167
Thermobacteroides acetoethylicus HTB2/W Fermenter L09163 8, 12, 109, 173
Thermoanaerobacterium thermosulfurigenes 4Bk Fermenter L09171 8, 109, 122
Moorella thermoautotrophica JW701k Fermenter X77849, L09168 8, 31, 109, 165
env.OS_ace1 Aerobic chemoorganotroph 3.3 L47197 121
env.OS_ace6 Aerobic chemoorganotroph 0.003 L47203 121
Isolate ac-18 Aerobic chemoorganotroph 0.01 U46747 86
Thermodesulfotobacterium Thermodesulfotobacterium commune Sulfate reducer L10662 158, 171, 174
Paraphyletic assemblage 2.5.1 Leptospirillum group OP-I-2 L22045 65
Paraphyletic assemblage 2.5.3 enviromental isolates L Enriched population 13 Aerobic chemoorganotroph 0.0000003 L04707 121, 147
OS-I-25 X67084-7 158
Paraphyletic assemblage 2.5.4 Nitrospina group K L04711 147, 162
Bacteria of uncertain lineage D X52547 159
F X52549 159
Q U42422 36
Archaea Methanobacterium thermoautotrophicum Methanogen X68720 89, 120, 173
a

All sequences are placed as they occur in the Ribosomal Database Project (75), release 6.1. Some sequences were previously reported in different lineages (e.g., see references 38 and 153), based on comparison to earlier releases. We caution that two sequences which appear in this release (OS-VI-L-4 and OP-I-6) are not included in the table, as there is good evidence of these being chimeric artifacts (65, 116). A few sequences which do not appear yet in this database are placed according to our own phylogenetic analyses. 

b

This may represent only a fraction of the population’s true physiological potential. 

c

Expressed as a percentage of S. cf. lividus cells determined from direct microscopic counts. The estimate was made from the reciprocal of number of S. cf. lividus cells present in the diluted mat sample used to inoculate the enrichment that led to the observation of a DGGE band or to the cultivation of an isolate (× 100), assuming that at least one cell of the population led to its enrichment or isolation. 

d

We used strain Y-7c-s, initially cultivated from a pH 5.5 spring at Clearwater Springs in Yellowstone National Park and provided by R. W. Castenholz, but several genetically similar strains are available (see reference 40). 

e

Percent similarities between the 16S rRNA sequences of bacteria previously cultivated from the mat and their closest relative among phylogenetically similar sequences detected in the mat indicate how different the two samplings of diversity are: 93.1% between S. cf. lividus Y-7c-s and type I, 81.6% between C. aurantiacus and type C, and 75.4% between T. roseum and type C. The relationships among type A/B cyanobacterial sequences and type C sequences are quantified in Fig. 2. The green sulfur bacterium-like sequences exhibit 82.9 to 90.2% sequence variation; the E-like green sulfur bacterium-like sequences form a cluster which exhibits ca. 6.9% sequence variation. We caution, however, that percent sequence similarity is a function of which regions of the sequences are being compared (i.e., of the balance between conserved and variable regions being analyzed), so that these similarity values, which are based on portions of the 16S rRNA molecule, may not be accurate estimates of similarities of the entire 16S rRNA sequences. 

f

Not cultivated from the Octopus Spring mat, but typical lipids were observed (176, 177). 

g

Not cultivated from the Octopus Spring mat, but cells of this morphology were observed (33). 

h

We could not find specific reference to prior cultivation of Thermus spp. from the Octopus Spring mat, though they have been cultivated from other nearby alkaline siliceous springs as well as from higher-temperature streamer communities in Octopus Spring. 

i

Incorrectly reported in reference 121. 

j

This designation is for the observation of a population as a DGGE band in an aerobic chemoorganotrophic enrichment culture (121); it is not the isolate cultivated from aerobic chemoorganotrophic enrichments and listed as ac-8 (86), whose 16S rRNA sequence is identical to that of type N. 

k

Thermoanaerobacter brockii, Thermoanaerobacter ethanolicus, and Thermoanaerobacterium thermosulfurigenes are new names for Thermoanaerobium brockii, Clostridium thermohydrosulfuricum, and Clostridium thermosulfurogenes, respectively (70); Moorella thermoautotrophica is the new name for Clostridium thermoautotrophicum (31).