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Last updated |
| August 10, 2003 |
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Lake Laysan |
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Laysan Water
Chemistry
Temperature and salinity in Lake Laysan varied little
around 23ºC and 80 ppt, respectively (See Fig. A). Chlorophyll a
concentrations did not exceed 1 mg/L (See
Fig. B). Hydrogen sulfide concentrations were low throughout the water
column, and decreased with depth (See Fig. B). DON comprised much of the
~550 mM total nitrogen pool (See Fig.
C), while NO3- and NH4+ concentrations
were each only fractions of total N (See Fig. D). Total phosphorus increased
from 8 to ~12 mM between 0.3 and 7.5 m,
mirroring increases in SNP with depth; SRP varied little around 3 mM
through the water column (See Fig. E). SRSi concentrations varied 5-fold
between 0.3 and 4 m (See Fig. F).
Laysan water chemistry figure
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Laysan Clones/cultures
Clone libraries based on partial 16S rDNA genes amplified from community
DNA from Lake Laysan water samples contained inserts that affiliated
with Archaea and Bacteria sequences in the public domain (Table
1). In total, 30 unique operational taxonomic units (OTUs) were
identified, where all members of a single OTU shared =97% identity.
The Bacteria were represented by 29 OTUs belonging to 19 families, or
other ranked or unclassified taxa in each of the five Proteobacteria
sub-divisions, the Bacteroidetes, Chloroflexi,
Firmicutes, Deinococcaceae,
Verrucomicrobiaceae, and Planctomycetales.
No OTU occurred in more than two depth samples from the lake, but the
a- and g-Proteobacteria
did occur throughout the water column; these sub-divisions also contained
the largest number of OTUs (Table 1).
All a-Proteobacteria
OTUs belonged in the Rhodobacteraceae.
Cloned representatives of the Bacteroidetes
included one OTU that affiliated with obligate psychrophiles (Psychroflexus
spp., Family Flavobacteriaceae) from
Antarctic sea-ice. The b-Proteobacteria,
Chloroflexi, Deinococci
and Verrucomicrobia were each represented
by just one OTU (Table 1).
Forty-two pure bacterial cultures derived from Lake Laysan.
On the basis of 16S rRNA homologies these cultures affiliated with 27
taxonomically distinct strains in 13 families or unclassified taxa in
the a-, g-,
and e-Proteobacteria,
Firmicutes, Bacteroidetes,
and the Chlorobiaceae (Table
1). Cultures from the g-Proteobacteria
belonged in the Vibrionaceae, Alteromonadaceae,
Halomonadaceae, and the Xanthomonas
group. Representatives of four a-Proteobacteria
families were cultivated, three of which were not represented in clone
libraries from the same sample.
Eight bacteria cultivated from Laysan shared <97%
16S rRNA sequence identity with bacteria in the public domain. Five of
the eight are a-Proteobacteria. Two cultures
belong in the Bacteroidetes; the closest
neighbors of one of these cultures is Psychroflexus
torquis, an obligate psychrophile from Antarctic sea-ice. Phenotypic
data including fatty acid and substrate assimilation support placement
of this strain as a new, mesophilic species in the genus Psychroflexus
(Donachie et al, in press). The only e-Proteobacterium
cultivated from Laysan shares <96% 16S rRNA identity with an Arcobacter
sp., its nearest cultivated neighbor based on 16S rDNA sequence identity.
All strains considered potentially novel in terms of 16S rRNA identities
have been characterized on the basis of whole cell fatty acid profiles,
substrate utilization, and other phenotypic properties. These data support
our contention that they are new species and in some cases new genera.
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| Laysan Clones
Table |
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| Division |
OTU |
Representative clone |
NT |
Closest relative |
Homology (%) |
Taxon |
Accession # |
| Euryarchaeota |
1 |
LA1-A10 |
640 |
Archaeon JDS-1 AF196290 |
527/532 (99.06) |
Halobacteriaceae |
AF513927 |
| a-Proteobacteria |
2 |
LA1-B32N |
1427 |
Roseobacter sp. AF098495 |
1359/1416 (95.97) |
Rhodobacteraceae |
AF513928 |
| |
3 |
LA1-B42N |
1421 |
Rhodobaca bogoriensis AF248638 |
1365/1424 (95.86) |
Rhodobacteraceae |
AF513929 |
| |
4 |
LA4-B49N |
1380 |
Uncultured Roseobacter AF245628 |
1120/1162 (96.39) |
Rhodobacteraceae |
AF513930 |
| |
5 |
LA7-B19N |
1424 |
Paracoccus sp. AB025192 |
1311/1399 (93.71) |
Rhodobacteraceae |
AF513933 |
| |
6 |
LAS-B23N
PH-B13 |
1426 |
a-Proteobacterium
AJ133762 |
1361/1413 (96.32) |
Rhodobacteraceae |
AF513934 |
| b-Proteobacteria |
7 |
LA1-B29N |
1492 |
Achromobacter xylosoxidans AF411021 |
1446/1490 (97.05) |
Alcaligenaceae |
AF513937 |
| g-Proteobacteria |
8 |
PH-B39N |
1497 |
Aeromonas bestiarum X60406 |
1491/1497 (99.60) |
Aeromonadaceae |
AF513938 |
| |
9 |
LAS-B15N, PH-B55N |
1494 |
Alteromonas sp. AF427478 |
1482/1493 (99.26) |
Alteromonadaceae |
AF513939 |
| |
10 |
LA4-B63N |
1491 |
Thiorhodovibrio winogradskyi AB016986 |
1407/1456 (96.63) |
Chromatiaceae |
AF513942 |
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11 |
LAS-B37N |
1504 |
Thiobacillus halophilus U58020 |
1492/1504 (99.20) |
Chromatiaceae |
AF513944 |
| |
12 |
LA1-A16 |
1002 |
Alkalispirillum mobile AF114783 |
923/975 (94.67) |
Ectothiorhodospiraceae |
AF513945 |
| |
13 |
LA7-B9 |
1477 |
Alcalilimnicola halodurans AJ404972 |
1389/1474 (94.23) |
Ectothiorhodospiraceae |
AF513947 |
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14 |
LA1-B44N |
1451 |
Thiomicrospira crunogena AF069959 |
1366/1432 (95.39) |
Piscirikettsia |
AF513948 |
| d-Proteobacteria |
15 |
LA30-B273 |
1518 |
Olavius algarvensis sulfate-reducing
endosymbiont AF328857 |
1374/1518 (90.51) |
d-Proteobacteria |
AF513951 |
| e-Proteobacteria |
16 |
LA4-B52N |
1471 |
Sulfurospirillum sp. AF357199 |
1366/1465 (93.24) |
unclassified |
AF513952 |
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17 |
LA7-A15N |
986 |
Sulfurospirillum arcachonense Y11561 |
901/958 (94.05) |
unclassified |
AF513953 |
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18 |
LA7-A3N |
1137 |
Campylobacter helveticus U03022 |
826/919 (89.88) |
Campylobacter |
AF513954 |
| Cytophagales |
19 |
LA1-B7 |
968 |
Flavobacterium sp. AF386740 |
941/953 (98.74) |
Flavobacteriaceae |
AF513955 |
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20 |
LA7-B21N |
1482 |
Uncultured CFB bacterium AF195429 |
904/979 (92.34) |
Cytophagales |
AF513957 |
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21 |
LAS-B39N |
1487 |
Psychroflexus torquis U85881 |
1381/1457 (94.78) |
Flavobacteriaceae |
AF513958 |
| Chloroflexi |
22 |
LAS-B16N |
1458 |
Uncultured bacterium AF142947 |
853/918 (92.92) |
Chloroflexi |
AF513960 |
| Actinobacteria |
23 |
LA1-B9 |
885 |
Unidentified Actinobacterium AJ292034 |
810/859 (94.30) |
Actinobacteridae |
AF513961 |
| Firmicutes |
25 |
PH-B53N |
1514 |
Bacillus sp. AB066347 |
1500/1506 (99.60) |
Bacillaceae |
AF513963 |
| Deinococcales |
26 |
LA7-B27N |
1483 |
Uncultured Deinococci bacterium
AY250871 |
504/559 (90.16) |
Deinococcaceae |
AF513964 |
| Verrucomicrobiaceae |
27 |
LA1-B30N |
1481 |
Uncultured Crater Lake bacterium AF316731 |
1061/1158 (91.62) |
Verrucomicrobiaceae |
AF513965 |
| Planctomycetales |
28 |
LA4-B39N |
1472 |
Uncultured bacterium AF234144 |
978/1095 (89.32) |
Planctomycetales |
AF513966 |
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29 |
LA4-B40N |
1458 |
Planctomyces brasiliensis AJ231190 |
1360/1431 (95.04) |
Planctomycetaceae |
AF513967 |
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30 |
LA7-A16N |
1014 |
Uncultured Planctomycete AF424502 |
794/936 (84.83) |
Planctomycetales |
AF513968 |
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| Laysan Cultures Table |
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| Taxon |
Culture1 |
Depth (m) 2 |
NT |
Closest relative |
Homology (%) |
Family/Group |
Accession # |
| a-Proteobacteria |
LA5 |
0.3 |
1364 |
a-Proteobacterium
AJ133762 |
1288/1366 (94.29) |
Rhodobacteraceae |
AF513437 |
| |
LA7 |
1 |
1363 |
Roseobacter sp. AF098495 |
1305/1366 (95.53) |
Rhodobacteraceae |
AF513438 |
| |
LA9 |
4 |
1280 |
Marine bacterium AJ002565 |
1194/1255 (95.14) |
Rhodobacteraceae |
AF513439 |
| |
LA19 |
1 |
1343 |
Glacial ice bacterium AF479378 |
1323/1334 (98.50) |
Sphingomonadaceae |
AF513440 |
| |
LA33B, LA25 |
0.3, 4 |
1384 |
a-Proteobacterium
AB015896 |
1299/1400 (92.79) |
Rhodobacteraceae |
AF513441 |
| |
LA38BS |
0.3 |
1254 |
Rhodovulum adriaticum D16418 |
1244/1252 (99.36) |
Rhodobacteraceae |
AF513442 |
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LA45 |
7.5 |
1398 |
Rhodospirillum salexigens M59070 |
1350/1374 (98.25) |
Rhodospirillaceae |
AF513443 |
| |
LA49 |
0.3 |
1241 |
Maricaulis virginensis AJ301667 |
1208/1209 (99.92) |
Rhodobacteraceae |
AF513444 |
| |
LA51 |
0.3 |
1182 |
a-Proteobacterium
AB010864 |
1168/1179 (99.07) |
Rhodobacteraceae |
AF513445 |
| |
LA52 |
7.5 |
1330 |
a-Proteobacterium
AB013079 |
1293/1313 (98.48) |
Rhizobiaceae |
AF513446 |
| g-Proteobacteria |
LA6, LA15, LA32B, LA38A, LA38C, LA39, LA40 |
0.3, 1, 0.3, 0.3 0.3, 0.3, 1 |
1436 |
Vibrio sp.3 AF064637 |
1428/1432 (99.72) |
Vibrionaceae |
AF513447 |
| |
LA13, LA4 |
7.5, 0.3 |
1437 |
Marinobacter sp. AF199440 |
1409/1429 (98.60) |
Alteromonadaceae |
AF513448 |
| |
LA18t, LA2, LA16, LA23 |
7.5, 0.3, 1, 4 |
1466 |
Salinivibrio costicola X74699 |
1439/1458 (98.56) |
Vibrionaceae |
AF513449 |
| |
LA26 |
4 |
1441 |
Idiomarina baltica AJ440214 |
1437/1440 (99.79) |
Alteromonadaceae |
AF513450 |
| |
LA34A, LA34B |
7.5, 7.5 |
1420 |
Marinobacter sp. U61848 |
1407/1411 (99.72) |
Alteromonadaceae |
AF513451 |
| |
LA37 |
7.5 |
1437 |
Stenotrophomonas maltophilia AB008509 |
1426/1435 (99.37) |
Xanthomonas |
AF513452 |
| |
LA44, LA43 |
7.5, 7.5 |
1420 |
Deleya salina X87217 |
1394/1413 (98.66) |
Halomonadaceae |
AF513453 |
| |
LA50 |
0.3 |
1418 |
Marinobacter sp. AF237685 |
1379/1418 (97.25) |
Alteromonadaceae |
AF513454 |
| e-Proteobacteria |
LA31B |
0.3 |
1402 |
Arcobacter sp. L42994 |
1345/1402 (95.93) |
Campylobacter |
AF513455 |
| Cytophagales |
LA1 |
0.3 |
1428 |
Psychroflexus torquis U85881 |
1350/1433 (94.21) |
Flavobacteriaceae |
AF513434 |
| (syn. CFB) |
LA8, LA11 |
1, 7.5 |
1405 |
Flavobacterium sp. AF386740 |
1343/1351 (99.41) |
Flavobacteriaceae |
AF513435 |
| |
LA48 |
0.3 |
1396 |
Flexibacter tractuosus M58789 |
1346/1391 (96.76) |
Flexibacteraceae |
AF513436 |
| Chlorobi |
LA53 |
0.3 |
1462 |
Prosthecochloris aestuarii AJ291826 |
1423/1452 (98.00) |
Chlorobiaceae |
AF513460 |
| Firmicutes |
LA10 |
4 |
1378 |
Bacillus pumilis AB048252 |
1344/1354 (99.26) |
Bacillaceae |
AF513456 |
| |
LA28, LA30 |
4, 0.3 |
1432 |
Glacial ice bacterium AF479336 |
1424/1424 (100) |
Bacillaceae |
AF513457 |
| |
LA38BB |
0.3 |
1434 |
Bacillus sp. AF169535 |
1369/1398 (97.93) |
Bacillaceae |
AF513458 |
| |
LA42 |
7.5 |
1488 |
Halobacillus trueperi AJ310149 |
1412/1441 (97.99) |
Bacillaceae |
AF513459 |
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