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Data Publisher for Earth & Environmental Science

Reintjes, Greta; Tegetmeyer, Halina; Wulf, Jörg; Bürgisser, Miriam; Fuchs, Bernhard M (2017): On-board sequencing of the microbial community of the South Pacific Gyre [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.882015

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Abstract:
Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of the seven most abundant bacterial clades (determined by 16S rRNA tag sequencing) of the South Pacific Gyre (SPG). Seawater samples were collected aboard the RV Sonne SO-245 "UltraPac"cruise from Antofagasta, Chile (17.12.2015) to Wellington, New Zealand (28.01.2016). A total of 15 stations were sampled at multiple depths from surface (20 m) to ~5000 m. Total cell counts (TCC, by DAPI staining) and FISH were carried out as described in Bennke et al. (2016). DAPI and FISH stained cells were visualised and counted automatically using a fully automated image acquisition and cell enumeration system (Bennke et al., 2016).
The cellular abundance of SAR11 clade, Prochlorococcus, AEGEAN-169 marine group, SAR86, SAR202, SAR324 and SAR406 were enumerated and are shown here in total (cell ml-1) and relative abundance (% TCC). For this study, a new probe specific for the AEGEAN-169 clade was designed and tested, based on the latest SILVA 16S rRNA database (refnr 128). We found that the microbial community within the SPG was highly similar to that of other oceanic gyres and showed a pronounced vertical distribution pattern. Two major differences which we observed, in comparison to previous studies of both the SPG and other oceanic Gyres, was a high abundance of the AEGEAN-169 marine group, a sister group of the SAR11 clade, and a low abundance of Prochlorococcus specifically in the surface waters of the central gyre.
Supplement to:
Reintjes, Greta; Tegetmeyer, Halina E; Bürgisser, Miriam; Orlic, Sandi; Tews, Ivo; Zubkov, Mikhail V; Voß, Daniela; Zielinski, Oliver; Quast, Christian; Glöckner, Frank Oliver; Amann, Rudolf; Ferdelman, Timothy G; Fuchs, Bernhard M (2019): On-Site Analysis of Bacterial Communities of the Ultraoligotrophic South Pacific Gyre. Applied and Environmental Microbiology, 85(14), https://doi.org/10.1128/AEM.00184-19
Related to:
Reintjes, Greta; Amann, Rudolf I; Arnosti, Carol; Fuchs, Bernhard M (2020): Microbial community composition and polysaccharide processing potential in the South Pacific Gyre. European Nucleotide Archive (ENA), insdc:PRJEB40503
Coverage:
Median Latitude: -30.101353 * Median Longitude: -121.254259 * South-bound Latitude: -39.310400 * West-bound Longitude: -170.000180 * North-bound Latitude: -23.491900 * East-bound Longitude: -84.562420
Date/Time Start: 2015-12-25T18:03:00 * Date/Time End: 2016-01-24T04:30:00
Minimum DEPTH, water: m * Maximum DEPTH, water: 5125 m
Event(s):
SO245_1-1  * Latitude: -23.503170 * Longitude: -84.562420 * Date/Time: 2015-12-25T18:03:00 * Elevation: -2764.4 m * Location: South Pacific Ocean * Campaign: SO245 (UltraPac, GEOTRACES) * Basis: Sonne_2 * Method/Device: CTD/Rosette (CTD-RO)
SO245_2-2  * Latitude: -23.491900 * Longitude: -90.029850 * Date/Time: 2015-12-27T07:25:00 * Elevation: -3890.9 m * Location: South Pacific Ocean * Campaign: SO245 (UltraPac, GEOTRACES) * Basis: Sonne_2 * Method/Device: CTD/Rosette (CTD-RO)
SO245_3-1  * Latitude: -23.499400 * Longitude: -95.295300 * Date/Time: 2015-12-29T18:03:00 * Elevation: -3772.3 m * Location: South Pacific Ocean * Campaign: SO245 (UltraPac, GEOTRACES) * Basis: Sonne_2 * Method/Device: CTD/Rosette (CTD-RO)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
Event labelEventReintjes, Greta
NumberNoReintjes, Greta
Station labelStationReintjes, Greta
DEPTH, waterDepth watermReintjes, GretaGeocode
SAR11 mix oligonucleotide FISH-probes targeting SAR11 cladeSAR11%Reintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
Prochlorococcus, targeted with PRO405 oligonucleotide FISH-probePRO405%Reintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
AEGEAN-169 marine group, targeted with the AEGEAN-169 mix oligonucleotide FISH-probesAEGEAN-169%Reintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
SAR86 clade, targeted with SAR86-1245 oligonucleotide FISH-probeSAR86-1245%Reintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
SAR202 clade, targeted with SAR202-312R oligonucleotide FISH-probeSAR202-312R%Reintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
10 SAR324 clade, targeted with SAR324-1412 oligonucleotide FISH-probeSAR324-1412%Reintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
11 SAR406 clade, targeted with SAR406-97 oligonucleotide FISH-probeSAR406-97%Reintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
12 Microbial abundance, cellsMicrobial abund#/mlReintjes, GretaFlow cytometryTotal cell counts (enumerated by DAPI) counted by flow cyctometry (FCM is flow cytometry)
13 SAR11 mix oligonucleotide FISH-probes targeting SAR11 cladeSAR11#/mlReintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
14 Prochlorococcus, targeted with PRO405 oligonucleotide FISH-probePRO405#/mlReintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
15 AEGEAN-169 marine group, targeted with the AEGEAN-169 mix oligonucleotide FISH-probesAEGEAN-169#/mlReintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
16 SAR86 clade, targeted with SAR86-1245 oligonucleotide FISH-probeSAR86#/mlReintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
17 SAR202 clade, targeted with SAR202-312R oligonucleotide FISH-probeSAR202-312R#/mlReintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
18 SAR324 clade, targeted with SAR324-1412 oligonucleotide FISH-probeSAR324#/mlReintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
19 SAR406 clade, targeted with SAR406-97 oligonucleotide FISH-probeSAR406#/mlReintjes, GretaCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
20 Accession number, geneticsAccess no genReintjes, Greta
Size:
2922 data points

Data

Download dataset as tab-delimited text — use the following character encoding:


Event

No

Station

Depth water [m]

SAR11 [%]

PRO405 [%]

AEGEAN-169 [%]

SAR86-1245 [%]

SAR202-312R [%]
10 
SAR324-1412 [%]
11 
SAR406-97 [%]
12 
Microbial abund [#/ml]
13 
SAR11 [#/ml]
14 
PRO405 [#/ml]
15 
AEGEAN-169 [#/ml]
16 
SAR86 [#/ml]
17 
SAR202-312R [#/ml]
18 
SAR324 [#/ml]
19 
SAR406 [#/ml]
20 
Access no gen
SO245_1-1 1SO245-01-012017.023.33.72.10.0593523100602138232219601228659insdc:ERS1883698
SO245_1-11SO245-01-015014.225.04.41.80.10.00.96854069753317128330089121324112065826insdc:ERS1883697
SO245_1-11SO245-01-01759.029.22.81.70.11.06593095900819278218527112744626329insdc:ERS1883696
SO245_1-11SO245-01-0110019.318.81.21.70.60.61.56979771347791311508027120754118383910539insdc:ERS1883695
SO245_1-11SO245-01-0112515.98.51.11.11.22.5464972736983943052085254562611531insdc:ERS1883694
SO245_1-11SO245-01-0115025.72.30.50.51.42.82.627577570847623314061434372376947032insdc:ERS1883693
SO245_1-11SO245-01-0140019.10.71.55.42.310933920895733162958722471insdc:ERS1883692
SO245_1-11SO245-01-0150018.10.81.84.91.510847119612900197452611660insdc:ERS1883691
SO245_2-2 2SO245-02-122027.018.33.41.80.054619314719999789185169995109insdc:ERS1883690
SO245_2-22SO245-02-125028.719.03.61.60.00.00.679214122702815082428359125162383174832insdc:ERS1883689
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SO245_2-22SO245-02-05100014.80.70.43.34.63.4548368094384236179325391886insdc:ERS1883680
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SO245_2-22SO245-02-02220016.60.56.14.54.2431087160198264319531802insdc:ERS1883678
SO245_2-22SO245-02-02350013.00.87.25.43.3317074125263228016991040insdc:ERS1883677
SO245_3-1 3SO245-03-015013.311.82.51.10.10.11.249659266047585481256454224474475810insdc:ERS1883676
SO245_3-13SO245-03-011007.814.21.90.80.40.31.26602635163394021123475245290522458121insdc:ERS1883675
SO245_3-13SO245-03-011253.725.71.50.60.61.3531764194091368237711312232446966insdc:ERS1883674
SO245_3-13SO245-03-0115020.215.31.90.40.71.72.2313088632754777760741101209853856982insdc:ERS1883673
SO245_3-13SO245-03-0117016.210.20.60.30.72.21.434851556390356532161912244075984879insdc:ERS1883672
SO245_3-13SO245-03-0120021.13.60.70.11.83.82.01567523313756271050166285359103151insdc:ERS1883671
SO245_3-13SO245-03-0130013.90.50.80.13.64.72.01072331493750480497381750612177insdc:ERS1883670
SO245_3-13SO245-03-0150017.00.40.33.25.21.86092910370238195193131681115insdc:ERS1883669
SO245_4-1 4SO245-04-136046.814.04.51.20.00.10.247028322009265981212105596141329847
SO245_4-14SO245-04-1310035.219.42.51.00.40.61.045725916100188525112034481173826524618insdc:ERS1883667
SO245_4-14SO245-04-1115017.931.41.11.00.81.01.24358607801913677347074533353044895100insdc:ERS1883666
SO245_4-14SO245-04-1117520.421.61.40.30.21.71.335165971633758884888116077459434677insdc:ERS1883665
SO245_4-14SO245-04-1120029.612.80.70.10.82.21.726211177559334191809367212356624535insdc:ERS1883664
SO245_4-14SO245-04-1122532.34.40.60.11.53.42.71772675732877641135106267759384751
SO245_4-14SO245-04-1125036.11.40.70.01.54.81.914984554094202310790226371632907insdc:ERS1883663
SO245_4-14SO245-04-1130029.80.01.00.05.24.92.1141077420410143928735069272892insdc:ERS1883662
SO245_4-14SO245-04-0750019.80.00.62.94.81.625770350896014957525124474123insdc:ERS1883661
SO245_4-14SO245-04-07100021.80.43.84.11.5577541260821421832339861insdc:ERS1883660
SO245_4-14SO245-04-01225014.30.27.94.71.63092944147424401454504
SO245_4-14SO245-04-01350012.50.26.65.80.73072138406120371785215insdc:ERS1883659
SO245_4-14SO245-04-0139000.57.55.72.13221015124221830673insdc:ERS1883658
SO245_5-1 5SO245-05-015444464
SO245_5-15SO245-05-012545.48.45.81.745883220811438312265207892
SO245_5-15SO245-05-015034.07.24.01.50.00.01.14902921668423539919612755098495197insdc:ERS1883657
SO245_5-15SO245-05-0110039.36.11.91.50.10.31.1514007202116313039766750536013885397insdc:ERS1883656
SO245_5-15SO245-05-0115026.315.90.91.20.40.91.04802231261727616345145859192144184898insdc:ERS1883655
SO245_5-15SO245-05-0117530.63.30.70.31.23.33.0474804145495154793181151956981543114244insdc:ERS1883654
SO245_5-15SO245-05-0120024.38.30.50.30.62.02.135772886772296201717930211170477477insdc:ERS1883653
SO245_5-15SO245-05-0122519.019.41.00.80.31.61.020171138295391121916151352433082037insdc:ERS1883652
SO245_5-15SO245-05-0125029.33.60.40.14.34.12.315345544951547867577659963383468insdc:ERS1883651
SO245_5-15SO245-05-0130024.70.40.40.25.25.02.213619033619558586313712368502969insdc:ERS1883650
SO245_5-15SO245-05-0140079700
SO245_5-15SO245-05-0150016.70.63.14.81.76558610931361205931221141insdc:ERS1883649
SO245_6-1 6SO245-06-115448238
SO245_6-16SO245-06-1110514200
SO245_6-16SO245-06-112050.67.85.62.0512899259527399552892810104insdc:ERS1883648
SO245_6-16SO245-06-1140512008
SO245_6-16SO245-06-116048.05.24.31.20.00.00.6497332238471256622118661170992984insdc:ERS1883647
SO245_6-16SO245-06-1180505279
SO245_6-16SO245-06-111009.50.20.10.6555502529398897783277insdc:ERS1883646
SO245_6-16SO245-06-1112543.011.02.20.90.60.45663352432976246712289492735682435insdc:ERS1883645
SO245_6-16SO245-06-0815029.522.81.00.90.40.90.947691214068910883149124054171741494292insdc:ERS1883644
SO245_6-16SO245-06-0817528.622.32.51.00.81.41.33660951048138163990063624307549424832insdc:ERS1883643
SO245_6-16SO245-06-0820033.912.51.30.20.92.21.4303226102733379943851637263866414154insdc:ERS1883642
SO245_6-16SO245-06-0822542.02.71.10.31.04.21.11854607783850452040464192977152114insdc:ERS1883641
SO245_6-16SO245-06-0825043.22.20.50.61.53.91.3151205653053311817937232959122011insdc:ERS1883640
SO245_6-16SO245-06-08275
SO245_6-16SO245-06-0830028.40.50.80.35.64.31.812077734301628906362672752052126insdc:ERS1883639
SO245_6-16SO245-06-0350023.40.44.04.11.9insdc:ERS1883638
SO245_6-16SO245-06-03100019.83.05.62.5insdc:ERS1883637
SO245_6-16SO245-06-01150012.74.25.52.0insdc:ERS1883636
SO245_6-16SO245-06-01250012.56.64.71.1
SO245_6-16SO245-06-01360014.36.74.5
SO245_7-4 7SO245-07-045391755
SO245_7-47SO245-07-042034.28.56.01.347976916403340780287866189
SO245_7-47SO245-07-045032.37.23.31.30.00.10.5470075151646337981565461111884232397
SO245_7-47SO245-07-0410034.19.02.11.10.10.30.9
SO245_7-47SO245-07-04125501012
SO245_7-47SO245-07-0415024.122.50.80.60.60.91.14372211053269828734102623253639354678
SO245_7-47SO245-07-0417516.127.43.91.00.71.21.742769068687116973168514405282349187142
SO245_7-47SO245-07-0420020.714.11.00.51.11.61.9323139667934549833611713352251066140
SO245_7-47SO245-07-0422535.58.70.50.11.63.51.722159978668193461042310361278453745
SO245_7-47SO245-07-0425029.52.60.50.13.04.31.9162105478704231827211491269382999
SO245_7-47SO245-07-0430028.00.40.90.46.44.52.1142512399605701226627916464423036
SO245_7-47SO245-07-0440076865
SO245_7-47SO245-07-0450018.40.65.24.9554121019633828872737
SO245_7-47SO245-07-046002590
SO245_8-1 8SO245-08-1010402312
SO245_8-18SO245-08-102038.87.16.01.639767015417728036239806164
SO245_8-18SO245-08-106027.75.12.01.40.00.10.941610111526021055836459921662913745
SO245_8-18SO245-08-1080556361
SO245_8-18SO245-08-1010023.28.91.40.90.20.50.84953111148634383570834408113923284012
SO245_8-18SO245-08-1012515.413.21.20.80.70.550624678063665715822425233412582
SO245_8-18SO245-08-1915019.725.71.00.80.40.80.84745079362012213845553938166137013654
SO245_8-18SO245-08-1917523.223.94.11.30.51.41.13847508910891955158524809200152714194
SO245_8-18SO245-08-1920023.78.51.00.20.82.21.129073968934247132762523223962513198
SO245_8-18SO245-08-1922532.93.30.30.23.60.61750135756258285253506353998
SO245_8-18SO245-08-1925029.22.20.40.23.24.31.7136148397412982477313434358682328
SO245_8-18SO245-08-10275120818
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SO245_8-18SO245-08-1040066453
SO245_8-18SO245-08-1045052501
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SO245_8-18SO245-08-1960039137
SO245_8-18SO245-08-1975071975
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SO245_8-18SO245-08-19125015908
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SO245_8-18SO245-08-19175011104
SO245_8-18SO245-08-19200010420
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SO245_8-18SO245-08-1930008564
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SO245_9-1 9SO245-09-015385825
SO245_9-19SO245-09-012534.78.34.41.745128215659537592200377717insdc:ERS1883586
SO245_9-19SO245-09-015034.78.02.31.30.10.11.0477814165658381771094260202875264778
SO245_9-19SO245-09-0110028.919.91.11.30.50.61.25006441445369942856076508245328045908
SO245_9-19SO245-09-0115026.924.92.20.70.30.81.6486344130729120905107483550141040377927insdc:ERS1883585
SO245_9-19SO245-09-0117529.111.81.00.30.22.11.82321256745527460225272041849444085insdc:ERS1883584
SO245_9-19SO245-09-0120032.12.91.10.41.23.60.71646415289946921762593204258451136insdc:ERS1883583
SO245_9-19SO245-09-0122528.31.31.00.42.53.92.21339343786317141299576333552372987insdc:ERS1883582
SO245_9-19SO245-09-0125024.40.30.80.62.54.11.0813681986226963548020423312830insdc:ERS1883581
SO245_9-19SO245-09-0130025.00.51.00.83.14.02.69147922906421915714285436502360insdc:ERS1883580
SO245_9-19SO245-09-0140077316
SO245_9-19SO245-09-0150021.51.31.64.11.676566164851003124831161202insdc:ERS1883579
SO245_10-1 10SO245-10-105452347
SO245_10-110SO245-10-1010461297
SO245_10-110SO245-10-102037.67.15.12.8469331176375333692370113235insdc:ERS1883578
SO245_10-110SO245-10-1040512628
SO245_10-110SO245-10-106029.912.62.01.40.10.11.1515908154411647981021571202585165727insdc:ERS1883577
SO245_10-110SO245-10-1080546740
SO245_10-110SO245-10-1010024.126.21.01.10.20.31.25516451327261442555627579288316006840insdc:ERS1883576
SO245_10-110SO245-10-1012535.527.23.41.20.41.660419821461116452320301737124179848insdc:ERS1883575
SO245_10-110SO245-10-0615027.316.51.60.90.41.52.4345314943745683954213108134750768288insdc:ERS1883574
SO245_10-110SO245-10-0617528.96.61.20.51.53.24.518038052148119052165830277857008117insdc:ERS1883573
SO245_10-110SO245-10-0620028.72.61.50.53.43.02.61588304558440662414794541647014098insdc:ERS1883572
SO245_10-110SO245-10-0622530.51.10.50.22.04.43.0148211452491571726326302365514432
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SO245_10-110SO245-10-10275113016
SO245_10-110SO245-10-0630023.90.41.01.02.84.63.99291622225400957929262042373633insdc:ERS1883570
SO245_10-110SO245-10-1035062738
SO245_10-110SO245-10-1040069819
SO245_10-110SO245-10-0350024.90.73.84.92.96530116253444244932001881insdc:ERS1883569
SO245_10-110SO245-10-0660052136
SO245_10-110SO245-10-0675048855
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SO245_10-110SO245-10-06125033841
SO245_10-110SO245-10-01150021.62.15.83.22815460705861633890insdc:ERS1883567
SO245_10-110SO245-10-06175021867
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