Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean)
Abstract
:1. Introduction
2. Experimental Section
2.1. Sampling Site and Sampling Procedure
2.2. Nucleic Acids Extraction and RT-PCR of Total RNA Templates
2.3. CARD-FISH Analysis
Probe | Sequence (5′ to 3′) of Probe | Target Organisms | % Formamide | References |
---|---|---|---|---|
Eub338 | GCTGCCTCCCGTAGGAGT | Bacteria | 55 | (Amann et al., 1990) [29] |
Cren537 | TGACCACTTGAGGTGCTG | Crenarchaea | 20 | (Teira et al., 2004) [31] |
Eury806 | CACAGCGTTTACACCTAG | Euryarchaea | 20 | (Teira et al., 2004) [31] |
Non338 | ACTCCTACGGGAGGCAGC | For non-specific probe binding | 55 | (Wallner et al., 1993) [33] |
2.4. Sequencing and Phylogenetic Analysis
2.5. Statistical Analysis
2.6. Nucleotide Sequence Accession Numbers
3. Results
3.1. Hydrological and Hydrochemical Conditions of the Sampling Site
3.2. CARD-FISH Distribution
3.3. Phylogenetic Analysis of 16S rDNA and 16S rRNA Bacterial Clones Retrieved from Different Depths
Bacterial or Archaeal Division | Genus/Clade | Closest Relative (EMBL Accession No.) | % Identity | MAW | LIW | TDW |
---|---|---|---|---|---|---|
Gammaproteobacteria | SAR 86 | Clone S23_686 (EF572587) | 99 | 8D-2R | ||
JL-ENTP-VE | Clone HOT157_350m7 (JN166339.1) | 100 | 2D-2R | |||
Alteromonadaceae | Alteromonas macleodii str. “Deep ecotype” (CP001103) | 99 | 10D | 3D-17R | ||
OM60 clade | Clone SHTA403 (GU235460) | 97 | 2D | |||
Umboniibacter | Umboniibacter marinipuniceus strain: KMM 3891 (AB467279) | 99 | 3D | |||
Pseudospirillum | Clone HOT157_350m9 (JN166361) | 99 | 2D-2R | 2D | ||
E01-9C-26 | Clone ASTS_SIM_500m_310 (KJ589919) | 99 | 2D | 5D-1R | 1D | |
E01-9C-26 | Clone PRTBB84 (HM798879) | 98 | 2D-1R | 1D | ||
Alphaproteobacteria | SAR 11 | Clone C146Chl358 (JX530113) | 99 | 5D | 3D | |
SAR 11 | Clone C146300253 (JX530857) | 99 | 2D | 1D | ||
SAR 11 | Clone PRTAB7655 (HM798613) | 98 | 3D | 3D | 1D | |
DB1-14 | Clone HglFeb5D7m (JX017019) | 98 | 5D-1R | |||
AEGEAN-169 | Clone SPOTSFEB02_70m27 (DQ009450) | 97 | 2D | 2D | ||
AEGEAN-169 | Cone 20162U78 (EU237459) | 99 | 2R | |||
S25-593 | Clone CTD005-32B-02 (DQ513053) | 99 | 4D-1R | |||
SAR 116 | Clone 20154U16 (EU237278) | 99 | 5D-1R | |||
SAR 116 | Clone SPOTSAUG01_5m101 (DQ009267) | 99 | 3D | |||
Deltaproteobacteria | SAR 324 | Clone SHAB608 (GQ348695) | 99 | 2D-2R | ||
OM27 | Clone 52-3-11 (JN018836) | 99 | 2D | |||
Planctomycetes | Clone OS2BR2-03 (JN233146) | 99 | 2R | |||
Verrucomicrobia | Clone SPOTSMAY03_150m14 (DQ009456) | 98 | 2D | |||
Acidobacteria | Clone J8P41000_1H01 (GQ351195) | 97 | 2R | 2D-2R | ||
Nitrospira | Clone HMMVPog-53 (AJ704710) | 95 | 2R | |||
Chloroflexi | Clone SAR250 (AY534097) | 99 | 2R | |||
Clone CTD005-79B-02 (AY704386) | 100 | 1R | 1D-2R | |||
Cyanobacteria | Prochlorococcus | Prochlorococcus marinus str. NATL2A (CP000095) | 100 | 10D-32R | ||
Synechococcus | Synechococcus sp. RS9920 (AY172830) | 99 | 6D-6R | |||
Geitlerinema | Geitlerinema sp. A28DM (FJ410907) | 100 | 18R | |||
Thaumarchaeota | MGI | Clone HF770_015N17 (DQ300532) | 99 | 9D-1R | 2D-2R | |
MGI | Clone TS_HP_RNAA_69 (AM937105) | 99 | 9D-5R | 8R | ||
MGI | Clone KM3_193_A03 (KF900772) | 99 | 10D-4R | |||
MGI | Clone MT793-NA08 (AB193963) | 99 | 2D-6R | |||
MGI | Clone SC5_2222_T2_E3 (KJ814656) | 99 | 33D-19R | 14D-69R | ||
MGI | Nitrosopumilus maritimus SCM1 (NR_102913) | 99 | 13D-8R | 1D | ||
Crenarchaeota | MBG | Clone TS_NB_DNAA_125 (AM937086) | 99 | 1D-4R | ||
PSL12 | Clone TS_HP_RNAA_67 (AM937090) | 100 | 2R | |||
PSL12 | Clone TS_NB_RNAA_25 (AM937096) | 100 | 3R | 1D | ||
PSL12 | Clone TS_NB_DNAA_66 (AM937087) | 99 | 4D-3R | |||
Euryarchaeota | MGII | Clone HF70_25A12 (DQ156469) | 99 | 4D-10R | ||
MGII | Clone HF200_89A11 (DQ156453) | 99 | 6D | 1D | ||
MGII | Clone HF770_037J18 (DQ300558) | 99 | 2D-5R | |||
MGII | Clone KM3-136-D10 (EF597686) | 99 | 1D-1R | 1D | ||
MGII | Clone HF4000_48H06 (DQ300561) | 99 | 4D | 2D-2R | ||
MGII | Clone PD_18 (JX103589) | 98 | 8D-2R |
3.4. Phylogenetic Analysis of 16S rDNA and 16S rRNA Archaeal Clones Retrieved from Different Depths
3.5. Rarefaction Analysis, Diversity Index and Coverage Values of Analysed Clone Libraries
3.6. Cluster Analyses of Clone Libraries
LIBSHUFF results between bacterial libraries | delta-C | p-value | LIBSHUFF results between archaeal libraries | delta-C | p-value |
---|---|---|---|---|---|
MAW 25 m (DNA vs. RNA) | 6.198 | 0.001 | MAW 25 m (DNA vs. RNA) | 0.019 | 0.824 |
LIW 500 m (DNA vs. RNA) | 3.528 | 0.001 | LIW 500 m (DNA vs. RNA) | 0.511 | 0.002 |
TDW 3000 m (DNA vs. RNA) | 7.647 | 0.001 | TDW 3000 m (DNA vs. RNA) | 0.090 | 0.037 |
Bacteria | R statistic | Significance level of sample statistic (%) | Archaea | R statistic | Significance level of sample statistic (%) |
---|---|---|---|---|---|
DNA-derived libraries | 0.048 | 0.8 | DNA-derived libraries | 0.378 | 0.1 |
MAW, LIW(D) | 0.053 | 0.3 | MAW, LIW (D) | 0.446 | 0.1 |
MAW, TDW(D) | 0.077 | 0.5 | MAW, TDW (D) | 0.470 | 0.1 |
LIW, TDW (D) | 0.000 | 46.4 | LIW, TDW (D) | −0.007 | 57.2 |
RNA-derived libraries | 0.302 | 0.1 | RNA-derived libraries | 0.476 | 0.1 |
MAW, LIW (R) | 0.311 | 0.1 | MAW, LIW (R) | 0.684 | 0.1 |
MAW, TDW (R) | 0.409 | 0.1 | MAW, TDW (R) | 0.842 | 0.1 |
LIW, TDW (R) | 0.037 | 15.2 | LIW, TDW (R) | 0.039 | 0.9 |
4. Discussion
5. Conclusions
Supplementary Materials
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
References
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Smedile, F.; Scarfi, S.; De Domenico, E.; Garel, M.; Glanville, H.; Gentile, G.; Cono, V.L.; Tamburini, C.; Giuliano, L.; Yakimov, M. Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean). J. Mar. Sci. Eng. 2015, 3, 845-865. https://doi.org/10.3390/jmse3030845
Smedile F, Scarfi S, De Domenico E, Garel M, Glanville H, Gentile G, Cono VL, Tamburini C, Giuliano L, Yakimov M. Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean). Journal of Marine Science and Engineering. 2015; 3(3):845-865. https://doi.org/10.3390/jmse3030845
Chicago/Turabian StyleSmedile, Francesco, Simona Scarfi, Emilio De Domenico, Marc Garel, Helen Glanville, Gabriella Gentile, Violetta La Cono, Cristian Tamburini, Laura Giuliano, and Michail Yakimov. 2015. "Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean)" Journal of Marine Science and Engineering 3, no. 3: 845-865. https://doi.org/10.3390/jmse3030845