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Bacterial taxa-area and distance-decay relationships in marine environments.

Zinger L, Boetius A, Ramette A - Mol. Ecol. (2014)

Bottom Line: Noticeably, bacterial TAR and DDR patterns did not correlate with each other both within and across ecosystem types, suggesting that (i) TAR cannot be directly derived from DDR and (ii) TAR and DDR may be influenced by different ecological factors.Nevertheless, we found marine bacterial TAR and DDR to be steeper in ecosystems associated with high environmental heterogeneity or spatial isolation, namely marine sediments and coastal environments compared with pelagic ecosystems.Hence, our study provides information on macroecological patterns of marine bacteria, as well as methodological and conceptual insights, at a time when biodiversity surveys increasingly make use of high-throughput sequencing technologies.

View Article: PubMed Central - PubMed

Affiliation: HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany; CNRS, Université Paul Sabatier, UMR5174 EDB, 118 route de Narbonne, Toulouse, F-31062, France.

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Effect of sequencing depth (a,c) and sampling effort (b,d) on z (a,b) and /β/ (c,d) obtained with 100 random resampling for each sequencing/sampling depth. A local-fitting algorithm (LOESS smoother, black continuous lines) was used, and numbers of samples/sequences were slightly modified for surface waters and coastal sediment to help to visualize changes in z and /β/. Continuous and dotted coloured straight lines correspond to slopes and their standard errors, respectively, obtained for the initial data set (Fig.1) for comparative purposes.
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fig03: Effect of sequencing depth (a,c) and sampling effort (b,d) on z (a,b) and /β/ (c,d) obtained with 100 random resampling for each sequencing/sampling depth. A local-fitting algorithm (LOESS smoother, black continuous lines) was used, and numbers of samples/sequences were slightly modified for surface waters and coastal sediment to help to visualize changes in z and /β/. Continuous and dotted coloured straight lines correspond to slopes and their standard errors, respectively, obtained for the initial data set (Fig.1) for comparative purposes.

Mentions: Overall, sequencing depth (i.e. the number of DNA amplicons sequenced) per sample affected the variability of z and β very weakly, and only when it was shallow (<500 sequences; Fig.3a, c). Increasing sequencing depth slightly reduced both z and /β/ regardless of ecosystem type, a feature less pronounced in surface- and deep-sea waters. Finally, z and /β/ started to stabilize at ∼4000 sequences and were always significantly larger in coastal sediments (W = 0, Holm-corrected P << 0.0001) as compared to other ecosystems.


Bacterial taxa-area and distance-decay relationships in marine environments.

Zinger L, Boetius A, Ramette A - Mol. Ecol. (2014)

Effect of sequencing depth (a,c) and sampling effort (b,d) on z (a,b) and /β/ (c,d) obtained with 100 random resampling for each sequencing/sampling depth. A local-fitting algorithm (LOESS smoother, black continuous lines) was used, and numbers of samples/sequences were slightly modified for surface waters and coastal sediment to help to visualize changes in z and /β/. Continuous and dotted coloured straight lines correspond to slopes and their standard errors, respectively, obtained for the initial data set (Fig.1) for comparative purposes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230465&req=5

fig03: Effect of sequencing depth (a,c) and sampling effort (b,d) on z (a,b) and /β/ (c,d) obtained with 100 random resampling for each sequencing/sampling depth. A local-fitting algorithm (LOESS smoother, black continuous lines) was used, and numbers of samples/sequences were slightly modified for surface waters and coastal sediment to help to visualize changes in z and /β/. Continuous and dotted coloured straight lines correspond to slopes and their standard errors, respectively, obtained for the initial data set (Fig.1) for comparative purposes.
Mentions: Overall, sequencing depth (i.e. the number of DNA amplicons sequenced) per sample affected the variability of z and β very weakly, and only when it was shallow (<500 sequences; Fig.3a, c). Increasing sequencing depth slightly reduced both z and /β/ regardless of ecosystem type, a feature less pronounced in surface- and deep-sea waters. Finally, z and /β/ started to stabilize at ∼4000 sequences and were always significantly larger in coastal sediments (W = 0, Holm-corrected P << 0.0001) as compared to other ecosystems.

Bottom Line: Noticeably, bacterial TAR and DDR patterns did not correlate with each other both within and across ecosystem types, suggesting that (i) TAR cannot be directly derived from DDR and (ii) TAR and DDR may be influenced by different ecological factors.Nevertheless, we found marine bacterial TAR and DDR to be steeper in ecosystems associated with high environmental heterogeneity or spatial isolation, namely marine sediments and coastal environments compared with pelagic ecosystems.Hence, our study provides information on macroecological patterns of marine bacteria, as well as methodological and conceptual insights, at a time when biodiversity surveys increasingly make use of high-throughput sequencing technologies.

View Article: PubMed Central - PubMed

Affiliation: HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany; CNRS, Université Paul Sabatier, UMR5174 EDB, 118 route de Narbonne, Toulouse, F-31062, France.

Show MeSH
Related in: MedlinePlus