Limits...
Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms.

Teeling H, Fuchs BM, Bennke CM, Krüger K, Chafee M, Kappelmann L, Reintjes G, Waldmann J, Quast C, Glöckner FO, Lucas J, Wichels A, Gerdts G, Wiltshire KH, Amann RI - Elife (2016)

Bottom Line: Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down to the genus level.Metagenome analyses also revealed recurrent patterns at the functional level, in particular with respect to algal polysaccharide degradation genes.We, therefore, hypothesize that even though there is substantial inter-annual variation between spring phytoplankton blooms, the accompanying succession of bacterial clades is largely governed by deterministic principles such as substrate-induced forcing.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Marine Microbiology, Bremen, Germany.

ABSTRACT
A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. We investigated such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down to the genus level. Metagenome analyses also revealed recurrent patterns at the functional level, in particular with respect to algal polysaccharide degradation genes. We, therefore, hypothesize that even though there is substantial inter-annual variation between spring phytoplankton blooms, the accompanying succession of bacterial clades is largely governed by deterministic principles such as substrate-induced forcing.

No MeSH data available.


Related in: MedlinePlus

Taxonomic classification of bacterioplankton metagenomesSampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing:  Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified (Supplementary file 9). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled basesDOI:http://dx.doi.org/10.7554/eLife.11888.007
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4829426&req=5

fig5: Taxonomic classification of bacterioplankton metagenomesSampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing:  Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified (Supplementary file 9). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled basesDOI:http://dx.doi.org/10.7554/eLife.11888.007

Mentions: We plotted contig GC contents versus coverage to evaluate our taxonomic classification, which in some cases allowed to assess the coherence of some of the clades (Figure 5). For example, Reinekea (Figure 5D,H,I) and the NS5 marine group (Figure 5H,L,M,O) were mostly represented by distinct clusters, whereas Polaribacter (Figure 5D,H,I) was almost always represented by at least two clusters indicating the presence of sub-populations. In general, the number of clusters increased from pre-bloom to mid-bloom situations and decreased slightly towards late bloom situations and notably towards post-bloom situations. This tendency was more evident in 2009, the year with the highest bloom intensity and the largest number of metagenome samples spanning a broader timespan (Figure 5A–F). It is noteworthy that high in situ abundance did not always correlate with good metagenome assemblies. SAR11 for example, while highly abundant in all metagenome datasets, yielded few large contigs, possibly due to population heterogeneity and presence of hyper-variable regions described in sequenced SAR11 genomes (Wilhelm et al., 2007).10.7554/eLife.11888.007Figure 5.Taxonomic classification of bacterioplankton metagenomes


Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms.

Teeling H, Fuchs BM, Bennke CM, Krüger K, Chafee M, Kappelmann L, Reintjes G, Waldmann J, Quast C, Glöckner FO, Lucas J, Wichels A, Gerdts G, Wiltshire KH, Amann RI - Elife (2016)

Taxonomic classification of bacterioplankton metagenomesSampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing:  Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified (Supplementary file 9). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled basesDOI:http://dx.doi.org/10.7554/eLife.11888.007
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829426&req=5

fig5: Taxonomic classification of bacterioplankton metagenomesSampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing:  Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified (Supplementary file 9). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled basesDOI:http://dx.doi.org/10.7554/eLife.11888.007
Mentions: We plotted contig GC contents versus coverage to evaluate our taxonomic classification, which in some cases allowed to assess the coherence of some of the clades (Figure 5). For example, Reinekea (Figure 5D,H,I) and the NS5 marine group (Figure 5H,L,M,O) were mostly represented by distinct clusters, whereas Polaribacter (Figure 5D,H,I) was almost always represented by at least two clusters indicating the presence of sub-populations. In general, the number of clusters increased from pre-bloom to mid-bloom situations and decreased slightly towards late bloom situations and notably towards post-bloom situations. This tendency was more evident in 2009, the year with the highest bloom intensity and the largest number of metagenome samples spanning a broader timespan (Figure 5A–F). It is noteworthy that high in situ abundance did not always correlate with good metagenome assemblies. SAR11 for example, while highly abundant in all metagenome datasets, yielded few large contigs, possibly due to population heterogeneity and presence of hyper-variable regions described in sequenced SAR11 genomes (Wilhelm et al., 2007).10.7554/eLife.11888.007Figure 5.Taxonomic classification of bacterioplankton metagenomes

Bottom Line: Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down to the genus level.Metagenome analyses also revealed recurrent patterns at the functional level, in particular with respect to algal polysaccharide degradation genes.We, therefore, hypothesize that even though there is substantial inter-annual variation between spring phytoplankton blooms, the accompanying succession of bacterial clades is largely governed by deterministic principles such as substrate-induced forcing.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Marine Microbiology, Bremen, Germany.

ABSTRACT
A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. We investigated such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down to the genus level. Metagenome analyses also revealed recurrent patterns at the functional level, in particular with respect to algal polysaccharide degradation genes. We, therefore, hypothesize that even though there is substantial inter-annual variation between spring phytoplankton blooms, the accompanying succession of bacterial clades is largely governed by deterministic principles such as substrate-induced forcing.

No MeSH data available.


Related in: MedlinePlus