Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization
Summary Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in‐situ hybridization and pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and c...
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| Published in | Environmental microbiology Vol. 17; no. 10; pp. 3500 - 3514 |
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| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Blackwell Publishing Ltd
01.10.2015
Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
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| Summary: | Summary
Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in‐situ hybridization and pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and coastal marine particles > 5 and > 10 μm respectively. Limnic particles were more abundant (average: 1 × 107 l−1), smaller in size (average areas: 471 versus 2050 μm2) and more densely colonized (average densities: 7.3 versus 3.6 cells 100 μm−2) than marine ones. Limnic particle‐associated (PA) bacteria harboured Alphaproteobacteria and Betaproteobacteria, and unlike previously suggested sizeable populations of Gammaproteobacteria, Actinobacteria and Bacteroidetes. Marine particles were colonized by Planctomycetes and Betaproteobacteria additionally to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. Large differences in individual particle colonization could be detected. High‐throughput sequencing revealed a significant overlap of PA and free‐living (FL) bacteria highlighting an underestimated connectivity between both fractions. PA bacteria were in 14/21 cases more diverse than FL bacteria, reflecting a high heterogeneity in the particle microenvironment. We propose that a ratio of Chao 1 indices of PA/FL < 1 indicates the presence of rather homogeneously colonized particles. The identification of different bacterial families enriched on either limnic or marine particles demonstrates that, despite the seemingly similar ecological niches, PA communities of both environments differ substantially. |
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| Bibliography: | ArticleID:EMI12466 Leibniz Society Croatian Science Foundation Max Planck Society German Academic Exchange Service DAAD German Science Foundation - No. GR1540-1/17 Fig. S1. Abundance (A) and size distribution (B) of particles with a diameter larger than 10 μm in limnic and marine systems. Boxes show 50% quartiles, whiskers 10 and 90 percentiles, and dots 5 and 95 percentiles. Full central line shows median and dashed line shows average. Fig. S2. Correlation between particle area (x-axis) and DAPI counts (y-axis); (A) overall and (B) separated into eight subsystems. Sample name abbreviations: EL and HL, epilimnion and hypolimnion of Lake Stechlin; NE and SW, north-eastern and south-western basins of Lake Grosse Fuchskuhle; 09 and 11, samples collected in 2009 and 2011 on Helgoland; AT and BT, samples collected above and below the thermocline along the Rovinj-Po transect in the Northern Adriatic Sea. Fig. S3. Bacterial cell density expressed as cells per 1000 μm3 and plotted per particle volume. Fig. S4. A model of available space for colonization in limnic and marine particles suggesting difference in available surfaces due to particle structure (A) and inner particle colonization in freshwater systems versus surface colonization alone in marine systems (B). In our limnic samples, both the inner core and the outer surface of the particles might have been colonized, whereas on marine particles, colonization had occurred mainly on the surface of a particle. This model shows four adjunct spheres of volume V as a limnic particle and a single sphere of volume 4V as a marine particle. The first would offer a surface area 1.6 times greater than the second. As particles are often fractal structures (Richardson et al., 1990), each hypothetical sphere can in turn offer additional sub niches for colonization. Fig. S5. Distribution of abundances of major phylogenetic groups (CARD - FISH) in four limnic (white field) and four marine (grey field) subsystems: (A) Alphaproteobacteria; (B) Betaproteobacteria; (C) Gammaproteobacteria; (D) Bacteroidetes; (E) Planctomycetes; (F) Actinobacteria. Boxes show 50% quartiles, whiskers 10 and 90 percentiles, and dots 5 and 95 percentiles. Full central line shows median and dashed line shows average. Sample name abbreviations: EL and HL, epilimnion and hypolimnion of Lake Stechlin; NE and SW, north-eastern and south-western basins of Lake Grosse Fuchskuhle; 09 and 11, samples collected in 2009 and 2011 on Helgoland; AT and BT, samples collected above and below the thermocline along the Rovinj-Po transect in the Northern Adriatic Sea. PA and FL refer to particle-associated and free-living respectively. Fig. S6. Non-metric multidimensional scaling analysis of 454 data for Lake Stechlin, and Lake Grosse Fuchskuhle (A), Helgoland (B) and the Northern Adriatic Sea (C). Stress levels for each analysis were 0.14, 0.11 and 0.1 respectively. The data were clustered based on phylogeny at the family level. Distances were calculated with the past software using the Bray-Curtis algorithm. Analysis of similarity (ANOSIM) results for the data are given in Supporting Information Table S5. Fig. S7. Sequence frequencies of major phylogenetic groups of free-living (FL) and particle-associated (PA) bacterial communities from limnic and marine systems separated according to the different basins. Fig. S8. Sequence frequencies of major bacterial taxa at the family level within the different groups, normalized to the total number of sequences in that group. To simplify the image, only families making up over 3% of the sequences of the respective phyla/class in at least one sample are shown. The list of families per groups is given in the legend table. Where no taxonomic information was available at the family level, taxonomy is provided at the level of class (cl) or order (or). The presence or absence of each family within the particle-associated (A) or free-living (F) fractions in limnic (L) or marine (M) systems is given by the 4 '+' or '-' symbols next to each family name. A symbol 'E' means that a group was enriched in the respective fraction in at least one sample. A red symbol 'E' appears in the cases when a group was simultaneously enriched on particles in at least one sample and depleted in other sample. Sample name abbreviations EL and HL, Lake Stechlin epilimnion and hypolimnion respectively; NE and SW, north-east and south-west basins of Lake Grosse Fuchskuhle respectively; 09 and 11, Helgoland 2009 and 2011 respectively; AT and BT, above and below the thermocline in the Northern Adriatic Sea respectively. 'PA' and FL' within the sample name refer to particle-associated and free-living fractions respectively. Curly brackets represent clustering at the nearest lower taxonomy (order or class). Table S1. CARD-FISH abundance data for specific groups. Table S2. Sequence quality and diversity data for each sample. Table S3. Sample composition of each Sample-group. Table S4. Summary of OTU comparison between homogeneous and heterogeneous PA communities. Table S5. Analysis of similarity (ANOSIM). Table S6. Contribution of individual taxa to difference between sample groups. Table S7. Abundance of identifiable taxonomic paths across the different samples. this supplementary table is available as a separate file. Table S8. List of the samples, sampling locations, sampling periods and the respective filtered fractions. Table S9. Oligonucleotide probes used in this study. Appendix S1. Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization. ark:/67375/WNG-060NJ19R-P istex:58B8A1666F90229DE395D504327D7AA5F4FB0F73 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1462-2912 1462-2920 |
| DOI: | 10.1111/1462-2920.12466 |