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, 6 (8), 1459-68

Unraveling Assembly of Stream Biofilm Communities

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Unraveling Assembly of Stream Biofilm Communities

Katharina Besemer et al. ISME J.

Abstract

Microbial biofilms assemble from cells that attach to a surface, where they develop into matrix-enclosed communities. Mechanistic insights into community assembly are crucial to better understand the functioning of natural biofilms, which drive key ecosystem processes in numerous aquatic habitats. We studied the role of the suspended microbial community as the source of the biofilm community in three streams using terminal-restriction fragment length polymorphism and 454 pyrosequencing of the 16S ribosomal RNA (rRNA) and the 16S rRNA gene (as a measure for the active and the bulk community, respectively). Diversity was consistently lower in the biofilm communities than in the suspended stream water communities. We propose that the higher diversity in the suspended communities is supported by continuous inflow from various sources within the catchment. Community composition clearly differed between biofilms and suspended communities, whereas biofilm communities were similar in all three streams. This suggests that biofilm assembly did not simply reflect differences in the source communities, but that certain microbial groups from the source community proliferate in the biofilm. We compared the biofilm communities with random samples of the respective community suspended in the stream water. This analysis confirmed that stochastic dispersal from the source community was unlikely to shape the observed community composition of the biofilms, in support of species sorting as a major biofilm assembly mechanism. Bulk and active populations generated comparable patterns of community composition in the biofilms and the suspended communities, which suggests similar assembly controls on these populations.

Figures

Figure 1
Figure 1
nMDS analysis of the microbial community compositions estimated by T-RFLP (a, b) and 454 pyrosequencing (c, d), calculated from the presence/absence-based Sørensen index (a, c) and the abundance-based Horn index (b, d). Kruskal's standardized stress values (S) below 0.2 indicated acceptable representation of the calculated similarities. Circles represent the bulk (16S rRNA gene based), crosses the active (16S rRNA-based) community compositions, brown the biofilm community humic stream, orange the biofilm community outflow stream, red the biofilm community confluence stream, green the suspended community humic stream, blue the suspended community outflow stream and turquoise the suspended community confluence stream.
Figure 2
Figure 2
nMDS analysis visualizing the results of a random sampling procedure to estimate the probability that the biofilm communities represented random samples of their respective suspended source communities. A total of 1000 random subsamples of the suspended communities were assembled for each sample pair. White circles represent the random subsamples of the suspended communities, red triangle the biofilm community and blue cube the suspended community; humic stream (a, b), outflow stream (c, d), confluence stream (e, f), bulk (a, c, e) and active (b, d, f) communities.
Figure 3
Figure 3
Microbial diversity in biofilm and suspended community, as estimated by T-RFLP (a) and 454 pyrosequencing (b), calculated as richness and the number equivalents of the Shannon entropy. A threshold of 0.2% contribution to the community was applied to the 454 pyrosequencing data to compare results from 454 pyrosequencing with T-RFLP analysis (c). con, confluence stream; hum, humic stream; out, outflow stream. Cross-hatched bars represent the biofilm community, solid bars the suspended community, green bars the bulk community and blue bars the active community.
Figure 4
Figure 4
Rank-abundance curves of biofilm and suspended communities for relative abundances obtained from 454 pyrosequencing data. Curves are displayed in log–log scale for clarity. Colors are same as in Figure 1.
Figure 5
Figure 5
‘True diversity' estimates (medians with 95% confidence interval) for the biofilm and suspended communities, calculated by fitting Sichel distribution curves to the abundance distributions obtained from the 454 pyrosequencing data. Colors are same as in Figure 1.
Figure 6
Figure 6
Relative abundances of the most important phylogenetic classes in the biofilm and suspended communities. Each pie chart represents the pooled data from all the three investigated streams.

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