Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1 - PubMed (original) (raw)
Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1
Sari Peura et al. ISME J. 2012 Sep.
Abstract
Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.
Figures
Figure 1
Non-metric multidimensional scaling ordination visualizing the Bray–Curtis distances of all 122 samples from the time-series data set from Lake Alinen Mustajärvi and 24 samples from the four lakes data set. The five lakes are represented by different symbols (▪=Nimetön, ▵=Mekkojärvi, +=Valkea Kotinen, •=Alinen Mustajärvi, 
=Valkea Mustajärvi) and the three separate depth layers are indicated by grey scale. The stress value is 17.3.
Figure 2
The mean proportion of unclassified reads using the naive Bayesian classifier in MOTHUR (a). The mean proportion of reads annotated with candidate divisions after classification with ARB; the proportion of OD1 reads is indicated in white (b). The proportion of reads annotated with typical freshwater tribes as described in Newton et al. (2011) (c). All panels present proportions from all sequences.
Figure 3
Mean DOC concentration (mg l−1) (a) and CH4 concentration (μ
M
) (b) in epilimnion and hypolimnion of Lakes Nimetön, Mekkojärvi, Valkea Kotinen, Alinen Mustajärvi and Valkea Mustajärvi.
Figure 4
Ternary plot showing the distribution of OTUs in the time-series data from Lake Alinen Mustajärvi (a). Axes represent the three depth layers of the lake (epilimnion, metalimnion and hypolimnion) and the percentage of reads associated with each layer for each OTU. The size of the symbol indicates number of reads associated with each OTU and taxonomic affiliation are indicated by colours. Pie charts indicating the proportion of reads affiliated with OTUs associated with epilimnion (b) and hypolimnion (c) as determined by Wilcoxon's signed-rank test using the time-series data set (false discovery rate _q_=0.021). Colours represent different phyla as in (a). In (a), OTUs represented by at least 50 reads are included, panels (b) and (c) include all OTUs represented by at least 20 reads in the time-series data set.
Figure 5
Proportion of all OD1-related sequences and of the 10 most abundant OD1-affiliated OTUs (a). The distribution of the distance from the centroid (b) determined from the temporal dynamics of the bacterial communities in the corresponding layers. The distance from the centroid was estimated by MJ Anderson's permutated analysis of beta-dispersion and represents a statistical measure for the variability of the communities over time.
Figure 6
Subnetworks organized around methane (a) and inorganic nitrogen (b) compounds. The subnetworks were extracted from the entire association network (see Supplementary Figure 2) and show all OTUs (nodes) correlating with the respective compound. Circles represent bacterioplankton OTUs where colours represent their taxonomic annotations at the phyla level as in Figure 3a. The size of the circles reflects the number of samples where each OTU could be detected. Blue solid lines (edges) indicate positive correlations and red dashed lines (edges) indicate negative correlations, whereas the width of the line reflects the LSA coefficient. Abbreviations for the environmental variables are translated as following: NH4, ammonium concentrations, NO, combined nitrate and nitrite concentrations and CH4, methane concentrations.
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