Lineage-specific responses of microbial communities to environmental change

Abstract

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

Fig 1

Divergent ecological patterns between parent and daughter taxa. The heat map shows relative abundances (number of 16S rRNA reads) of each OTU defined at a 75%, 81%, 85%, 87%, 93%, or 99.5% sequence identity cutoff. Relative abundances are normalized by OTU to show relative change in abundance of each OTU over time and depth. OTUs were assigned a taxonomic classification if 95% of the reads in an OTU were classified identically or labeled with an asterisk if mixed. OTUs were left unlabeled if the reads they contained could not be classified with confidence to the specified taxonomic resolution. Bold labels highlight OTUs defined at the 99.5% cutoff that show the “opportunistic starting at mix” pattern as shown in Table 1. A similar figure using the freshwater classifications from Newton et al. (19) is shown in Fig. S4 in the supplemental material.

Fig 2

Summarizing correlations of ecological preference among sister taxa. Correlations of change in abundance of sister OTUs when controlling for depth (temporal patterns) or time (spatial patterns) were summed at each cutoff and represented in the bar graph as the number of strong correlations among sister OTUs normalized by the total number of comparisons made among sister OTUs. Negative and positive correlations are shown in red and blue, respectively. The 81% and 87% cutoffs are not shown because no strong correlations were found. See Fig. S6 in the supplemental material for a network diagram displaying correlations among OTUs.

Fig 3

Assessing ecological differences among highly related genotypes of Polynucleobacter using two phylogenetic markers. Each heat map and dendrogram depicts the relative abundance of each dereplicated sequence (genotype) over time and the genetic similarity among genotypes using the V2 16S rRNA pyrosequencing data (A) and the protein-encoding phylogenetic marker (ccoN) (B). Abundances are relative to the total number of 16S rRNA sequences in each sample. Genotypes represent unique 16S rRNA sequences that were classified as belonging to the Polynucleobacter genus (A) and unique ccoN sequences amplified with primers specific for the Polynucleobacter genus (B). The two dominant genotypes in the 0-m and 4-m depths are outlined in each heat map. Asterisks and striped boxes signify that a ccoN clone library was not constructed for day 3 at 0 m.

Fig 4

A bloom of one highly resolved OTU corresponds to a drop in community diversity. The top and middle plots show change in phylogenetic diversity and richness (number of OTUs) in the hypolimnion, with OTUs defined at the 99.5% sequence identity cutoff used for both analyses (comparable to Shade et al. [25]; Fig. 3). The lower plot shows relative abundance (number of reads) of OTU 3.5.10.10.12.1733, the most abundant OTU defined at the 99.5% cutoff, and OTU 3, the most abundant OTU in the data set.