Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time
Year: 2021
Type: article
Abstract: After the acceptance of our manuscript, we became aware of an error in our approach used to analyze the bacterial community associated with Microcystis. We only removed DNA sequence reads from Microcystis after the calculation of relative abundance rather than before. In turn, Microcystis abundance may have introduced errors into results on community composition in the ordination and hierarchical clustering. To assess this, we re-computed the hierarchical clustering and ordination analysis using relative abundance values for the microbiome calculated after Microcystis read removal. The results of the analysis with single Microcystis colonies alone do not change substantially. The correlations with community dissimilarity and sampling date and Microcystis oligotype are still significant and ANOSIM R values increased from 0.41 to 0.43 (for sampling date) and 0.49 to 0.53 (for Microcystis oligotype), respectively (p = 1x10-4 in both cases; figure 1, correction of previous figure 5). Hierarchical clustering assignments changed for 2 of the 44 colonies sequenced (colonies MC2019-108 and MC2019-126). The clusters that now contain these colonies correspond better with the sampling date and Microcystis oligotype of the other member colonies. Temporal trends in the relative abundance of key phycosphere taxa as well as their specificity to certain Microcystis oligotypes were not impacted by the analysis error (figure 2, correction of previous figure 4). The relative abundances reported in original Figure 2 (depicted as percent of total community on single colonies, including Microcystis) remain unaltered to show the contribution of non-Microcystis bacterial reads to total reads in single colonies. The results of the ordination and hierarchical clustering analysis including bulk samples changed more substantially (Results and Discussion subsection “Microcystis phycosphere communities are dissimilar from bulk community samples” in the original publication). Microbial communities were separated into 6 major hierarchical clustering groups rather than 4 (figure 3, correction of previous figure 3). The membership of the clustering is still significantly correlated with sample type (ANOSIM R = 0.6758, P = 0.001), but the correlation is lower than previously calculated (ANOSIM R = 0.7534, P = 1x10-5). The lower correlation can be explained by the 100 μm retentate communities, which were divided among multiple clusters (clusters A, C, and F) that included single colony and other bulk community sample types in some cases (figure 4, correction of previous figure S11). The clustering of samples within these three clusters is correlated with the relative abundance of Microcystis (Mantel ρ = 0.5037, P = 1x10-4, figure 5), which suggests that non-Microcystis communities in bulk phytoplankton seston heavily dominated by Microcystis can more closely resemble non-Microcystis communities associated with some single Microcystis colonies than described in the original manuscript. However, the clustering of single colony-associated communities together with 100 μm retentate communities was limited to 17 colonies in hierarchical cluster C (figures 3 and 4), and non-Microcystis communities ordinated along NMDS1 are separated along a gradient transitioning from single colonies to bulk community samples (figure 3). When viewed with NMDS2, only 2 single colony communities appear to overlap with 100 μm retentate communities along NMDS1, while 5 single colony communities appear to overlap with 100 μm retentate samples along NMDS1 when viewed with NMDS3 (figure 3). Furthermore, the relative abundance of Microcystis in 100 μm retentate samples that clustered with whole water and < 105 μm samples was not significantly higher than that of 100 μm retentate samples that clustered with single Microcystis colonies (Pairwise Wilcox Test, P > 0.05, figure 5). Therefore, even when the relative abundance of Microcystis in bulk samples is high, differences in bacterial community composition between bulk phytoplankton seston and single Microcystis colonies cannot be explained solely by Microcystis relative abundance in bulk seston, which supports the original conclusion of the manuscript that bacterial communities not associated with the Microcystis phycosphere are a major constituent of bacterial communities in bulk seston. Shifts in non-Microcystis communities in whole Lake Erie water are still significantly correlated with month (ANOSIM R remained at ~0.36, P = 1x10-4; figure 6, correction of previous figure S9) and chlorophyll a concentration (Mantel ρ decreased from ~0.40 to ~0.37 while P remained at 1x10-4; figure 7, correction of previous figure S10). The updated results do not substantially change the implications or interpretation of the study, and the updated analysis is included in the GitHub site (https://github.com/Geo-omics/Characterizing-individual-Microcystis-colony-phycosphere-communities) in addition to the originally submitted analysis. We sincerely apologize for any inconvenience that this oversight has caused readers. Smith, D.J., Tan, J.Y., Powers, M.A., Lin, X.N., Davis, T.W. and Dick, G.J. (2021), Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time. Environ Microbiol. https://doi.org/10.1111/1462-2920.15514
Source: Environmental Microbiology
Authors: Derek J. Smith, James Y. Tan, McKenzie A. Powers, Xiaoxia N. Lin, Timothy W. Davis, Gregory J. Dick
Language: English
Subfield: Environmental Chemistry
Field: Environmental Science
Domain: Physical Sciences
Open Access status: bronze
OpenAlex ID: W4245234810