Metagenomic Identification of Bacterioplankton Taxa and Pathways Involved in Microcystin Degradation in Lake Erie

Abstract

Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

“…In contrast with other studies, examining soil and sediment-bound microbial communities (Bissett et al, 2013;Sun et al, 2013), which have observed a lack of correlations between absolute abiotic measurements and 16S rRNA OTU relative abundances, numerous correlations were observed between biotic and abiotic factors. Although consideration should be made that such approaches, wherein relative abundances are used to derive correlations between species, may overestimate the numbers of true correlations (Friedman, 2012;r14933), this analysis was effective at classifying factors characteristic of the three observed periods, namely summer, autumn and winter periods, also observed in the dbRDA analysis (Figure 2).…”

“…Studies have pointed to a number of actinobacteria as associated with particles, with several demonstrating the acI-C and acIV lineages form speciesspecific associations with cyanobacteria (Allgaier et al, 2007). Similar increases were observed for the particle-associated betI and betIV (Figure 4g), which have been noted for their attachment to prokaryotic (Bagatini et al, 2014) and eukaryotic phytoplankton (Paver et al, 2013), as well as the metabolism of the cyanobacterial toxin microcystin (Mou et al, 2013). Among the Bacteroidetes, bacI-A, bacIII-B, bacIV-B and bacVI-B (Figure 4f) were more dominant during periods of high biovolume.…”

“…However, the bacterial community associated with Aphanocapsa and Geitlerinema differed to that of the autumn period with a greater number of OTUs identified as belonging to the Verrucomicrobial orders Opitutales and Spartobacteriales. The Verrucomicrobia have previously been reported in cyanobacterial blooms and metagenomic analysis, suggesting that they possess numerous pathways for the assimilation of cyanobacterial extracellular polymeric substances, as well as exudates (Mou et al, 2013;Bagatini et al, 2014). The bacterial groups associated with the cyanobacteria Microcystis, Oscillatoria, Sphaerospermopsis and Cuspidothrix were overrepresented by particleassociated groups, including betI, acI-C, acIV-C (Allgaier et al, 2007;Paver et al, 2013;Bagatini et al, 2014) and the methylotrophic taxon betIV, and Methylophiliaceae .…”

“…Na levels and EC were only slightly higher in the summer bloom period (average [Na] = 28.2 p.p.m., average EC = 399 μS cm − 1 ) than in the autumn period (average [Na] = 18.9 p.p.m., average EC = 361 μS-cm − 1 ). Although it is unlikely that Na concentration was sufficient to suppress the growth of any cyanobacterial species, several studies have demonstrated a link between ionic flux and toxin production (Pomati et al, 2004;Wilhelm et al, 2011;Carneiro et al, 2013), presenting a credible route through which subtle changes in Na concentrations may influence, via secondary and tertiary mechanisms, the cyanobacterial and bacterial community composition Mou et al, 2013).…”

Microcystin-LR Biodegradation by Bacillus sp.: Reaction Rates and Possible Genes Involved in the Degradation

“…Farhadkhani et al [63] observed that TOC did not significantly impact the microbial community growth during MC-LR degradation, which is similar to our observation in the current study. Mou et al [38] reported that in a biodegradation study of MC-LR, the degrading bacteria did not use MC-LR as a carbon source and MC-LR might be removed via a xenobiotic method. This may be the reason why the degradation of MC-LR did not lead to an increase in total bacteria concentration in this study.…”