Methanogenesis has traditionally been assumed to occur only in anoxic environments, yet there is mounting, albeit indirect, evidence of methane (CH 4 ) production in oxic marine and freshwaters. Here we present the first direct, ecosystem-scale demonstration of methanogenesis in oxic lake waters. This methanogenesis appears to be driven by acetoclastic production, and is closely linked to algal dynamics. We show that oxic water methanogenesis is a significant component of the overall CH 4 budget in a small, shallow lake, and provide evidence that this pathway may be the main CH 4 source in large, deep lakes and open oceans. Our results challenge the current global understanding of aquatic CH 4 dynamics, and suggest a hitherto unestablished link between pelagic CH 4 emissions and surface-water primary production. This link may be particularly sensitive to widespread and increasing human influences on aquatic ecosystem primary productivity.

There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic prokaryotes that use light as a secondary energy source to complement the consumption of organic matter. Despite this metabolic flexibility and their widespread distribution, their low relative abundances suggest that they may be subjected to strong regulatory processes. However, there is still little information on the regulation of AAP abundance, particularly in freshwaters. Here, we used a lake mesocosm experiment to address the top-down regulation of freshwater AAP by protists and zooplankton under 2 contrasting nutrient regimes. Our results support the hypothesis that freshwater AAP are subject to intense top-down regulation, and are selectively removed by grazers. The average gross growth rate of AAP was ca. 1.5 times higher, and grazing loss rates 1.6 times higher than those of the bulk bacterial community. Our results further indicate that whereas protists are the main predators of AAP, zooplankton may account for over a third of AAP losses, and both exhibit a greater selectivity for AAP relative to total bacteria. The mechanistic underpinning of this selectivity is still unclear, but it may be related to the average larger cell size of AAP, and to their higher potential growth rates relative to the bulk bacterial community. Our results further suggest that AAP may play a disproportionate role in the nutrition of lake zooplankton, and in the trophic transfer of organic carbon in lake food webs.KEY WORDS: Aerobic anoxygenic phototrophic bacteria · Grazing loss rate · Selective predation · Photoheterotrophy · Freshwater Resale or republication not permitted without written consent of the publisher FREE REE ACCESS CCESSContribution to AME Special 5 'SAME 13: progress and perspectives in aquatic microbial ecology ' Aquat Microb Ecol 76: 71-83, 2015 Lamy et al. , Mašín et al. 2012, Fauteux et al. 2015. Two possible hypotheses may explain their low in situ abundances: either light-derived energy has little effect on the growth and competitiveness of AAP, or, if there is an effect, there are other factors, unrelated to phototrophy, that may limit the ecological success of AAP bacteria more than that of other bacterial groups. Experimental evidence from marine environments suggests that AAP bacteria may have higher growth rates than the average bacteria (Koblízek et al. 2007, and therefore their generally low abundance should be due to high losses, either via grazing or viral infection. Indeed, the only study so far to have explored the different controls of the abundance of this group showed that protist grazing was the main regulator of the abundance of marine AAP bacteria . Beyond this marine study, however, there is still little information on the regulation of AAP abundance and activity, especially for inland waters, despite the fact that these photoheterotrophic mic robes have also been shown to be widespread in freshwater planktonic food webs (Mašín et al. 2008, Medová et al. 2011, Mašín et al. 2012, Cuperová et al. 2013,...

Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in‐depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs.