Active bacteria and archaea cells fixing bicarbonate in the dark along the water column of a stratified eutrophic lagoon

Abstract

We studied the carbon dioxide fixation activity in a stratified hypereutrophic karstic lagoon using a combination of fingerprinting techniques targeting bacterial and archaeal 16S rRNA genes, functional gene cloning [the acetyl-CoA carboxylase (accC)], and isotopic labelling ((14)C-bicarbonate) coupled to single-cell analyses [microautoradiography combined with catalyzed reported deposition-FISH (MAR-CARD-FISH)]. The microbial planktonic community was dominated by bacteria with maximal abundances of archaea just below the oxic/anoxic transition zone (7% of total cells). In situ incubations with radiolabelled bicarbonate showed maximal photoassimilation activity in the oxic epilimnion, whereas dark CO(2) fixation was consistently observed throughout the water column, with a maximum at the oxic/anoxic interface (8.6 mg C m(-3) h(-1)). The contributions of light and dark carbon fixation activities in the whole water column were 69% and 31% of the total C incorporated, respectively. MAR-CARD-FISH incubations corroborated these results and revealed that the highest fraction of bacterial and archaeal cells actively uptaking bicarbonate in the light was found at the surface. The bacterial community was mainly composed of green sulfur bacteria (Chlorobi) and members of the Betaproteobacteria and the Bacteroidetes. The archaeal assemblage was composed of phylotypes of the Miscellaneous Crenarchaeotic Group and a few methanogens. Clone libraries of the accC gene showed an absolute dominance of bacterial carboxylases. Our results suggest that the dark carbon fixation activity measured was mainly related to CO(2) incorporation by heterotrophs rather than to the activity of true chemoautotrophs.

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

“…MCG are likely to access substrates that are physically or chemically recalcitrant. This conclusion is in agreement with findings from previous literature (Biddle et al, 2006;Lipp et al, 2008;Takano et al, 2010;Webster et al, 2010;Lliró s et al, 2011).…”

Microbial Ecology of Lake Kivu

“…The small contribution of archaea to the planktonic microbial community is a common trait for freshwater environments (Casamayor and Borrego 2009 ) . In this regard, values below 10% of total prokaryotes have usually been reported for different freshwater lakes (Pernthaler et al 1998 ;Jürgens et al 2000 ;Llirós et al 2011 ) , although higher archaeal abundances have been reported (>20% of total cells) in some oligotrophic (Urbach et al 2007 ;Auguet and Casamayor 2008 ) or oligomesotrophic (Callieri et al 2009 ) freshwater lakes.…”

Some Mixotrophic Flagellate Species Selectively Graze on Archaea

“…In the last decade, several studies have shown the broad distribution and abundance of Archaea in aquatic ecosystems (50)(51)(52) and their potential relevance in the sulfur, nitrogen, and carbon cycles (33,(53)(54)(55). However, their specific ecological interactions within the microbial communities remain largely unknown.…”

“…Occasionally, some biases of the probe-hybridizing members of the phylum Bacteroidetes have been reported (32)(33)(34). This doubling hybridization can inflate the Archaea counts.…”