Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3

Abstract

Anaerobic nitrate-dependent Fe(II) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. Although Fe(II) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent Fe(II) oxidation were from environments of circumneutral pH. The present study was conducted in Lake Grosse Fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the objective of identifying, characterizing and enumerating the microorganisms responsible for this process. The incubations of sediment under chemolithotrophic nitratedependent Fe(II)-oxidizing conditions have shown the enrichment of TM3 group of uncultured Actinobacteria. A time-course experiment done on these Actinobacteria showed a consumption of Fe(II) and nitrate in accordance with the expected stoichiometry (1:0.2) required for nitratedependent Fe(II) oxidation. Quantifications done by most probable number showed the presence of 1 Â 10 4 autotrophic and 1 Â 10 7 heterotrophic nitrate-dependent Fe(II) oxidizers per gram fresh weight of sediment. The analysis of microbial community by 16S rRNA gene amplicon pyrosequencing showed that these actinobacterial sequences correspond to B0.6% of bacterial 16S rRNA gene sequences. Stable isotope probing using 13 CO 2 was performed with the lake sediment and showed labeling of these Actinobacteria. This indicated that they might be important autotrophs in this environment. Although these Actinobacteria are not dominant members of the sediment microbial community, they could be of functional significance due to their contribution to the regeneration of Fe(III), which has a critical role as an electron acceptor for anaerobic microorganisms mineralizing sediment organic matter. To the best of our knowledge this is the first study to show the autotrophic nitrate-dependent Fe(II)-oxidizing nature of TM3 group of uncultured Actinobacteria.

Methane emission from feather moss stands

“…Cloning and sequencing of both mcrA (Conrad, Klose, Noll, Kemnitz, & Bodelier, ) and archaeal 16S rRNA genes were performed using Marburg feather moss sample‐1 for identification of the T‐RFs and for phylogenetic analysis of the methanogens according to the procedure described before (Kanaparthi et al., ). Neighbor‐joining phylogenetic tree of 16S rRNA gene sequences was constructed using ARB after aligning the sequences with SINA aligner.…”

“…DNA was extracted from the moss samples using the Soil DNA extraction kit (Machery-Nagel, D€ uren, Germany) according to the manufacturer's instructions. The community finger print was determined by terminal restriction fragment length polymorphism (T-RFLP) as described before (Kanaparthi, Pommerenke, Casper, & Dumont, 2013). In brief, PCR amplification of 16S rRNA gene was performed using FAM labeled ARCH109-F and ARCH934-R primers (Grosskopf, Janssen, & Liesack, 1998).…”

“…Cloning and sequencing of both mcrA (Conrad, Klose, Noll, Kemnitz, & Bodelier, 2008) and archaeal 16S rRNA genes were performed using Marburg feather moss sample-1 for identification of the T-RFs and for phylogenetic analysis of the methanogens according to the procedure described before (Kanaparthi et al, 2013).…”

Assessment of methane and carbon dioxide emissions in two sub‐basins of a small acidic bog lake artificially divided 30 years ago

“…Initially, the division was conducted to enable wholelake experiments in food-web manipulation (Kasprzak, 1993;Koschel, 1995). Over the decades of division, research in Lake Grosse Fuchskuhle has covered several other topics: plankton studies (Glöckner et al, 2000;Hehmann et al, 2001;Macek, Simek, & Bittl, 2001), microorganisms and microbial activity (Grossart et al, 2008;Kanaparthi, Pommerenke, Casper, & Dumont, 2013;Simek et al, 1998), basic limnology and geographical settings (Burkert et al, 2004;Kasprzak, 1993;Koschel, 1995;Richter, 1997;Succow & Jeschke, 1986), and CH 4 and CO 2 cycle (Casper et al, 2003;Chan, Wolf, Hepperle, & Casper, 2002;Conrad, Claus, & Casper, 2010), among others. The two most contrasting basins, namely south-west basin (SW) (characterised by a low pH of 4.4 and DOC of 37.3 mg/L) and the north-east basin (NE) (with a pH of 6.5 and DOC of 16.4 mg/L), were selected for this study (Figure 1).…”

Characteristics of the cultivable bacteria from sediments associated with two deep-sea hydrothermal vents in Okinawa Trough

“…In the absence of photosynthesis, the food chain in the vent system relies on chemoautotrophic prokaryotes, which produce complex organic molecules with energy obtained by oxidizing the inorganic compounds available in the environments. Studies have shown that some chemoautotrophic microorganisms, such as Thioreductor, Sulfurovum, and Sulfurimonas, can use reduced sulfur compounds, Fe(II), Mn(II), H 2 , and CH 4 as electron donors to obtain energy and fix carbon, thus providing a basis for hydrothermal vent ecosystems (Biddle et al 2012;Inagaki et al 2004;Kanaparthi et al 2013;Mino et al 2014;Nakagawa et al 2005a). In addition, heterotrophic bacteria were also rich in hydrothermal systems (Rajasabapathy et al 2014), and they play important roles in carbon and nitrogen cycling by decomposing particulate organic materials (Zhou et al 2009a, b).…”