Genetic Diversity of Hydrogen-Producing Bacteria in an Acidophilic Ethanol-H₂-Coproducing System, Analyzed Using the [Fe]-Hydrogenase Gene

Abstract

Hydrogen gas (H 2 ) produced by bacterial fermentation of biomass can be a sustainable energy source. The ability to produce H 2 gas during anaerobic fermentation was previously thought to be restricted to a few species within the genera Clostridium and Enterobacter. This work reports genomic evidence for the presence of novel H 2 -producing bacteria (HPB) in acidophilic ethanol-H 2 -coproducing communities that were enriched using molasses wastewater. The majority of the enriched dominant populations in the acidophilic ethanol-H 2 -coproducing system were affiliated with low-G؉C-content gram-positive bacteria, Bacteroidetes, and Actinobacteria, based on the 16S rRNA gene. However, PCR primers designed to specifically target bacterial hydA yielded 17 unique hydA sequences whose amino acid sequences differed from those of known HPB. The putative ethanol-H 2 -coproducing bacteria comprised 11 novel phylotypes closely related to Ethanoligenens harbinense, Clostridium thermocellum, and Clostridium saccharoperbutylacetonicum. Furthermore, analysis of the alcohol dehydrogenase isoenzyme also pointed to an E. harbinense-like organism, which is known to have a high conversion rate of carbohydrate to H 2 and ethanol. We also found six novel HPB that were associated with lactate-, propionate-, and butyrate-oxidizing bacteria in the acidophilic H 2 -producing sludge. Thus, the microbial ecology of mesophilic and acidophilic H 2 fermentation involves many other bacteria in addition to Clostridium and Enterobacter.

[FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism

“…The H 2 evolution activity of [FeFe]-hydrogenase is 10-to 100-fold greater than that of the [NiFe]-hydrogenase (Frey, 2002), an observation that is consistent with the physiological role of most [NiFe]-hydrogenase in H 2 uptake (Vignais et al, 2001). Recently, PCR primers for the specific amplification of the large subunit of the [FeFe]hydrogenase gene (hydA) were developed to examine the diversity of hydA as a proxy for fermentative bacteria in a H 2 -generating saline microbial-mat system (Boyd et al, 2009b) and in a H 2 -generating anaerobic bioreactor (Xing et al, 2008). The results of these studies, as well as those from a number of metagenomic investigations that include the deep subsurface (Chivian et al, 2008) and termite hindgut environments (Warnecke et al, 2007), collectively indicate a widespread distribution and diversity of [FeFe]-hydrogenase in nature.…”

The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities

“…Non-targeted metagenomic and metatranscriptomic sequencing may identify and quantify the hydrogenase genes, but not in a cost-effective manner. Previous studies characterizing the hydrogenase genes present in microbial communities have only targeted specific subgroups of hydrogenases (Roeselers et al, 2008;Xing et al, 2008;Boyd et al, 2009). In this study, we focused on the most widespread hydrogenases, the (NiFe) (including (NiFeSe)) and (FeFe) hydrogenases, and demonstrated the most broadly targeted approach to date to characterize diverse hydrogenase genes present and expressed in a microbial community.…”

Clostridium perfringens septicemia in a long-beaked common dolphin Delphinus capensis: an etiology of gas bubble accumulation in cetaceans

“…During the decomposition process, destruction of tissues by the body's enzymes (autolysis) and microorganisms from the intestines and the environment (putrefaction) occurs (Vass 2001). Some of these microorganisms are fermentive H 2 -producing bacteria, which are restricted to a few genera, such as Clostridium and Enterobacter (Xing et al 2008). In this case, the hydrogen was likely produced while the dolphin was alive, by the C. perfringens cultured from multiple organs and presumed to be the rodshaped bacterium associated with the gas margins identified on histopathology.…”