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

Marshall, Ian P. G.; Berggren, Dusty R. V.; Azizian, Mohammad F.; Burow, Luke C; Semprini, Lewis; Spormann, Alfred M.

doi:10.1038/ismej.2011.136

Cited by 34 publications

(30 citation statements)

References 55 publications

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“…Dehaloccoides , which was the sole group belonging to Chloroflexi detected in the present study, is able to catalyze reductive dehalogenation using H 2 as electron donors (He et al ., ), while syntrophic growth with hydrogenotrophic methanogens was reported for the species in Chloroflexi isolated from paddy field soil (Yamada et al ., ). No [FeFe]‐hydrogenase gene related to Chloroflexi was detected in the other environments tested (Boyd et al ., , ; Schmidt et al ., , ) except in a reductive dechlorinating soil column (Marshall et al ., ). Therefore, Chloroflexi may be unique among the H 2 ‐producing bacteria in the paddy field soil, and elucidation of the roles of the members in Chloroflexi in H 2 production and consumption in paddy field soil needs further investigations.…”

Section: Resultsmentioning

confidence: 97%

Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil

Baba

Kimura

Asakawa

et al. 2013

FEMS Microbiol Lett

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Hydrogen (H2) is one of the most important intermediates in the anaerobic decomposition of organic matter. Although the microorganisms consuming H2 in anaerobic environments have been well documented, those producing H2 are not well known. In this study, we elucidated potential members of H2‐producing bacteria in a paddy field soil using clone library analysis of [FeFe]‐hydrogenase genes. The [FeFe]‐hydrogenase is an enzyme involved in H2 metabolism, especially in H2 production. A suitable primer set was selected based on the preliminary clone library analysis performed using three primer sets designed for the [FeFe]‐hydrogenase genes. Soil collected in flooded and drained periods was used to examine the dominant [FeFe]‐hydrogenase genes in the paddy soil bacteria. In total, 115 and 108 clones were analyzed from the flooded and drained paddy field soils, respectively. Homology and phylogenetic analysis of the clones showed the presence of diverse [FeFe]‐hydrogenase genes mainly related to Firmicutes, Deltaproteobacteria, and Chloroflexi. Predominance of Deltaproteobacteria and Chloroflexi suggests that the distinct bacterial community possessed [FeFe]‐hydrogenase genes in the paddy field soil. Our study revealed the potential members of H2‐producing bacteria in the paddy field soil based on their genetic diversity and the distinctiveness of the [FeFe]‐hydrogenase genes.

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Section: Resultsmentioning

confidence: 97%

Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil

Baba

Kimura

Asakawa

et al. 2013

FEMS Microbiol Lett

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“…In a study using a hydrogenase-specific microarray (23), it was possible to detect [NiFe]-hydrogenase genes in a microbial mat, but obviously this technique is limited to those genes available in the databases.…”

Section: Discussionmentioning

confidence: 99%

“…A few studies already attempted to analyze the occurrence of these hydrogenases in the environment by using primers specific for one group of the nine different known groups and subgroups of [NiFe]-hydrogenases (9,21,22) or by using a microarray with a specific set of genes (23), but there is no study that tried to unravel the whole set present.…”

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confidence: 99%

hypD as a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters

Beimgraben

Gutekunst

Opitz

et al. 2014

Appl Environ Microbiol

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Hydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H 2 cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown.[NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of A tmospheric hydrogen concentrations result from a number of counteracting processes. H 2 is mainly produced due to photooxidation of methane and other hydrocarbons in the upper atmosphere and due to fossil fuel and biomass burning. By far the largest proportion of hydrogen (80 to 90%) is consumed by microorganisms in the soil, whereas the remaining part reacts with OH radicals (1, 2). Since OH radicals are important for the degradation of methane, hydrogen levels indirectly control the amount of this trace gas. Currently, the atmospheric concentration of H 2 is about 0.5 ppm (2).The processes governing hydrogen concentrations and exchange in marine and freshwater environments are poorly described. In general, it seems that tropical surface waters act as hydrogen sources contributing about 6% to the global hydrogen production (2). Possible causes of H 2 evolution are photochemical processes in the surface layers as well as nitrogen fixation (3-6). Thorough flux analysis is still lacking. On the other hand, investigations of temperate surface waters showed net hydrogen uptake that could be assigned to microorganisms (7).Three classes of hydrogenases, the enzymes involved in hydrogen turnover, are known. Their classification is based on their active site metal ions being either a single [Fe] Although they are phylogenetically related, it is not possible to derive degenerated primers for the amplification of [NiFe]-hydrogenase genes, because their signature motifs are too scattered and too short. However, all [NiFe]-hydrogenases ultimately depend on the presence of six maturation genes, hypABCDEF (10). The most promising candidate of all maturation genes is the highly conserved hypD, encoding a protein with a ferredoxin:thioredoxin reductase-like [4Fe-4S] cluster and additional cysteine residues that probably work as a redox cascade. In concert with HypC, it works as a scaffold protein that allows the insertion of the Fe(CN) 2 (CO) in the correct oxidation state into the active site of the [NiFe]-hydrogenases (11-17).Since hydrogen leakage from anaerobic habitats is negligible and does not contribute to a significant extent to H 2 levels in the atmosphere (18)(19)(20), microbial influence on its atmospheric concentration apart from nitrogen fixation mainly relies on [NiFe]-hydrogenases. A few studies already attempted to analyze the occurrence o...

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“…To find linkages between rdhA genes, we constructed and used a tiling DNA microarray targeting 293 rdhA of known and unknown substrate specificity. The tiling microarray method avoids false‐positive gene detection to a greater extent than traditional microarray methods that rely on a smaller number of probes targeting each gene (Marshall et al ., ). We used this rdhA ‐based approach to identify different strains within a population based on the covariance of rdhA genes using hierarchical clustering, analogous to finding patterns of gene coregulation from pure‐culture microarray data (Eisen et al ., ) or differential coverage binning of metagenomes (Albertsen et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Inferring community dynamics of organohalide-respiring bacteria in chemostats by covariance ofrdhAgene abundance

Marshall

Azizian

Semprini

et al. 2013

FEMS Microbiol Ecol

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We have developed a novel approach to identifying and quantifying closely related organohalide-respiring bacteria. Our approach made use of the unique genomic associations of specific reductive dehalogenase subunit A encoding genes (rdhA) that exist in known strains of Dehalococcoides mccartyi and Desulfitobacterium and the distinguishing covariance pattern of observed rdhA genes to assign genes to unknown strains. To test this approach, we operated five anaerobic reductively dechlorinating chemostats for 3-4 years with tetrachloroethene and trichloroethene as terminal electron acceptors and lactate/formate as electron donors. The presence and abundance of rdhA genes were determined comprehensively at the community level using a custom-developed Reductive Dehalogenase Chip (RDH Chip) DNA microarray and used to define putative strains of Dehalococcoides mccartyi and Desulfitobacterium sp. This monitoring revealed that stable chemical performance of chemostats was reflected by a stable community of reductively dechlorinating bacteria. However, perturbations introduced by, for example, electron donor limitation or addition of the competing electron acceptor sulfate led to overall changes in the chemostat performance, including incomplete reduction in the chloroethene substrates, and in the population composition of reductively dehalogenating bacteria. Interestingly, there was a high diversity of operationally defined D. mccartyi strains between the chemostats with almost all strains unique to their specific chemostats in spite of similar selective pressure and similar inocula shared between chemostats.

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

Cited by 34 publications

References 55 publications

Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil

Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil

hypD as a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters

Inferring community dynamics of organohalide-respiring bacteria in chemostats by covariance ofrdhAgene abundance

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