Expression and Association of Group IV Nitrogenase NifD and NifH Homologs in the Non-Nitrogen-Fixing Archaeon<i>Methanocaldococcus jannaschii</i>

Staples, Christopher R.; Lahiri, Surobhi; Raymond, Jason; Herbulis, Lindsay Von; Mukhophadhyay, Biswarup; Blankenship, Robert E.

doi:10.1128/jb.00876-07

Cited by 57 publications

(52 citation statements)

References 52 publications

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“…However, it should be borne in mind that probably not all of the detected nifH sequences came from active diazotrophic microorganisms. For example, most of the NifH sequences from the originally defined "cluster IV" are not well characterized, and some are found not to be involved in N 2 fixation (9,17,64). Although it is currently unknown whether the microorganisms that carry the novel nifH sequences from most of our newly defined classes are functional for active N 2 fixation in natural environments, our study extends the diversity and evolutionary complexity of the nifH gene sequences.…”

Section: Discussionmentioning

confidence: 82%

Environment-Dependent Distribution of the Sediment nifH -Harboring Microbiota in the Northern South China Sea

Dang

Yang

et al. 2013

Appl Environ Microbiol

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fThe South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N 2 fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH 4 ؉ concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N 2 fixation and NH 4 ؉ production. Several other environmental factors, including sediment pore water PO 4 3؊ concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery.

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Section: Discussionmentioning

confidence: 82%

Environment-Dependent Distribution of the Sediment nifH -Harboring Microbiota in the Northern South China Sea

Dang

Yang

et al. 2013

Appl Environ Microbiol

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“…In agreement, known methanogens missing such pathways require acetate or complex exogenous nutrients (for example, yeast extract or rumen fluid) for growth (Whitman et al, 1982;Miller and Wolin, 1985;Tanner and Wolfe, 1988;Zellner et al, 1989;Miller and Lin, 2002). In addition, unlike most methanogens, the WSA2 genomes are also deficient in nitrogen fixation genes (that is, Nif) though they do encode non-nitrogenfixing NifD-and NifH-like genes (NflDH; Figure 2a; Staples et al, 2007). Thus, the draft genomes suggest that WSA2 may be incapable of both autotrophy and nitrogen fixation, a rarity among known methanogens.…”

Section: Physiologymentioning

confidence: 75%

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

et al. 2016

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The ecophysiology of one candidate methanogen class WSA2 (or Arc I) remains largely uncharacterized, despite the long history of research on Euryarchaeota methanogenesis. To expand our understanding of methanogen diversity and evolution, we metagenomically recover eight draft genomes for four WSA2 populations. Taxonomic analyses indicate that WSA2 is a distinct class from other Euryarchaeota. None of genomes harbor pathways for CO 2 -reducing and aceticlastic methanogenesis, but all possess H 2 and CO oxidation and energy conservation through H 2 -oxidizing electron confurcation and internal H 2 cycling. As the only discernible methanogenic outlet, they consistently encode a methylated thiol coenzyme M methyltransferase. Although incomplete, all draft genomes point to the proposition that WSA2 is the first discovered methanogen restricted to methanogenesis through methylated thiol reduction. In addition, the genomes lack pathways for carbon fixation, nitrogen fixation and biosynthesis of many amino acids. Acetate, malonate and propionate may serve as carbon sources. Using methylated thiol reduction, WSA2 may not only bridge the carbon and sulfur cycles in eutrophic methanogenic environments, but also potentially compete with CO 2 -reducing methanogens and even sulfate reducers. These findings reveal a remarkably unique methanogen 'Candidatus Methanofastidiosum methylthiophilus' as the first insight into the sixth class of methanogens 'Candidatus Methanofastidiosa'.

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“…Cluster III contained putative anaerobes including sulfate reducing genera of the Deltaproteobacteria , and genera such as Clostridium . Cluster IV contained nifH paralogs that are thought to function in metabolic processes other than nitrogen fixation (e.g., Young, 2005; Staples et al, 2007). …”

Section: Resultsmentioning

confidence: 99%

Diazotroph Diversity in the Sea Ice, Melt Ponds, and Surface Waters of the Eurasian Basin of the Central Arctic Ocean

et al. 2016

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The Eurasian basin of the Central Arctic Ocean is nitrogen limited, but little is known about the presence and role of nitrogen-fixing bacteria. Recent studies have indicated the occurrence of diazotrophs in Arctic coastal waters potentially of riverine origin. Here, we investigated the presence of diazotrophs in ice and surface waters of the Central Arctic Ocean in the summer of 2012. We identified diverse communities of putative diazotrophs through targeted analysis of the nifH gene, which encodes the iron protein of the nitrogenase enzyme. We amplified 529 nifH sequences from 26 samples of Arctic melt ponds, sea ice and surface waters. These sequences resolved into 43 clusters at 92% amino acid sequence identity, most of which were non-cyanobacterial phylotypes from sea ice and water samples. One cyanobacterial phylotype related to Nodularia sp. was retrieved from sea ice, suggesting that this important functional group is rare in the Central Arctic Ocean. The diazotrophic community in sea-ice environments appear distinct from other cold-adapted diazotrophic communities, such as those present in the coastal Canadian Arctic, the Arctic tundra and glacial Antarctic lakes. Molecular fingerprinting of nifH and the intergenic spacer region of the rRNA operon revealed differences between the communities from river-influenced Laptev Sea waters and those from ice-related environments pointing toward a marine origin for sea-ice diazotrophs. Our results provide the first record of diazotrophs in the Central Arctic and suggest that microbial nitrogen fixation may occur north of 77°N. To assess the significance of nitrogen fixation for the nitrogen budget of the Arctic Ocean and to identify the active nitrogen fixers, further biogeochemical and molecular biological studies are needed.

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Expression and Association of Group IV Nitrogenase NifD and NifH Homologs in the Non-Nitrogen-Fixing ArchaeonMethanocaldococcus jannaschii

Cited by 57 publications

References 52 publications

Environment-Dependent Distribution of the Sediment nifH -Harboring Microbiota in the Northern South China Sea

Environment-Dependent Distribution of the Sediment nifH -Harboring Microbiota in the Northern South China Sea

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

Diazotroph Diversity in the Sea Ice, Melt Ponds, and Surface Waters of the Eurasian Basin of the Central Arctic Ocean

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