New Nitrogen-Fixing Microorganisms Detected in Oligotrophic Oceans by Amplification of Nitrogenase (
            <i>nifH</i>
            ) Genes

Zehr, Jonathan P.; Mellon, Mark T.; Zani, Sabino

doi:10.1128/aem.64.12.5067-5067.1998

Cited by 102 publications

(20 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA extracts were treated with ezDNase™ and converted into cDNA using the SuperScript ® IV First Strand Synthesis System with ezDNase™ enzyme kit (Invitrogen) following the recommendation of the supplier. Nested PCR amplification of nifH genes from cDNA sample and full control (i.e., sample following extraction, cDNA conversion, and amplification) were conducted in triplicate (with one negative PCR control) according to the modified protocol of Zehr et al., 1998 from Jayakumar et al., 2017. Amplification was verified by gel electrophoresis and cDNA amplicons were pooled and sent with total DNA extracts for nifH and 16S rRNA gene sequencing using bTEFAP ® and Illumina MiSeq300 at the MRDNA ® facility (Shallowater, TX, USA).…”

Section: Methodsmentioning

confidence: 99%

Ammonium Sensitivity of Biological Nitrogen Fixation by Anaerobic Diazotrophs in Cultures and Benthic Marine Sediments

et al. 2022

View full text Add to dashboard Cite

Biological nitrogen fixation (BNF) is the dominant source of new bioavailable nitrogen (N) in the ocean (Gruber & Galloway, 2008;Zhang et al., 2020). By replenishing fixed N lost by denitrification and anammox, BNF promotes N availability and marine productivity. Present in a subset of diverse prokaryotes termed diazotrophs, all BNF is catalyzed by the enzyme nitrogenase in a complex, energy-intensive reaction that reduces dinitrogen (N 2 ) into ammonia (NH 3 ), which is subsequently incorporated into cell material. Diazotrophs thus function as natural gatekeepers for ecosystem N input and are critically important in oligotrophic systems, such as tropical and subtropical marine surface waters (

show abstract

Section: Methodsmentioning

confidence: 99%

Ammonium Sensitivity of Biological Nitrogen Fixation by Anaerobic Diazotrophs in Cultures and Benthic Marine Sediments

et al. 2022

View full text Add to dashboard Cite

show abstract

“…One of the cyanobacteria, i.e., Trichodesmium, has been traditionally considered the most dominant diazotrophic genus, but it is now clear that marine diazotrophs are more diverse. Non-cyanobacterial diazotrophs which are not constrained by light may also conduct N 2 fixation below the twilight zone (Zehr et al 1998, Riemann et al 2010, Luo et al 2012. They can be detected in a wide range of environments such as nutrient-rich, cold, temperate zones, and the dark and deep oceans (Benavides et al 2018).…”

mentioning

confidence: 99%

Dinitrogen fixation rates in the Bay of Bengal during summer monsoon

Saxena

Sahoo

Khan

et al. 2020

Environ. Res. Commun.

View full text Add to dashboard Cite

Biological dinitrogen (N 2 ) fixation exerts an important control on oceanic primary production by providing bioavailable form of nitrogen (such as ammonium) to photosynthetic microorganisms. N 2 fixation is dominant in nutrient poor and warm surface waters. The Bay of Bengal is one such region where no measurements of phototrophic N 2 fixation rates exist. The surface water of the Bay of Bengal is generally nitrate-poor and warm due to prevailing stratification and thus, could favour N 2 fixation. We commenced the first N 2 fixation study in the photic zone of the Bay of Bengal using 15 N 2 gas tracer incubation experiment during summer monsoon 2018. We collected seawater samples from four depths (covering the mixed layer depth of up to 75 m) at eight stations. N 2 fixation rates varied from 4 to 75 μmol N m −2 d −1 . The contribution of N 2 fixation to primary production was negligible (<1%). However, the upper bound of observed N 2 fixation rates is higher than the rates measured in other oceanic regimes, such as the Eastern Tropical South Pacific, the Tropical Northwest Atlantic, and the Equatorial and Southern Indian Ocean.

show abstract

“…The diversity of marine diazotrophs has long been thought to be restricted to members of the phylum Cyanobacteria . However, culture-independent approaches, like those targeting the nifH gene or metagenomic and metatranscriptomic analyses from various oceanic samples demonstrated the presence in abundance of non-cyanobacterial diazotrophs (NCD, (Zehr et al, 1998; Delmont et al, 2018; Farnelid et al, 2019; Geisler et al, 2019; Kapili et al, 2020; Delmont et al, 2022)). Despite these observations, few marine NCD have been brought to culture (Farnelid et al, 2014; Martinez-Perez et al, 2018), hampering in depth understanding of their ecophysiology and contribution to global N budget in oceans.…”

Section: Discussionmentioning

confidence: 99%

“…More and more evidence show the presence in all oceans of previously overlooked nitrogen-fixers, not affiliated to the phylum Cyanobacteria . Indeed, culture-independent approaches based on the amplification or immunodetection of the nifH gene, a gene encoding a subunit of the nitrogenase, conserved among diazotrophs and considered as a biomarker for diazotrophy, have demonstrated the presence of marine Non-Cyanobacterial Diazotrophs (NCDs) (Zehr et al, 1998) in the water column attached to particles (undefined aggregates, faecal pellets) (Farnelid et al, 2019; Geisler et al, 2019) and in deep sea sediments (Kapili et al, 2020). Moreover, Tara Oceans expeditions provide metagenomic data from diverse oceanic locations, depths and size fractions, coupled with physical and chemical information (Karsenti et al, 2011; Planes et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph

Joublin-Delavat

Touahri

Morot

et al. 2022

Preprint

View full text Add to dashboard Cite

Nitrogen (N2) fixation, or diazotrophy, supports a large part of primary production in oceans. In these environments, diazotrophic cyanobacteria are known to largely contribute to N2 fixation. However, culture-independent approaches highlighted the presence in abundance of non-cyanobacterial diazotrophs (NCD) in all open oceans and in estuarine environments. Unfortunately, the ecophysiology of marine NCD remains elusive, mostly because of the low number of isolated NCD and because of the lack of available genetic tools for these isolates. Here, a dual genetic and functional approach allowed unveiling the ecophysiology of a marine NCD affiliated to the species Vibrio diazotrophicus. We developed genetic tools for this strain, leading to the obtention of the first genetic mutant of a marine NCD, deleted in its nifH gene. Physiological characterization of the mutant was performed using a soft-gellan assay, demonstrating that the nifH mutant in not able to grow in nitrogen-deprived media, while in trans complementation restores the wild type phenotype. Furthermore, we demonstrated here that V. diazotrophicus produces a thick biofilm under diazotrophic conditions, suggesting biofilm production as an adaptive response of this NCD to cope with the inhibition of nitrogen-fixation by molecular oxygen. Finally, the genomic signature of V. diazotrophicus is essentially absent from metagenomic data of Tara Ocean expeditions, despite having been isolated from various marine environments. This suggests that a hidden NCD diversity occurs in those environments, but unveiling this diversity requires additional sampling strategies. Given the increasing evidence that marine NCD play a major role in the biogeochemical cycle of nitrogen and carbon (by fueling the biological carbon pump), an in depth characterization of their ecophysiology is needed. We think that the genetically tractable V. diazotrophicus strain used in this study may serve as an ideal model to study the ecophysiology of these overlooked procaryotic group.

show abstract

New Nitrogen-Fixing Microorganisms Detected in Oligotrophic Oceans by Amplification of Nitrogenase ( nifH ) Genes

Cited by 102 publications

References 17 publications

Ammonium Sensitivity of Biological Nitrogen Fixation by Anaerobic Diazotrophs in Cultures and Benthic Marine Sediments

Ammonium Sensitivity of Biological Nitrogen Fixation by Anaerobic Diazotrophs in Cultures and Benthic Marine Sediments

Dinitrogen fixation rates in the Bay of Bengal during summer monsoon

Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph

Contact Info

Product

Resources

About