Activity and distribution of diazotrophic communities across the Cape Verde Frontal Zone in the Northeast Atlantic Ocean

Hallstrøm, Søren; Benavides, Mar; Salamon, Ellen R.; Arı́stegui, Javier; Riemann, Lasse

doi:10.1007/s10533-022-00940-w

Cited by 4 publications

(1 citation statement)

References 109 publications

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“…However, qPCR data can allow for quantitative comparisons in abundances even if there are limitations in converting to cell number and biomass. We stress that qPCR data have demonstrated important characteristics of the biogeography of diazotrophs, including seasonality (Church et al 2009; Bentzon‐Tilia et al 2015; Cabello et al 2016; Tang and Cassar 2019), biogeography (Shiozaki et al 2017; Hallstrøm et al 2022) and hotspots or blooms of uncultivated or difficult to detect organisms (Goebel et al 2008; Moisander et al 2010). This has led to invaluable insights into the environmental drivers of diazotrophic taxa now known to be of key importance to marine N cycling.…”

Section: Diazotroph Qpcr Data Are Valuablementioning

confidence: 96%

Quantification of gene copy numbers is valuable in marine microbial ecology: A comment to Meiler et al. (2022)

Zehr

Riemann

2023

Limnology & Oceanography

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Section: Diazotroph Qpcr Data Are Valuablementioning

confidence: 96%

Quantification of gene copy numbers is valuable in marine microbial ecology: A comment to Meiler et al. (2022)

Zehr

Riemann

2023

Limnology & Oceanography

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Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Turk‐Kubo

Gradoville

Cheung

et al. 2022

FEMS Microbiology Reviews

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Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

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Global biogeography of N₂-fixing microbes:nifHamplicon database and analytics workflow

Morando,

Magasin,

Cheung

et al. 2024

Preprint

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Marine nitrogen (N) fixation is a globally significant biogeochemical process carried out by a specialized group of prokaryotes (diazotrophs), yet our understanding of their ecology is constantly evolving. Although marine dinitrogen (N2)-fixation is often ascribed to cyanobacterial diazotrophs, indirect evidence suggests that non-cyanobacterial diazotrophs (NCDs) might also be important. One widely used approach for understanding diazotroph diversity and biogeography is polymerase chain reaction (PCR)-amplification of a portion of thenifHgene, which encodes a structural component of the N2-fixing enzyme complex, nitrogenase. An array of bioinformatic tools exists to processnifHamplicon data, however, the lack of standardized practices has hindered cross-study comparisons. This has led to a missed opportunity to more thoroughly assess diazotroph biogeography, diversity, and their potential contributions to the marine N cycle. To address these knowledge gaps a bioinformatic workflow was designed that standardizes the processing ofnifHamplicon datasets originating from high-throughput sequencing (HTS). Multiple datasets are efficiently and consistently processed with a specialized DADA2 pipeline to identify amplicon sequence variants (ASVs). A series of customizable post-pipeline stages then detect and discard spuriousnifHsequences and annotate the subsequent quality-filterednifHASVs using multiple reference databases and classification approaches. This newly developed workflow was used to reprocess nearly all publicly availablenifHamplicon HTS datasets from marine studies, and to generate a comprehensivenifHASV database containing 7909 ASVs aggregated from 21 studies that represent the diazotrophic populations in the global ocean. For each sample, the database includes physical and chemical metadata obtained from the Simons Collaborative Marine Atlas Project (CMAP). Here we demonstrate the utility of this database for revealing global biogeographical patterns of prominent diazotroph groups and highlight the influence of sea surface temperature. The workflow andnifHASV database provide a robust framework for studying marine N2fixation and diazotrophic diversity captured bynifHamplicon HTS. Future datasets that target understudied ocean regions can be added easily, and users can tune parameters and studies included for their specific focus. The workflow and database are available, respectively, in GitHub (https://github.com/jdmagasin/nifH-ASV-workflow) and Figshare (https://doi.org/10.6084/m9.figshare.23795943.v1).

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Activity and distribution of diazotrophic communities across the Cape Verde Frontal Zone in the Northeast Atlantic Ocean

Cited by 4 publications

References 109 publications

Quantification of gene copy numbers is valuable in marine microbial ecology: A comment to Meiler et al. (2022)

Quantification of gene copy numbers is valuable in marine microbial ecology: A comment to Meiler et al. (2022)

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Global biogeography of N₂-fixing microbes:nifHamplicon database and analytics workflow

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Activity and distribution of diazotrophic communities across the Cape Verde Frontal Zone in the Northeast Atlantic Ocean

Cited by 4 publications

References 109 publications

Quantification of gene copy numbers is valuable in marine microbial ecology: A comment to Meiler et al. (2022)

Quantification of gene copy numbers is valuable in marine microbial ecology: A comment to Meiler et al. (2022)

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Global biogeography of N2-fixing microbes:nifHamplicon database and analytics workflow

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Global biogeography of N₂-fixing microbes:nifHamplicon database and analytics workflow