Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens

Biological dinitrogen (N2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N2 fixation by NCDs and propose a conceptual framework for aggregate-associated N2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.

[1]  L. Riemann,et al.  Pelagic N2 fixation dominated by sediment diazotrophic communities in a shallow temperate estuary , 2021, Limnology and Oceanography.

[2]  D. Capone,et al.  Nitrogen fixation within the water column associated with two hypoxic basins in the Southern California Bight , 2011 .

[3]  T. Thiel Nitrogen Fixing Organisms: Pure and Applied Aspects , 1991 .

[4]  H. Ploug Small‐scale oxygen fluxes and remineralization in sinking aggregates , 2001 .

[5]  J. Cole,et al.  BACTERIAL GROWTH EFFICIENCY IN NATURAL AQUATIC SYSTEMS , 1998 .

[6]  I. Berman‐Frank,et al.  Dissolved Organic Matter Influences N2 Fixation in the New Caledonian Lagoon (Western Tropical South Pacific) , 2018, Front. Mar. Sci..

[7]  L. Riemann,et al.  Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection. , 2016, Trends in microbiology.

[8]  J. Hall,et al.  Mass sedimentation of picoplankton embedded in organic aggregates , 2000 .

[9]  H. Grossart,et al.  Bacterial production and growth efficiencies: Direct measurements on riverine aggregates , 2000 .

[10]  A. Alldredge,et al.  Can Microscale Chemical Patches Persist in the Sea? Microelectrode Study of Marine Snow, Fecal Pellets , 1987, Science.

[11]  G. Likens,et al.  Sulfate inhibition of molybdenum-dependent nitrogen fixation by planktonic cyanobacteria under seawater conditions: a non-reversible effect , 2003, Hydrobiologia.

[12]  E. Rahav,et al.  Direct Detection of Heterotrophic Diazotrophs Associated with Planktonic Aggregates , 2019, Scientific Reports.

[13]  L. Riemann,et al.  Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters , 2010 .

[14]  W. S. Silver Microbial ecology. , 1967, Science.

[15]  Samuel T. Wilson,et al.  Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies , 2019, The ISME Journal.

[16]  R. Fulweiler,et al.  Nitrogen fixation: A poorly understood process along the freshwater‐marine continuum , 2021, Limnology and Oceanography Letters.

[17]  A. Waite,et al.  Embedding and slicing of intact in situ collected marine snow , 2018 .

[18]  C. Santinelli DOC in the Mediterranean Sea , 2015 .

[19]  H. Grossart,et al.  Bacterial growth and grazing on diatom aggregates: Respiratory carbon turnover as a function of aggregate size and sinking velocity , 2000 .

[20]  Tom O. Delmont,et al.  Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean , 2021, The ISME Journal.

[21]  L. Stal,et al.  Dominance of unicellular cyanobacteria in the diazotrophic community in the Atlantic Ocean , 2014 .

[22]  Mark V Brown,et al.  Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs , 2021, PeerJ.

[23]  B. Jørgensen,et al.  Anoxic aggregates - an ephemeral phenomenon in the pelagic environment? , 1997 .

[24]  Meaghan C. Daley,et al.  Longitudinal variability of diazotroph abundances in the subtropical North Atlantic Ocean , 2016 .

[25]  Farooq Azam,et al.  Microbial Control of Oceanic Carbon Flux: The Plot Thickens , 1998, Science.

[26]  N. Musat,et al.  NanoSIMS chemical imaging combined with correlative microscopy for biological sample analysis. , 2016, Current opinion in biotechnology.

[27]  A. Alldredge,et al.  In situ settling behavior of marine snow1 , 1988 .

[28]  A. White,et al.  Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments , 2017, Front. Microbiol..

[29]  E. Carpenter,et al.  The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica , 2020, FEMS microbiology ecology.

[30]  R. Colwell,et al.  Enumeration, Isolation, and Characterization of N2-Fixing Bacteria from Seawater , 1985, Applied and environmental microbiology.

[31]  K. Daly,et al.  Assessing the Impacts of Oil-associated Marine Snow Formation and Sedimentation during and after the Deepwater Horizon Oil Spill , 2016 .

[32]  E. Rahav,et al.  Contribution of Heterotrophic Diazotrophs to N2 Fixation in a Eutrophic River: Free-Living vs. Aggregate-Associated , 2022, Frontiers in Microbiology.

[33]  W. Wanek,et al.  Application of stable‐isotope labelling techniques for the detection of active diazotrophs , 2017, Environmental microbiology.

[34]  J. LaRoche,et al.  Methodological Underestimation of Oceanic Nitrogen Fixation Rates , 2010, PloS one.

[35]  A. Knapp The sensitivity of marine N2 fixation to dissolved inorganic nitrogen , 2012, Front. Microbio..

[36]  D. Vaulot,et al.  Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga , 2012, Science.

[37]  R. Beinart,et al.  Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean , 2014, The ISME Journal.

[38]  U. Riebesell,et al.  Effects of rising temperature on the formation and microbial degradation of marine diatom aggregates , 2009 .

[39]  David C. Smith,et al.  Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution , 1992, Nature.

[40]  L. Riemann,et al.  Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean. , 2015, Environmental microbiology.

[41]  L. Proctor Nitrogen-fixing, photosynthetic, anaerobic bacteria associated with pelagic copepods , 1997 .

[42]  Noah L. Walcutt,et al.  Assessment of holographic microscopy for quantifying marine particle size and concentration , 2020, Limnology and oceanography, methods.

[43]  A. Bowie,et al.  Homeostasis drives intense microbial trace metal processing on marine particles , 2021, Limnology and Oceanography.

[44]  J. Zehr Nitrogen fixation by marine cyanobacteria. , 2011, Trends in microbiology.

[45]  J. Fortney,et al.  NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity. , 2020, Environmental microbiology.

[46]  S. Chisholm,et al.  Nutrient gradients in the western North Atlantic Ocean: Relationship to microbial community structure and comparison to patterns in the Pacific Ocean , 2001 .

[47]  R. Amann,et al.  GeneFISH--an in situ technique for linking gene presence and cell identity in environmental microorganisms. , 2010, Environmental Microbiology.

[48]  J. R. Collins,et al.  Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre , 2018, The ISME Journal.

[49]  Kishori M. Konwar,et al.  Microbial ecology of expanding oxygen minimum zones , 2012, Nature Reviews Microbiology.

[50]  L. Riemann,et al.  N-fixation and related O2 constraints on model marine diazotroph Pseudomonas stutzeri BAL361 , 2018 .

[51]  P. Falkowski,et al.  Iron availability, cellular iron quotas, and nitrogen fixation in Trichodesmium , 2001 .

[52]  D. Capone,et al.  Emerging patterns of marine nitrogen fixation , 2011, Nature Reviews Microbiology.

[53]  C. Turley,et al.  Biogeochemical significance of attached and free-living bacteria and the flux of particles in the NE Atlantic Ocean , 1994 .

[54]  Francisco M. Cornejo-Castillo,et al.  Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A , 2020, The ISME journal.

[55]  E. Trembath-Reichert,et al.  Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses , 2015, The ISME Journal.

[56]  M. Mills,et al.  Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean , 2018, Proceedings of the National Academy of Sciences.

[57]  H. Grossart,et al.  Limnetic macroscopic organic aggregates (lake snow): Occurrence, characteristics, and microbial dynamics in Lake Constance , 1993 .

[58]  L. Proctor,et al.  Molecular evidence for zooplankton-associated nitrogen-fixing anaerobes based on amplification of the nifH gene , 1999 .

[59]  H. Grossart,et al.  Microbial ecology of organic aggregates in aquatic ecosystems , 2002 .

[60]  H. Claustre,et al.  Multi-faceted particle pumps drive carbon sequestration in the ocean , 2019, Nature.

[61]  A. Waite,et al.  Hard and soft plastic resin embedding for single‐cell element uptake investigations of marine‐snow‐associated microorganisms using nano‐scale secondary ion mass spectrometry , 2018, Limnology and Oceanography: Methods.

[62]  Q. Jeangros,et al.  Correlation of fluorescence microscopy, electron microscopy, and NanoSIMS stable isotope imaging on a single tissue section , 2020, Communications Biology.

[63]  T. Ferdelman,et al.  Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre , 2011, The ISME Journal.

[64]  J. Granger,et al.  The Contamination of Commercial 15N2 Gas Stocks with 15N–Labeled Nitrate and Ammonium and Consequences for Nitrogen Fixation Measurements , 2014, PloS one.

[65]  B. Fuchs,et al.  Metabolic versatility of a novel N2‐fixing Alphaproteobacterium isolated from a marine oxygen minimum zone , 2018, Environmental microbiology.

[66]  A. Onifade,et al.  Direct detection of iro B, stn and hil A virulence genes in Salmonella enterica serovar typhimurium from non-ripened cheese , 2022, Bulletin of the National Research Centre.

[67]  C. Duarte,et al.  Dilution limits dissolved organic carbon utilization in the deep ocean , 2015, Science.

[68]  K. Hyde,et al.  Rates of dinitrogen fixation and the abundance of diazotrophs in North American coastal waters between Cape Hatteras and Georges Bank , 2012 .

[69]  L. Riemann,et al.  Putative N-2-fixing heterotrophic bacteria associated with dinoflagellate-Cyanobacteria consortia in the low-nitrogen Indian Ocean , 2010 .

[70]  L. Riemann,et al.  Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters , 2018, Front. Microbiol..

[71]  J. Gasol,et al.  Patterns of bacterial diversity in the marine planktonic particulate matter continuum , 2017, The ISME Journal.

[72]  S. Bonaglia,et al.  Aerobic and anaerobic nitrogen transformation processes in N2-fixing cyanobacterial aggregates , 2015, The ISME Journal.

[73]  J. LaRoche,et al.  Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype , 2015, PloS one.

[74]  F. Azam,et al.  Oceanography: Sea snow microcosms , 2001, Nature.

[75]  E. Rahav,et al.  Microbial metabolism of transparent exopolymer particles during the summer months along a eutrophic estuary system , 2015, Front. Microbiol..

[76]  J. Audinot,et al.  The effect of FISH and CARD-FISH on the isotopic composition of (13)C- and (15)N-labeled Pseudomonas putida cells measured by nanoSIMS. , 2014, Systematic and applied microbiology.

[77]  Samuel T. Wilson,et al.  A critical review of the 15N2 tracer method to measure diazotrophic production in pelagic ecosystems , 2020, Limnology and Oceanography: Methods.

[78]  E. Rahav,et al.  Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline , 2016, Scientific Reports.

[79]  L. Riemann,et al.  Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries , 2014, The ISME Journal.

[80]  H. Paerl,et al.  Oxygen-Poor Microzones as Potential Sites of Microbial N2 Fixation in Nitrogen-Depleted Aerobic Marine Waters , 1987, Applied and environmental microbiology.

[81]  D. Bianchi,et al.  Global niche of marine anaerobic metabolisms expanded by particle microenvironments , 2018, Nature Geoscience.

[82]  A. Hochman,et al.  Mechanism of nitrogenase switch-off by oxygen , 1987, Journal of bacteriology.

[83]  C. Lamborg,et al.  The oceanographic toolbox for the collection of sinking and suspended marine particles , 2015 .

[84]  Sarah K. Hu,et al.  Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean , 2019, Proceedings of the National Academy of Sciences.

[85]  U. Riebesell,et al.  Polysaccharide aggregation as a potential sink of marine dissolved organic carbon , 2004, Nature.

[86]  Leyden Fernández,et al.  Non‐cyanobacterial diazotrophs dominate nitrogen‐fixing communities in permafrost thaw ponds , 2020, Limnology and Oceanography.

[87]  A. Alldredge,et al.  In situ settling behavior of marine snow ' , 2022 .

[88]  Stefan Bertilsson,et al.  Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria , 2011, PloS one.

[89]  M. Kuypers,et al.  Detecting metabolic activities in single cells, with emphasis on nanoSIMS. , 2012, FEMS microbiology reviews.

[90]  Reiner Schlitzer,et al.  Depth‐dependent elemental compositions of particulate organic matter (POM) in the ocean , 2003 .

[91]  L. Guidi,et al.  Sinking Organic Particles in the Ocean—Flux Estimates From in situ Optical Devices , 2020, Frontiers in Marine Science.

[92]  A. Burd,et al.  Aggregation in the Marine Environment , 1998 .

[93]  Alice L. Alldredge,et al.  Characteristics, dynamics and significance of marine snow , 1988 .

[94]  L. Riemann,et al.  Deep Into Oceanic N2 Fixation , 2018, Front. Mar. Sci..

[95]  P. Sprent,et al.  Nitrogen Fixing Organisms , 1990 .

[96]  P. Masqué,et al.  Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles , 2020, Frontiers in Microbiology.

[97]  S. Bonnet,et al.  Mesopelagic N2 Fixation Related to Organic Matter Composition in the Solomon and Bismarck Seas (Southwest Pacific) , 2015, PloS one.

[98]  H. Harada,et al.  Gold-ISH: a nano-size gold particle-based phylogenetic identification compatible with NanoSIMS. , 2014, Systematic and applied microbiology.

[99]  R. Sherrell,et al.  Sampling for particulate trace element determination using water sampling bottles: methodology and comparison to in situ pumps , 2012 .

[100]  David M. Karl,et al.  Dinitrogen fixation in the world's oceans , 2002 .

[101]  Hervé Claustre,et al.  Major role of particle fragmentation in regulating biological sequestration of CO2 by the oceans , 2020, Science.

[102]  André W. Visser,et al.  Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles , 2020, Nature Communications.

[103]  P. Raimbault,et al.  High abundance of diazotrophic picocyanobacteria (<3 µm) in a Southwest Pacific coral lagoon , 2008 .

[104]  E. Rahav,et al.  Heterotrophic Nitrogen Fixation at the Hyper-Eutrophic Qishon River and Estuary System , 2020, Frontiers in Microbiology.

[105]  H. Itoh,et al.  Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers , 2021, mSphere.

[106]  U. Riebesell,et al.  Impact of increasing carbon dioxide on dinitrogen and carbon fixation rates under oligotrophic conditions and simulated upwelling , 2021, Limnology and Oceanography.

[107]  I. Berman‐Frank,et al.  Heterotrophic and autotrophic contribution to dinitrogen fixation in the Gulf of Aqaba , 2015 .

[108]  H. Paerl Microzone formation: Its role in the enhancement of aquatic N2 fixation' , 1985 .

[109]  M. Ribbe,et al.  Nitrogen Fixation , 2011, Methods in Molecular Biology.

[110]  周文刚 Emerging Patterns , 2017, Encyclopedia of Machine Learning and Data Mining.

[111]  H. Grossart,et al.  Microbial degradation of organic carbon and nitrogen on diatom aggregates , 2001 .

[112]  J. Zehr,et al.  Nitrogen fixation: Nitrogenase genes and gene expression , 2001 .

[113]  I. Berman‐Frank,et al.  Dinitrogen fixation in aphotic oxygenated marine environments , 2013, Front. Microbiol..