The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks

ABSTRACT Reduced nitrogen species are key nutrients for biological productivity in the oceans. Ammonium is often present in low and growth-limiting concentrations, albeit peaks occur during collapse of algal blooms or via input from deep sea upwelling and riverine inflow. Autotrophic phytoplankton exploit ammonium peaks by storing nitrogen intracellularly. In contrast, the strategy of heterotrophic bacterioplankton to acquire ammonium is less well understood. This study revealed the marine bacterium Phaeobacter inhibens DSM 17395, a Roseobacter group member, to have already depleted the external ammonium when only ∼⅓ of the ultimately attained biomass is formed. This was paralleled by a three-fold increase in cellular nitrogen levels and rapid buildup of various nitrogen-containing intracellular metabolites (and enzymes for their biosynthesis) and biopolymers (DNA, RNA and proteins). Moreover, nitrogen-rich cells secreted potential RTX proteins and the antibiotic tropodithietic acid, perhaps to competitively secure pulses of external ammonium and to protect themselves from predation. This complex response may ensure growing cells and their descendants exclusive provision with internal nitrogen stocks. This nutritional strategy appears prevalent also in other roseobacters from distant geographical provenances and could provide a new perspective on the distribution of reduced nitrogen in marine environments, i.e. temporary accumulation in bacterioplankton cells.

[1]  B. Blasius,et al.  Non-Redfield, nutrient synergy and flexible internal elemental stoichiometry in a marine bacterium , 2017, FEMS microbiology ecology.

[2]  R. Rabus,et al.  Photometric Determination of Ammonium and Phosphate in Seawater Medium Using a Microplate Reader , 2017, Journal of Molecular Microbiology and Biotechnology.

[3]  D. Schomburg,et al.  Native plasmids restrict growth of Phaeobacter inhibens DSM 17395: Energetic costs of plasmids assessed by quantitative physiological analyses. , 2016, Environmental microbiology.

[4]  H. Vlamakis,et al.  Dynamic metabolic exchange governs a marine algal-bacterial interaction , 2016, eLife.

[5]  J. Collett,et al.  Increasing importance of deposition of reduced nitrogen in the United States , 2016, Proceedings of the National Academy of Sciences.

[6]  Maxwell Z. Wilson,et al.  Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink , 2016, Proceedings of the National Academy of Sciences.

[7]  A. Steinbüchel,et al.  Features of the biotechnologically relevant polyamide family “cyanophycins” and their biosynthesis in prokaryotes and eukaryotes , 2016, Critical reviews in biotechnology.

[8]  Milton H. Saier,et al.  The Transporter Classification Database (TCDB): recent advances , 2015, Nucleic Acids Res..

[9]  Peter D. Karp,et al.  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases , 2015, Nucleic Acids Res..

[10]  L. Gram,et al.  Influence of Iron on Production of the Antibacterial Compound Tropodithietic Acid and Its Noninhibitory Analog in Phaeobacter inhibens , 2015, Applied and Environmental Microbiology.

[11]  L. Gram,et al.  Phaeobacter inhibens from the Roseobacter clade has an environmental niche as a surface colonizer in harbors. , 2015, Systematic and applied microbiology.

[12]  G. Larsson,et al.  Regulating the production of (R)-3-hydroxybutyrate in Escherichia coli by N or P limitation , 2015, Front. Microbiol..

[13]  Antje Chang,et al.  BRENDA in 2015: exciting developments in its 25th year of existence , 2014, Nucleic Acids Res..

[14]  L. Gram,et al.  Biofilm formation is not a prerequisite for production of the antibacterial compound tropodithietic acid in Phaeobacter inhibens DSM17395 , 2014, Journal of applied microbiology.

[15]  Haiwei Luo,et al.  Evolutionary Ecology of the Marine Roseobacter Clade , 2014, Microbiology and Molecular Reviews.

[16]  A. Buchan,et al.  Master recyclers: features and functions of bacteria associated with phytoplankton blooms , 2014, Nature Reviews Microbiology.

[17]  Jeroen S. Dickschat,et al.  Biosynthesis of the antibiotic tropodithietic acid by the marine bacterium Phaeobacter inhibens. , 2014, Chemical communications.

[18]  Haiwei Luo,et al.  Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters , 2014, The ISME Journal.

[19]  V. Meas-Yedid,et al.  The Intracellular Bacteria Chlamydia Hijack Peroxisomes and Utilize Their Enzymatic Capacity to Produce Bacteria-Specific Phospholipids , 2014, PloS one.

[20]  Hans-Peter Klenk,et al.  Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). , 2014, Environmental microbiology.

[21]  Hans V. Westerhoff,et al.  Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective , 2013, Microbiology and Molecular Reviews.

[22]  Richard D. Smith,et al.  Proteomic and Transcriptomic Analyses of “Candidatus Pelagibacter ubique” Describe the First PII-Independent Response to Nitrogen Limitation in a Free-Living Alphaproteobacterium , 2013, mBio.

[23]  M. Göker,et al.  Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395. , 2013, International journal of systematic and evolutionary microbiology.

[24]  B. Blasius,et al.  Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395 , 2013, Proteomics.

[25]  R. Reinhardt,et al.  Dynamics of amino acid utilization in Phaeobacter inhibens DSM 17395 , 2013, Proteomics.

[26]  R. Reinhardt,et al.  Adaptation of Phaeobacter inhibens DSM 17395 to growth with complex nutrients , 2013, Proteomics.

[27]  L. Gram,et al.  Disruption of Cell-to-Cell Signaling Does Not Abolish the Antagonism of Phaeobacter gallaeciensis toward the Fish Pathogen Vibrio anguillarum in Algal Systems , 2013, Applied and Environmental Microbiology.

[28]  H. Sarmento,et al.  Phytoplankton species‐specific release of dissolved free amino acids and their selective consumption by bacteria , 2013 .

[29]  T. Thomas,et al.  Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life , 2012, The ISME Journal.

[30]  Niels Klitgord,et al.  Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis , 2012, Nucleic acids research.

[31]  R. Amann,et al.  Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom , 2012, Science.

[32]  R. Reinhardt,et al.  Physiological and Proteomic Adaptation of “Aromatoleum aromaticum” EbN1 to Low Growth Rates in Benzoate-Limited, Anoxic Chemostats , 2012, Journal of bacteriology.

[33]  J. Armengaud,et al.  Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria* , 2011, Molecular & Cellular Proteomics.

[34]  Paul Bowness,et al.  Discovery of Candidate Serum Proteomic and Metabolomic Biomarkers in Ankylosing Spondylitis* , 2011, Molecular & Cellular Proteomics.

[35]  S. Schulz,et al.  Tropodithietic Acid Production in Phaeobacter gallaeciensis Is Regulated by N-Acyl Homoserine Lactone-Mediated Quorum Sensing , 2011, Journal of bacteriology.

[36]  R. Kolter,et al.  The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis. , 2011, Nature chemistry.

[37]  W. Eisenreich,et al.  Studies on the Mechanism of Ring Hydrolysis in Phenylacetate Degradation , 2011, The Journal of Biological Chemistry.

[38]  R. Kudela,et al.  Nitrogen cycle of the open ocean: from genes to ecosystems. , 2011, Annual review of marine science.

[39]  J. Huisman,et al.  Pulsed nitrogen supply induces dynamic changes in the amino acid composition and microcystin production of the harmful cyanobacterium Planktothrix agardhii. , 2010, FEMS microbiology ecology.

[40]  I. Linhartova,et al.  RTX proteins: a highly diverse family secreted by a common mechanism , 2010, FEMS microbiology reviews.

[41]  D. Stahl,et al.  Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria , 2009, Nature.

[42]  Xiao-Jiang Feng,et al.  Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli , 2009, Molecular systems biology.

[43]  D. Schomburg,et al.  Growth phase‐dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter‐clade , 2009, Proteomics.

[44]  Dietmar Schomburg,et al.  MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. , 2009, Analytical chemistry.

[45]  L. Gram,et al.  Phaeobacter and Ruegeria Species of the Roseobacter Clade Colonize Separate Niches in a Danish Turbot (Scophthalmus maximus)-Rearing Farm and Antagonize Vibrio anguillarum under Different Growth Conditions , 2008, Applied and Environmental Microbiology.

[46]  Karsten Suhre,et al.  MassTRIX: mass translator into pathways , 2008, Nucleic Acids Res..

[47]  R. Rabus,et al.  Solvent Stress Response of the Denitrifying Bacterium “Aromatoleum aromaticum” Strain EbN1 , 2008, Applied and Environmental Microbiology.

[48]  F. Azam,et al.  Microbial structuring of marine ecosystems , 2007, Nature Reviews Microbiology.

[49]  F. Winkler,et al.  The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel , 2007, Proceedings of the National Academy of Sciences.

[50]  H. Biebl,et al.  Environmental biology of the marine Roseobacter lineage. , 2006, Annual review of microbiology.

[51]  J. A. Camargo,et al.  Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: A global assessment. , 2006, Environment international.

[52]  Ulf Riebesell,et al.  The regulation of carbon and nutrient assimilation in diatoms is significantly different from green algae. , 2006, Protist.

[53]  M. Moran,et al.  Overview of the Marine Roseobacter Lineage , 2005, Applied and Environmental Microbiology.

[54]  A. Görg,et al.  Current two‐dimensional electrophoresis technology for proteomics , 2004, Proteomics.

[55]  D. Kirchman,et al.  The uptake of inorganic nutrients by heterotrophic bacteria , 1994, Microbial Ecology.

[56]  R. Rabus,et al.  Evaluation of Two-Dimensional Difference Gel Electrophoresis for Protein Profiling , 2003, Journal of Molecular Microbiology and Biotechnology.

[57]  H. Grossart,et al.  Possible Quorum Sensing in Marine Snow Bacteria: Production of Acylated Homoserine Lactones by Roseobacter Strains Isolated from Marine Snow , 2002, Applied and Environmental Microbiology.

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

[59]  J. C. Goldman,et al.  Rapid nitrogen uptake by marine bacteria , 2001 .

[60]  Walker O. Smith,et al.  Temperature effects on export production in the open ocean , 2000 .

[61]  M. Merrick,et al.  The glnKamtB operon. A conserved gene pair in prokaryotes. , 2000, Trends in genetics : TIG.

[62]  P. Falkowski,et al.  Biogeochemical Controls and Feedbacks on Ocean Primary Production , 1998, Science.

[63]  J. Randerson,et al.  Primary production of the biosphere: integrating terrestrial and oceanic components , 1998, Science.

[64]  N. Anderson,et al.  Analysis of changes in acute‐phase plasma proteins in an acute inflammatory response and in rheumatoid arthritis using two‐dimensional gel electrophoresis , 1998, Electrophoresis.

[65]  Rainer Storn,et al.  Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces , 1997, J. Glob. Optim..

[66]  R. Storn,et al.  Differential Evolution - A simple and efficient adaptive scheme for global optimization over continuous spaces , 2004 .

[67]  M. Heldal,et al.  Content of carbon, nitrogen, oxygen, sulfur and phosphorus in native aquatic and cultured bacteria , 1996 .

[68]  I. Obernosterer,et al.  Phytoplankton extracellular release and bacterial growth: dependence on the inorganic N:P ratio , 1995 .

[69]  J. C. Goldman,et al.  Ammonium regeneration and carbon utilization by marine bacteria grown on mixed substrates , 1991 .

[70]  T. Egli,et al.  Dynamics of microbial growth and cell composition in batch culture. , 1990, FEMS microbiology reviews.

[71]  L. Ingber Very fast simulated re-annealing , 1989 .

[72]  T. Stanley Species differences. , 1988, British journal of anaesthesia.

[73]  David L. Kirchman,et al.  Utilization of inorganic and organic nitrogen by bacteria in marine systems1 , 1986 .

[74]  W. Admiraal,et al.  Nitrogen metabolism of marine planktonic diatoms: Excretion, assimilation and cellular pools of free amino acids in seven species with different cell size , 1986 .

[75]  D. Kleiner Bacterial ammonium transport , 1985 .

[76]  Q. Dortch,et al.  Species differences in accumulation of nitrogen pools in phytoplankton , 1984 .

[77]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[78]  Ian Morris,et al.  Extracellular release of carbon by marine phytoplankton; a physiological approach1 , 1980 .

[79]  M. M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[80]  M. R. Droop,et al.  Vitamin B12 and Marine Ecology. IV. The Kinetics of Uptake, Growth and Inhibition in Monochrysis Lutheri , 1968, Journal of the Marine Biological Association of the United Kingdom.

[81]  A. L. Chaney,et al.  Modified reagents for determination of urea and ammonia. , 1962, Clinical chemistry.

[82]  A. C. Redfield The biological control of chemical factors in the environment. , 1960, Science progress.

[83]  T. Horiuchi RNA DEGRADATION AND DNA AND PROTEIN SYNTHESIS OF E. COLI B. IN A PHOSPHATE DEFICIENT MEDIUM , 1959 .

[84]  J. Duguid,et al.  The influence of cultural conditions on polysaccharide production by Aerobacter aerogenes. , 1953, Journal of general microbiology.

[85]  O. H. Lowry,et al.  Protein measurement with the Folin phenol reagent. , 1951, The Journal of biological chemistry.

[86]  J. Monod,et al.  Recherches sur la croissance des cultures bactériennes , 1942 .