scholarly journals Lipidomic Analysis of Roseobacters of the Pelagic RCA Cluster and Their Response to Phosphorus Limitation

2020 ◽  
Vol 11 ◽  
Author(s):  
Eleonora Silvano ◽  
Mingyu Yang ◽  
Mathias Wolterink ◽  
Helge-Ansgar Giebel ◽  
Meinhard Simon ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Phosphorus Limitation ◽  
Membrane Lipid ◽  
Polar Regions ◽  
Lipidomic Analysis ◽  
Betaine Lipids ◽  
Oceanic Climate ◽  
Gas Metabolism ◽  
Marine Heterotrophic Bacteria ◽  
Ruegeria Pomeroyi

The marine roseobacter-clade affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic roseobacter counterparts such as Ruegeria pomeroyi DSS-3 and Phaeobacter sp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodeling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol (PG) and phosphatidylethanolamine (PE), RCA bacteria synthesize a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation.

scholarly journals Lipidomic analysis of roseobacters of the pelagic RCA cluster and their response to phosphorus limitation

2020 ◽  
Author(s):  
Eleonora Silvano ◽  
Mingyu Yang ◽  
Mathias Wolterink ◽  
Helge-Ansgar Giebel ◽  
Meinhard Simon ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Phosphorus Limitation ◽  
Membrane Lipid ◽  
Polar Regions ◽  
Lipidomic Analysis ◽  
Betaine Lipids ◽  
Oceanic Climate ◽  
Gas Metabolism ◽  
Marine Heterotrophic Bacteria ◽  
Ruegeria Pomeroyi

AbstractThe marine roseobacter-clade Affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic roseobacter counterparts such as Ruegeria pomeroyi DSS-3 and Phaeobacter sp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodelling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol and phosphatidylethanolamine, RCA bacteria synthesise a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation.

scholarly journals Structure-Function Analysis Indicates that an Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage by DddK

2019 ◽  
Vol 85 (8) ◽  
Author(s):  
Ming Peng ◽  
Xiu-Lan Chen ◽  
Dian Zhang ◽  
Xiu-Juan Wang ◽  
Ning Wang ◽  
...  
Keyword(s):  
Water Molecule ◽  
Active Site ◽  
Dimethyl Sulfide ◽  
Catalytic Mechanism ◽  
Heterotrophic Bacteria ◽  
Function Analysis ◽  
Cloud Condensation Nuclei ◽  
Oxidation Products ◽  
Condensation Nuclei ◽  
Marine Heterotrophic Bacteria

ABSTRACT The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases, generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei and, thus, may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria; many of them contain the DMSP lyase DddK, and their dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the β-elimination reaction of DMSP. Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its neighboring His96. To further probe this mechanism, we purified and characterized the DddK protein from Pelagibacter ubique strain HTCC1062 and determined the crystal structures of wild-type DddK and its Y64A and Y122A mutants (bearing a change of Y to A at position 64 or 122, respectively), where the Y122A mutant is complexed with DMSP. The structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its deprotonation. Our data indicate that an active water molecule in the active site of DddK plays an important role in the deprotonation of Tyr64 and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding of DMS generation by SAR11 bacteria. IMPORTANCE The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which form cloud condensation nuclei that influence the reflectivity of clouds and, thereby, global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, and many of them contain DMSP lyase DddK to cleave DMSP, generating DMS. In this study, based on structural analyses and mutational assays, we revealed the catalytic mechanism of DddK, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.

scholarly journals Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacteriumZobellia galactanivoransDsijT

2016 ◽  
Vol 18 (12) ◽  
pp. 4610-4627 ◽  
Author(s):  
Tristan Barbeyron ◽  
François Thomas ◽  
Valérie Barbe ◽  
Hanno Teeling ◽  
Chantal Schenowitz ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Driving Forces ◽  
Marine Heterotrophic Bacteria ◽  
Carbohydrate Catabolism

A mineralogical characterization of biogenic calcium carbonates precipitated by heterotrophic bacteria isolated from cryophilic polar regions

Geobiology ◽  
2014 ◽  
Vol 12 (6) ◽  
pp. 542-556 ◽  
Author(s):  
J. Ronholm ◽  
D. Schumann ◽  
H. M. Sapers ◽  
M. Izawa ◽  
D. Applin ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Polar Regions ◽  
Mineralogical Characterization ◽  
Calcium Carbonates

scholarly journals Facilitation of Robust Growth of Prochlorococcus Colonies and Dilute Liquid Cultures by “Helper” Heterotrophic Bacteria

2008 ◽  
Vol 74 (14) ◽  
pp. 4530-4534 ◽  
Author(s):  
J. Jeffrey Morris ◽  
Robin Kirkegaard ◽  
Martin J. Szul ◽  
Zackary I. Johnson ◽  
Erik R. Zinser
Keyword(s):  
Solid Medium ◽  
Heterotrophic Bacteria ◽  
Cell Concentration ◽  
Preliminary Evidence ◽  
Critical Threshold ◽  
Semisolid Medium ◽  
Marine Heterotrophic Bacteria ◽  
Pure Cultures ◽  
Novel Method ◽  
Axenic Cultures

ABSTRACT Axenic (pure) cultures of marine unicellular cyanobacteria of the Prochlorococcus genus grow efficiently only if the inoculation concentration is large; colonies form on semisolid medium at low efficiencies. In this work, we describe a novel method for growing Prochlorococcus colonies on semisolid agar that improves the level of recovery to approximately 100%. Prochlorococcus grows robustly at low cell concentrations, in liquid or on solid medium, when cocultured with marine heterotrophic bacteria. Once the Prochlorococcus cell concentration surpasses a critical threshold, the “helper” heterotrophs can be eliminated with antibiotics to produce axenic cultures. Our preliminary evidence suggests that one mechanism by which the heterotrophs help Prochlorococcus is the reduction of oxidative stress.

scholarly journals The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans

2014 ◽  
Vol 81 (5) ◽  
pp. 1799-1812 ◽  
Author(s):  
Agnès Groisillier ◽  
Aurore Labourel ◽  
Gurvan Michel ◽  
Thierry Tonon
Keyword(s):  
Abc Transporter ◽  
Biochemical Characterization ◽  
Heterotrophic Bacteria ◽  
Dry Weight ◽  
Sole Source ◽  
Content Type ◽  
Wide Range ◽  
Marine Heterotrophic Bacteria ◽  
Operon Gene ◽  
Living Organisms

ABSTRACTMannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria.Zobellia galactanivorans(Flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH ofZ. galactanivoranswas active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K+. Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture ofZ. galactanivoransin the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes ofFlavobacteriaceaeamong the 76 publicly available at the time of the analysis. It is not conserved in allBacteroidetes; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes.

scholarly journals Metabolic strategies of sharing pioneer bacteria mediating fresh macroalgae breakdown

2021 ◽  
Author(s):  
Maéva Brunet ◽  
Nolwen Le Duff ◽  
Tristan Barbeyron ◽  
François Thomas
Keyword(s):  
Extracellular Enzymes ◽  
Heterotrophic Bacteria ◽  
Physical Contact ◽  
Brown Macroalgae ◽  
Resistance Proteins ◽  
Biomass Turnover ◽  
Macroalgal Biomass ◽  
Marine Heterotrophic Bacteria ◽  
Metabolic Strategies ◽  
Polysaccharide Utilization Loci

Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of pioneer bacteria within the flavobacterial genus Zobellia to initiate the degradation of fresh brown macroalgae, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans DsijT could use macroalgae as a sole carbon source and extensively degrade algal tissues without requiring physical contact, via the secretion of extracellular enzymes. This indicated a sharing behaviour, whereby pioneers release public goods that can fuel other bacteria. Comparisons of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include stress resistance proteins, type IX secretion system proteins and novel uncharacterized Polysaccharide Utilization Loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the niche, metabolism and evolution of pioneer degraders, as well as their cooperative interactions within microbial communities, as key players in macroalgal biomass turnover.

Sign in / Sign up

Export Citation Format

Share Document