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.

scholarly journals Inhibition of Extracellular Enzymes Exposed to Cyanopeptides

2020 ◽  
Vol 74 (3) ◽  
pp. 122-128
Author(s):  
Christine M. Egli ◽  
Regiane S. Natumi ◽  
Martin R. Jones ◽  
Elisabeth M.-L. Janssen
Keyword(s):  
Extracellular Enzymes ◽  
Heterotrophic Bacteria ◽  
Hydrolytic Enzymes ◽  
Aquatic Organisms ◽  
Freshwater Ecosystems ◽  
Cyanobacterial Blooms ◽  
Biologically Relevant ◽  
Metabolic Functions ◽  
Harmful Cyanobacterial Blooms ◽  
Quality Assessments

Harmful cyanobacterial blooms in freshwater ecosystems produce bioactive secondary metabolites including cyanopeptides that pose ecological and human health risks. Only adverse effects of one class of cyanopeptides, microcystins, have been studied extensively and have consequently been included in water quality assessments. Inhibition is a commonly observed effect for enzymes exposed to cyanopeptides and has mostly been investigated for human biologically relevant model enzymes. Here, we investigated the inhibition of ubiquitous aquatic enzymes by cyanobacterial metabolites. Hydrolytic enzymes are utilized in the metabolism of aquatic organisms and extracellularly by heterotrophic bacteria to obtain assimilable substrates. The ubiquitous occurrence of hydrolytic enzymes leads to the co-occurrence with cyanopeptides especially during cyanobacterial blooms. Bacterial leucine aminopeptidase and alkaline phosphatase were exposed to cyanopeptide extracts of different cyanobacterial strains ( Microcystis aeruginosa wild type and microcystin-free mutant, Planktothrix rubescens) and purified cyanopeptides. We observed inhibition of aminopeptidase and phosphatase upon exposure, especially to the apolar fractions of the cyanobacterial extracts. Exposure to the dominant cyanopeptides in these extracts confirmed that purified microcystins, aerucyclamide A and cyanopeptolin A inhibit the aminopeptidase in the low mg L–1 range while the phosphatase was less affected. Inhibition of aquatic enzymes can reduce the turnover of nutrients and carbon substrates and may also impair metabolic functions of grazing organisms.

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

scholarly journals Dual Agarolytic Pathways in a Marine Bacterium, Vibrio sp. Strain EJY3: Molecular and Enzymatic Verification

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Sora Yu ◽  
Eun Ju Yun ◽  
Dong Hyun Kim ◽  
So Young Park ◽  
Kyoung Heon Kim
Keyword(s):  
Marine Bacteria ◽  
Marine Bacterium ◽  
Extracellular Enzymes ◽  
Alternative Pathway ◽  
Recombinant Enzymes ◽  
Red Macroalgae ◽  
Macroalgal Biomass ◽  
Sugar Unit ◽  
Branching Point

ABSTRACT Vibrio sp. strain EJY3 is an agarolytic marine bacterium that catabolizes 3,6-anhydro-l-galactose (AHG), a monomeric sugar unit of agarose. While the AHG catabolic pathway in EJY3 has been discovered recently, the complete agarolytic system of EJY3 remains unclear. We have identified five enzymes, namely, the β-agarases VejGH50A, VejGH50B, VejGH50C, and VejGH50D and the α-neoagarooligosaccharide (NAOS) hydrolase VejGH117, involved in the agarolytic system of EJY3. Based on the characterization of recombinant enzymes and intracellular metabolite analysis, we found that EJY3 catabolizes agarose via two different agarolytic pathways. Among the four β-agarases of EJY3, VejGH50A, VejGH50B, and VejGH50C were found to be extracellular agarases, producing mainly neoagarotetraose (NeoDP4) and neoagarobiose. By detecting intracellular NeoDP4 in EJY3 grown on agarose, NeoDP4 was observed being taken up by cells. Intriguingly, intracellular NeoDP4 acted as a branching point for the two different downstream agarolytic pathways. First, via the well-known agarolytic pathway, NeoDP4 was depolymerized into monomeric sugars by the exo-type β-agarase VejGH50D and the α-NAOS hydrolase VejGH117. Second, via the newly found alternative agarolytic pathway, NeoDP4 was depolymerized into AHG and agarotriose (AgaDP3) by VejGH117, and AgaDP3 then was completely depolymerized into monomeric sugars by sequential reactions of the agarolytic β-galactosidases (ABG) VejABG and VejGH117. Therefore, by experimentally verifying agarolytic enzymatic activity and transport of NeoDP4 into EJY3 cells, we revealed that EJY3 possesses both the known pathway and the newly discovered alternative pathway that involves α-NAOS hydrolase and ABG. IMPORTANCE Agarose is the main polysaccharide of red macroalgae and is composed of galactose and 3,6-anhydro-l-galactose. Many marine bacteria possess enzymes capable of depolymerizing agarose into oligomers and then depolymerizing the oligomers into monomers. Here, we experimentally verified that both a well-known agarolytic pathway and a novel agarolytic pathway exist in a marine bacterium, Vibrio sp. strain EJY3. In agarolytic pathways, agarose is depolymerized mainly into 4-sugar-unit oligomers by extracellular enzymes, which are then transported into cells. The imported oligomers are intracellularly depolymerized into galactose and 3,6-anhydro-l-galactose by two different agarolytic pathways, using different combinations of intracellular enzymes. These results elucidate the depolymerization routes of red macroalgal biomass in the ocean by marine bacteria and provide clues for developing industrial processes for efficiently producing sugars from red macroalgae.

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 A newly isolated roseophage represents a distinct member of Siphoviridae family

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Lanlan Cai ◽  
Ruijie Ma ◽  
Hong Chen ◽  
Yunlan Yang ◽  
Nianzhi Jiao ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Genomic Analysis ◽  
Wide Distribution ◽  
Dinoroseobacter Shibae ◽  
Population Structures ◽  
Marine Heterotrophic Bacteria ◽  
Distinct Member ◽  
Biological Entities

Abstract Background Members of the Roseobacter lineage are a major group of marine heterotrophic bacteria because of their wide distribution, versatile lifestyles and important biogeochemical roles. Bacteriophages, the most abundant biological entities in the ocean, play important roles in shaping their hosts’ population structures and mediating genetic exchange between hosts. However, our knowledge of roseophages (bacteriophages that infect Roseobacter) is far behind that of their host counterparts, partly reflecting the need to isolate and analyze the phages associated with this ecologically important bacterial clade. Methods vB_DshS-R4C (R4C), a novel virulent roseophage that infects Dinoroseobacter shibae DFL12T, was isolated with the double-layer agar method. The phage morphology was visualized with transmission electron microscopy. We characterized R4C in-depth with a genomic analysis and investigated the distribution of the R4C genome in different environments with a metagenomic recruitment analysis. Results The double-stranded DNA genome of R4C consists of 36,291 bp with a high GC content of 66.75%. It has 49 genes with low DNA and protein homologies to those of other known phages. Morphological and phylogenetic analyses suggested that R4C is a novel member of the family Siphoviridae and is most closely related to phages in the genus Cronusvirus. However, unlike the Cronusvirus phages, R4C encodes an integrase, implying its ability to establish a lysogenic life cycle. A terminal analysis shows that, like that of λ phage, the R4C genome utilize the ‘cohesive ends’ DNA-packaging mechanism. Significantly, homologues of the R4C genes are more prevalent in coastal areas than in the open ocean. Conclusions Information about this newly discovered phage extends our understanding of bacteriophage diversity, evolution, and their roles in different environments.

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