Mesonia hitae sp. nov., isolated from the seawater of the South Atlantic Ocean

A Gram-negative, non-motile, non-spore-forming, aerobic and short rod-shaped bacterial strain R32^T, was isolated from seawater of the South Atlantic Ocean. Strain R32^T grew at 10-40 °C (optimum 28 °C), at pH 6.0-8.0 (optimum 7.0), and in the presence of 3-8 % NaCl (w/v) (optimum 5 %). Cells were oxidase- and catalase-positive. The 16S rRNA gene sequence of strain R32^T shared the highest similarities with Mesonia oceanica (98.3 %), followed by Salegentibacter salarius (93.0 %), Salegentibacter mishustinae (92.8 %), Salegentibacter salegens (92.5 %) and Mesonia maritima (92.4 %). The dominant fatty acids were iso-C_15 : 0 (32.7 %) and iso-C_17 : 0 3-OH (21.1 %). Menaquinone-6 (MK-6) was detected as the sole respiratory quinone. The polar lipids found were phosphatidylethanolamine, three aminolipids and three unidentified lipids. The DNA G+C content was 35.0 mol%. The ANI value and dDDH value between strain R32^T and the Salegentibacter and Mesonia species were 70.5-85.8 % and 18.7-30.5 %, respectively. Based on the results of the polyphasic characterization, strain R32^T is considered to represent a novel species of the genus Mesonia, for which the name Mesonia hitae sp. nov. is proposed. The type strain is R32^T (=MCCC 1A09780^T=KCTC 72004^T).

Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkaonoic Acid (PHA) Storage Polymers at Low Temperature

Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, Halomonas sp. 363 and Paracoccus sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of Halomonas sp. 363 carries three phaC synthase genes and transcribes genes along three PHA pathways (I to III), whereas Paracoccus sp. 392 carries only one phaC gene and transcribes genes along one pathway (I). Thus, Halomonas sp. 363 has a versatile repertoire of phaC genes and pathways enabling production of both short- and medium-chain-length PHA products. IMPORTANCE Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, Halomonas sp. 363 and Paracoccus sp. 392, are able to produce various types of PHA from inexpensive carbon sources. Halomonas sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.

Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance

Paenarthrobacter sp. GOM3, which is a strain that represents a new species-specific context within the genus Paenarthrobacter, is clearly a branched member independent of any group described thus far. This strain was recovered from marine sediments in the Gulf of Mexico, and despite being isolated from a consortium capable of growing with phenanthrene as a sole carbon source, this strain could not grow successfully in the presence of this substrate alone. We hypothesized that the GOM3 strain could participate in the assimilation of intermediate metabolites for the degradation of aromatic compounds. To date, there are no experimental reports of Paenarthrobacter species that degrade polycyclic aromatic hydrocarbons (PAHs) or their intermediate metabolites. In this work, we report genomic and experimental evidence of metabolic benzoate, gentisate, and protocatechuate degradation by Paenarthrobacter sp. GOM3. Gentisate was the preferred substrate with the highest volumetric consumption rate, and genomic analysis revealed that this strain possesses multiple gene copies for the specific transport of gentisate. Furthermore, upon analyzing the GOM3 genome, we found five different dioxygenases involved in the activation of aromatic compounds, suggesting its potential for complete remediation of PAH-contaminated sites in combination with strains capable of assimilating the upper PAH degradation pathway. Additionally, this strain was characterized experimentally for its pathogenic potential and in silico for its antimicrobial resistance. An overview of the potential ecological role of this strain in the context of other members of this taxonomic clade is also reported.

Mle046 Is a Marine Mesophilic MHETase-Like Enzyme

Accumulation of plastics in the oceans presents a major threat to diverse ecosystems. The introduction of biodegradable plastics into the market aims to alleviate the ecological burden caused by recalcitrant plastics. Poly (butylene adipate-co-terephthalate) (PBAT) is a biodegradable commercial plastic that can be biodegraded similarly to polyethylene terephthalate (PET) by PETase-like enzymes and MHETases. The role of MHETases is to hydrolyze the intermediate degradation product of PET, mono-2-hydroxyethyl terephthalate (MHET) to its monomers. We recently identified a homolog of the MHETase of the PET-degrading bacterium Ideonella sakaiensis, Mle046, from a marine microbial consortium. In this consortium, Mle046 was highly expressed when a PBAT-based blend film (PF) was supplied as the sole carbon source. In this study, we recombinantly expressed and biochemically characterized Mle046 under different conditions. Mle046 degrades MHET but also 4-(4-hydroxybutoxycarbonyl) benzoic acid (Bte), the intermediate of PF degradation. Mle046 is a mesophilic enzyme adapted to marine conditions, which rapidly degrades MHET to terephthalate and ethylene glycol at temperatures between 20 and 40°C. Mle046 degradation rates were similar for Bte and MHET. Despite its mesophilic tendency, Mle046 retains a considerable amount of activity at temperatures ranging from 10 to 60°C. In addition, Mle046 is active at a range of pH values from 6.5 to 9. These characteristics make Mle046 a promising candidate for biotechnological applications related to plastic recycling.

Paraliobacillus salinarum sp. nov., isolated from saline soil in Yingkou, China

A novel Gram-stain-positive, facultatively aerobic, slightly halophilic, endospore-forming bacterium, designated G6-18^T, was isolated from saline soil collected in Yingkou, Liaoning, PR China. Cells of strain G6-18^T grew at 10-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 8.0) and in the presence of 2-15 % (w/v) NaCl (optimum, 5 %). The strain could be clearly distinguished from the related species of the genus Paraliobacillus by its phylogenetic position and biochemical characteristics. It presented MK-7 as the major quinone and the dominant cellular fatty acids were iso-C_16 : 0, anteiso-C_15 : 0, C_16 : 0 and iso-C_14 : 0. The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol as the major components. The G+C content of strain G6-18^T genome was 35.3 mol%. 16S rRNA analysis showed that strain G6-18^T had the highest similarity to Paraliobacillus ryukyuensis DSM 15140^T, reaching 97.0 %, followed by Paraliobacillus quinghaiensis CGMCC 1.6333^T with a value of 96.3 %. The average nucleotide identity values between strain G6-18^T and Paraliobacillus ryukyuensis DSM 15140^T, Paraliobacillus sedimins KCTC 33762^T, Paraliobacillus quinghaiensis CGMCC 1.6333^T and Paraliobacillus zengyii DSM 107811^T were 74.3, 72.0, 73.2 and 72.8 %, respectively, and the digital DNA-DNA hybridization values between strain G6-18^T and the neighbouring strains were 15.6, 13.8, 14.2 and 14.2 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic inferences, strain G6-18^T represents a novel species of the genus Paraliobacillus, for which the name Paraliobacillus salinarum sp. nov. (=CGMCC 1.12058^T=DSM 25428^T) is proposed.

Biologically Active Antimicrobial Compounds from Marine Microorganisms (2005-2019)

INTRODUCTION

The increase in contagious diseases like nosocomial infections, urinary tract infections, and meningitis has led to the emergence of antimicrobial resistance urgently needs new antimicrobial medication with new modes of action. Some of the antibiotics present in the market have been obtained from terrestrial plants, or extracted semisynthetically from materials which can be fermented.

METHODS

Marine microorganisms account for approximately 80% of sea biomass. They are essential for the survival and well-being of aquatic habitats due to their indispensable contribution to biogeochemical cycles and biological processes. In marine ecosystems, microorganisms live as microbial communities in seawater, where symbiotic relationships are formed, and their ecological functions are fulfilled.

RESULTS

Marine microorganisms remain the largest, most diverse and most exciting source of structurally and functionally complex antimicrobial agents. They are extremely involved in their structure and functions. Enormous biological wealth lies in marine habitats. These microorganisms are potential sources of novel antimicrobial compounds to combat the most infectious diseases like nosocomial infections, and urinary tract infections.

CONCLUSION

This study deals with biologically active antimicrobial compounds taken from marine microorganism source, which was reported between the years 2005 and 2019. This review highlights their chemical groups, their bioactivities and sources. Marine microorganism exploitation techniques have also been reported by the authors.

Isolation and identification of marine Bacillus altitudinis KB1 from coastal Kerala: asparaginase producer

L-asparaginase is a target for many researchers as its properties against cancer, especially leukaemia, and protective agents reduce acrylamide in fried food. In this study, the water samples from Thumba Arattuvazhi Beach in Kerala were screened for l-asparaginase producing microorganisms. This was followed by colourimetric screening using modified M9 media with 0.009% Phenol red dye and using l-asparagine as a sole nitrogen source. Then, the Nessler assay was performed to quantify the enzyme. Molecular identification was made by 16SrRNA sequencing and aligned the sequence with GeneBank for phylogenetic tree construction using BLAST. Seawater was serially diluted for 10-1 to 10-6 using nutrient agar plates. A total of 19 bacterial colonies were isolated. The colonies were evaluated to produce l-asparaginase according to the pink zone around the colonies on the modified M9 medium using a red phenol indicator. The KB1 sample was selected for further studies according to plate colour assay. Nessler assay of L-asparaginase quantified as 2.537 IU/ml. Molecular characterisation showed the sequence association with Bacillus altitudinis the sequence submitted in Genebank as B. altitudinis KB1 strain. The l-asparaginase II gene (AnsB) was amplified based on the entire length of the hypothetical protein of annotated genome with accession number CP022319.2. The l-asparaginase activity in this study was 57% higher than the reference organism B. altitudinis BITHSP010. The l-asparaginase producing bacterium B. altitudinis KB1 from a marine source in Kerala can produce asparaginase, which can be utilised for biotechnology applications.

How Do Quorum-Sensing Signals Mediate Algae-Bacteria Interactions?

Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae-bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products of tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally, how microalgae can modulate these small molecules to dampen their effects.

A Glycolipid Glycosyltransferase with Broad Substrate Specificity from the Marine Bacterium "Candidatus Pelagibacter sp." Strain HTCC7211

In the marine environment, phosphorus availability significantly affects the lipid composition in many cosmopolitan marine heterotrophic bacteria, including members of the SAR11 clade and the Roseobacter clade. Under phosphorus stress conditions, nonphosphorus sugar-containing glycoglycerolipids are substitutes for phospholipids in these bacteria. Although these glycoglycerolipids play an important role as surrogates for phospholipids under phosphate deprivation, glycoglycerolipid synthases in marine microbes are poorly studied. In the present study, we biochemically characterized a glycolipid glycosyltransferase (GT_cp) from the marine bacterium “Candidatus Pelagibacter sp.” strain HTCC7211, a member of the SAR11 clade. Our results showed that GT_cp is able to act as a multifunctional enzyme by synthesizing different glycoglycerolipids with UDP-glucose, UDP-galactose, or UDP-glucuronic acid as sugar donors and diacylglycerol (DAG) as the acceptor. Analyses of enzyme kinetic parameters demonstrated that Mg²⁺ notably changes the enzyme’s affinity for UDP-glucose, which improves its catalytic efficiency. Homology modeling and mutational analyses revealed binding sites for the sugar donor and the diacylglycerol lipid acceptor, which provided insights into the retaining mechanism of GT_cp with its GT-B fold. A phylogenetic analysis showed that GT_cp and its homologs form a group in the GT4 glycosyltransferase family. These results not only provide new insights into the glycoglycerolipid synthesis mechanism in lipid remodeling but also describe an efficient enzymatic tool for the future synthesis of bioactive molecules.

IMPORTANCE The bilayer formed by membrane lipids serves as the containment unit for living microbial cells. In the marine environment, it has been firmly established that phytoplankton and heterotrophic bacteria can replace phospholipids with nonphosphorus sugar-containing glycoglycerolipids in response to phosphorus limitation. However, little is known about how these glycoglycerolipids are synthesized. Here, we determined the biochemical characteristics of a glycolipid glycosyltransferase (GT_cp) from the marine bacterium “Candidatus Pelagibacter sp.” strain HTCC7211. GT_cp and its homologs form a group in the GT4 glycosyltransferase family and can synthesize neutral glycolipids (monoglucosyl-1,2-diacyl-sn-glycerol [MGlc-DAG] and monogalactosyl [MGal]-DAG) and monoglucuronic acid diacylglycerol (MGlcA-DAG). We also uncovered the key residues for DAG binding through molecular docking, site-direct mutagenesis, and subsequent enzyme activity assays. Our data provide new insights into the glycoglycerolipid synthesis mechanism in lipid remodeling.

Evaluation of the Relationships Between Microbiota and Metabolites in Soft-Type Ripened Cheese Using an Integrated Omics Approach

Cheese ripening is effected by various microorganisms and results in the characteristic flavors of cheese. Owing to the complexity of the microbiota involved, the relationship between microorganisms and components during ripening remains unclear. In this study, metagenomics and metabolomics were integrated to reveal these relationships in three kinds of surface mold-ripened cheeses and two kinds of bacterial smear-ripened cheeses. The microbiota is broadly divided into two groups to correspond with different cheese types. Furthermore, surface mold-ripened cheese showed similar microbiota regardless of the cheese variety, whereas bacterial smear-ripened cheese showed specific microbiota characterized by marine bacteria (MB) and halophilic and alkaliphilic lactic acid bacteria for each cheese variety. In the metabolite analysis, volatile compounds suggested differences in cheese types, although organic acids and free amino acids could not determine the cheese characteristics. On the other hand, Spearman correlation analysis revealed that the abundance of specific bacteria was related to the formation of specific organic acids, free amino acids, and volatile compounds. In particular, MB was positively correlated with esters and pyrazines, indicating their contribution to cheese quality. These methodologies and results further our understanding of microorganisms and allow us to select useful strains for cheese ripening.

A new glance at the chemosphere of macroalgal-bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

Symbiosis is a dominant form of life that has been observed numerous times in marine ecosystems. For example, macroalgae coexist with bacteria that produce factors that promote algal growth and morphogenesis. The green macroalga Ulva mutabilis (Chlorophyta) develops into a callus-like phenotype in the absence of its essential bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. Spatially resolved studies are required to understand symbiont interactions at the microscale level. Therefore, we used mass spectrometry profiling and imaging techniques with high spatial resolution and sensitivity to gain a new perspective on the mutualistic interactions between bacteria and macroalgae. Using atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionisation high-resolution mass spectrometry (AP-SMALDI-HRMS), low-molecular-weight polar compounds were identified by comparative metabolomics in the chemosphere of Ulva. Choline (2-hydroxy-N,N,N-trimethylethan-1-aminium) was only determined in the alga grown under axenic conditions, whereas ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was found in bacterial presence. Ectoine was used as a metabolic marker for localisation studies of Roseovarius sp. within the tripartite community because it was produced exclusively by these bacteria. By combining confocal laser scanning microscopy (cLSM) and AP-SMALDI-HRMS, we proved that Roseovarius sp. MS2 settled mainly in the rhizoidal zone (holdfast) of U. mutabilis. Our findings provide the fundament to decipher bacterial symbioses with multicellular hosts in aquatic ecosystems in an ecologically relevant context. As a versatile tool for microbiome research, the combined AP-SMALDI and cLSM imaging analysis with a resolution to level of a single bacterial cell can be easily applied to other microbial consortia and their hosts. The novelty of this contribution is the use of an in situ setup designed to avoid all types of external contamination and interferences while resolving spatial distributions of metabolites and identifying specific symbiotic bacteria.

A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria, and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here, we identified a novel ATP-dependent DMSP lyase, DddX. DddX belongs to the acyl-CoA synthetase superfamily and is distinct from the eight other known DMSP lyases. DddX catalyses the conversion of DMSP to DMS via a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. DddX is found in several Alphaproteobacteria, Gammaproteobacteria, and Firmicutes, suggesting that this new DMSP lyase may play an overlooked role in DMSP/DMS cycles.

The global sulfur cycle is a collection of geological and biological processes that circulate sulfur-containing compounds through the oceans, rocks and atmosphere. Sulfur itself is essential for life and important for plant growth, hence its widespread use in fertilizers.

Marine organisms such as bacteria, algae and phytoplankton produce one particular sulfur compound, called dimethylsulfoniopropionate, or DMSP, in massive amounts. DMSP made in the oceans gets readily converted into a gas called dimethyl sulfide (DMS), which is the largest natural source of sulfur entering the atmosphere. In the air, DMS is converted to sulfate and other by-products that can act as cloud condensation nuclei, which, as the name suggests, are involved in cloud formation. In this way, DMS can influence weather and climate, so it is often referred to as ‘climate-active’ gas.

At least eight enzymes are known to cleave DMSP into DMS gas with a few by-products. These enzymes are found in algae, bacteria and fungi, and are referred to as lyases, for the way they breakdown their target compounds (DMSP, in this case). Recently, researchers have identified some bacteria that produce DMS from DMSP without using known DMSP lyases. This suggests there are other, unidentified enzymes that act on DMSP in nature, and likely contribute to global sulfur cycling.

Li, Wang et al. set out to uncover new enzymes responsible for converting the DMSP that marine bacteria produce into gaseous DMS. One new enzyme called DddX was identified and found to belong to a superfamily of enzymes quite separate to other known DMSP lyases. Li, Wang et al. also showed how DddX drives the conversion of DMSP to DMS in a two-step reaction, and that the enzyme is found across several classes of bacteria. Further experiments to characterise the protein structure of DddX also revealed the molecular mechanism for its catalytic action.

This study offers important insights into how marine bacteria generate the climatically important gas DMS from DMSP, leading to a better understanding of the global sulfur cycle. It gives microbial ecologists a more comprehensive perspective of these environmental processes, and provides biochemists with data on a family of enzymes not previously known to act on sulfur-containing compounds.

Structural basis of chitin utilization by a GH20 β-N-acetylglucosaminidase from Vibrio campbellii strain ATCC BAA-1116

Crystal structures of a GH20 β-N-acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.

Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β-N-acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA-1116. Crystal structures of wild-type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N-terminal carbohydrate-binding domain linked to a small α+β domain and a C-terminal (β/α)₈ catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).

Microscopic techniques to evaluate the biofilm formation ability of a marine bacterium Pseudomonas aeruginosa PFL-P1 on different substrata

Biofilm formation in bacteria is strongly affected by the nature of substrata. Different substrata such as glass, polystyrene, steel, ceramic, and rubber were used to assess the biofilm forming ability of a marine bacterium Pseudomonas aeruginosa PFL-P1 using a scanning electron microscope (SEM), atomic force microscope (AFM), and confocal laser scanning microscope (CLSM). The bacterium formed dense biofilms with varied aggregation on different substrata. SEM study revealed small rod-shaped cells with diverse arrangements within the biofilms on all the substrata under study. The AFM study revealed the highest roughness of 545 nm on the ceramic substratum. The biofilms formed on ceramic substratum were characterized with maximum roughness (742 nm), maximum peak height (1,480 nm), and maximum arithmetic mean height (611 nm), significantly higher than all the other substrata (p < .05). AFM studies confirmed that P. aeruginosa PFL-P1 exhibited biofilm heterogeneity on all the substrata. The CLSM study indicated a higher fraction of nucleic acids to α-polysaccharides ratio in the biofilms. COMSTAT analysis revealed the highest biofilm biomass of ~18 μm³ /μm² on the ceramic substratum. The maximum biofilm thickness of ~50 μm in the native state on the ceramic substratum was significantly higher than glass (p = .0015), polystyrene (p = .0001), steel (p = .0035), and rubber substrata (p = .0001). The higher surface roughness of ceramic substratum is accountable for more area for colonization, as evident from higher biomass and thickness of the biofilm. This study provides insight into the substratum properties, which modulate the biofilm forming ability in bacteria.

Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria

Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms remain largely unknown, hindering our understanding of the ecological roles of marine microorganisms in the ocean carbon cycle. Here, we studied the phylogenetic distribution of nine types of polysaccharide-degrading enzymes in marine bacterial genomes. First, we manually compiled a reference sequence database containing 961 experimentally verified enzymes. With this reference database, we annotated 9,335 enzyme sequences from 2,182 high-quality marine bacterial genomes, revealing extended distribution for six enzymes at the phylum level and for all nine enzymes at lower taxonomic levels. Next, phylogenetic analyses revealed intra-clade diversity in the encoding potentials and phylogenetic conservation of a few enzymes at the genus level. Lastly, our analyses revealed correlations between enzymes, with alginate lyases demonstrating the most extensive correlations with others. Intriguingly, chitinases showed negative correlations with cellulases, alginate lyases, and agarases in a few genera. This result suggested that intra-genus lifestyle differentiation occurred many times in marine bacteria and that the utilization of polysaccharides may act as an important driver in the recent ecological differentiation of a few lineages. This study expanded our knowledge of the phylogenetic distribution of polysaccharide enzymes and provided insights into the ecological differentiation of marine bacteria.

Diversity of Bacterioplankton and Bacteriobenthos from the Veracruz Reef System, Southwestern Gulf of Mexico

Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.

Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate

Polyhydroxyalkanoates (PHAs) are biodegradable bioplastics that can be manufactured sustainably and represent a promising green alternative to petrochemical-based plastics. Here, we describe the complete genome of a new marine PHA-producing bacterium-Photobacterium ganghwense (strain C2.2), which we have isolated from the Black Sea seashore. This new isolate is psychrotolerant and accumulates PHA when glycerol is provided as the main carbon source. Transmission electron microscopy, specific staining with Nile Red visualized via epifluorescence microscopy and gas chromatography analysis confirmed the accumulation of PHA. This is the only PHA-producing Photobacterium for which we now have a complete genome sequence, allowing us to investigate the pathways for PHA production and other secondary metabolite synthesis pathways. The de novo assembly genome, obtained using open-source tools, comprises two chromosomes (3.5, 2 Mbp) and a megaplasmid (202 kbp). We identify the entire PHA synthesis gene cluster that encodes a class I PHA synthase, a phasin, a 3-ketothiolase, and an acetoacetyl-CoA reductase. No conventional PHA depolymerase was identified in strain C2.2, but a putative lipase with extracellular amorphous PHA depolymerase activity was annotated, suggesting that C2.2 is unable to degrade intracellular PHA. A complete pathway for the conversion of glycerol to acetyl-CoA was annotated, in accordance with its ability to convert glycerol to PHA. Several secondary metabolite biosynthetic gene clusters and a low number of genes involved in antibiotic resistance and virulence were also identified, indicating the strain's suitability for biotechnological applications.

Effect of polymer type on the colonization of plastic pellets by marine bacteria

Plastic is omnipresent in the oceans and serves as a surface for biofilm-forming microorganisms. Plastic debris comprises different polymers, which may influence microbial colonization; here, we evaluated whether polymer type affects bacterial biofilm formation. Quantifying the biofilm on polyethylene (PE), polypropylene (PP) or polystyrene (PS) pellets by six marine bacterial strains (Vibrio,Pseudoalteromonas,Phaeobacter) demonstrated that each strain had a unique colonization behavior with either a preference for PS or PP over the other polymer types or no preference for a specific plastic type. PE, PP and PS pellets were exposed to natural seawater microbiota using free-living or total communities as inoculum. Microbial assembly as determined by 16S rRNA (V4) amplicon sequencing was affected by the composition of the initial inoculum and also by the plastic type. Known polymer and hydrocarbon degraders such as Paraglaciecola, Oleibacter and Hydrogenophaga were found in the plastic biofilms. Thus, on a community level, bacterial colonization on plastic is influenced by the microorganisms as well as the polymer type, and also individual strains can demonstrate polymer-specific colonization.

Phylogenetic Revision of the Genus Aliivibrio: Intra- and Inter-Species Variance Among Clusters Suggest a Wider Diversity of Species

Genus Aliivibrio is known to harbor species exhibiting bioluminescence as well as pathogenic behavior affecting the fish farming industry. Current phylogenetic understanding of Aliivibrio has largely remained dormant after reclassification disentangled it from the Vibrio genus in 2007. There is growing evidence of wider diversity, but until now the lack of genomes and selective use of type strains have limited the ability to compare and classify strains firmly. In this study, a total of 143 bacterial strains, including 51 novel sequenced strains, were used to strengthen phylogenetic relationships in Aliivibrio by exploring intra-species and inter-species relations. Multilocus sequence analysis (MLSA), applying the six housekeeping genes 16S ribosomal RNA (rRNA), gapA, gyrB, pyrH, recA, and rpoA, inferred 12 clades and a singular branch in Aliivibrio. Along with four new phylogenetic clades, the MLSA resolved prior inconsistencies circumscribing Aliivibrio wodanis and formed a unique clade we propose as the novel species Aliivibrio sp. “friggae.” Furthermore, phylogenetic assessment of individual marker genes showed gyrB, pyrH, and recA superior to the 16S rRNA gene, resolving accurately for most species clades in Aliivibrio. In this study, we provide a robust phylogenetic groundwork for Aliivibrio as a reference point to classification of species.

Use of Quorum Sensing Inhibition Strategies to Control Microfouling

Interfering with the quorum sensing bacterial communication systems has been proposed as a promising strategy to control bacterial biofilm formation, a key process in biofouling development. Appropriate in vitro biofilm-forming bacteria models are needed to establish screening methods for innovative anti-biofilm and anti-microfouling compounds. Four marine strains, two Pseudoalteromonas spp. and two Vibrio spp., were selected and studied with regard to their biofilm-forming capacity and sensitivity to quorum sensing (QS) inhibitors. Biofilm experiments were performed using two biofilm cultivation and quantification methods: the xCELLigence^® system, which allows online monitoring of biofilm formation, and the active attachment model, which allows refreshment of the culture medium to obtain a strong biofilm that can be quantified with standard staining methods. Although all selected strains produced acyl-homoserine-lactone (AHL) QS signals, only the P. flavipulchra biofilm, measured with both quantification systems, was significantly reduced with the addition of the AHL-lactonase Aii20J without a significant effect on planktonic growth. Two-species biofilms containing P. flavipulchra were also affected by the addition of Aii20J, indicating an influence on the target bacterial strain as well as an indirect effect on the co-cultured bacterium. The use of xCELLigence^® is proposed as a time-saving method to quantify biofilm formation and search for eco-friendly anti-microfouling compounds based on quorum sensing inhibition (QSI) strategies. The results obtained from these two in vitro biofilm formation methods revealed important differences in the response of biosensor bacteria to culture medium and conditions, indicating that several strains should be used simultaneously for screening purposes and the cultivation conditions should be carefully optimized for each specific purpose.

Global Expansion of Pacific Northwest Vibrio parahaemolyticus Sequence Type 36

We report transcontinental expansion of Vibrio parahaemolyticus sequence type 36 into Lima, Peru. From national collections, we identified 7 isolates from 2 different Pacific Northwest complex lineages that surfaced during 2011–2016. Sequence type 36 is likely established in environmental reservoirs. Systematic surveillance enabled detection of these epidemic isolates.

Induction of Extracellular Aminopeptidase Production by Peptides in Some Marine Bacterial Species

Bacterial extracellular aminopeptidases are key enzymes in protein processing in oligotrophic seawater. To the best of our knowledge, the regulation of aminopeptidase production in microbes inhabiting seawater has not yet been reported. The present study attempted to experimentally clarify which organic materials affect bacterial extracellular aminopeptidase production by nutrient-rich and starved cells growing in artificial seawater using Photobacterium, Alteromonas, Ruegeria, and Sulfitobacter. In all four species, we found that peptides induced bacterial extracellular aminopeptidase production. Amino acids led to cell growth with markedly lower aminopeptidase production by Photobacterium and Sulfitobacter, but not by Alteromonas and Ruegeria. These results suggest that the extracellular aminopeptidases of marine bacteria are primarily produced on demand in response to the presence of relevant substrates (peptides) in seawater. Peptidyl substances may be regulatory nutrients for marine bacterial growth in aquatic environments.

Aniba rosaeodora (Var. amazonica Ducke) Essential Oil: Chemical Composition, Antibacterial, Antioxidant and Antitrypanosomal Activity

Aniba rosaeodora is one of the most widely used plants in the perfumery industry, being used as medicinal plant in the Brazilian Amazon. This work aimed to evaluate the chemical composition of A. rosaeodora essential oil and its biological activities. A. rosaeodora essential oil presented linalool (93.60%) as its major compound. The A. rosaeodora essential oil and linalool showed activity against all the bacteria strains tested, standard strains and marine environment bacteria, with the lower minimum inhibitory concentration being observed for S. aureus. An efficient antioxidant activity of A. rosaeodora essential oil and linalool (EC₅₀: 15.46 and 6.78 µg/mL, respectively) was evidenced by the inhibition of the 2,2-azinobis- (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical. The antitrypanosomal activity of A. rosaeodora essential oil and linalool was observed at high concentrations against epimatigote forms (inhibitory concentration for 50% of parasites (IC₅₀): 150.5 ± 1.08 and 198.6 ± 1.12 µg/mL, respectively), and even higher against intracellular amastigotes of T. cruzi (IC₅₀: 911.6 ± 1.15 and 249.6 ± 1.18 µg/mL, respectively). Both A. rosaeodora essential oil and linalool did not exhibit a cytotoxic effect in BALB/c peritoneal macrophages, and both reduced nitrite levels in unstimulated cells revealing a potential effect in NO production. These data revealed the pharmacological potential of A. rosaeodora essential oil and linalool, encouraging further studies.

An Overview on Industrial and Medical Applications of Bio-Pigments Synthesized by Marine Bacteria

Marine bacterial species contribute to a significant part of the oceanic population, which substantially produces biologically effectual moieties having various medical and industrial applications. The use of marine-derived bacterial pigments displays a snowballing effect in recent times, being natural, environmentally safe, and health beneficial compounds. Although isolating marine bacteria is a strenuous task, these are still a compelling subject for researchers, due to their promising avenues for numerous applications. Marine-derived bacterial pigments serve as valuable products in the food, pharmaceutical, textile, and cosmetic industries due to their beneficial attributes, including anticancer, antimicrobial, antioxidant, and cytotoxic activities. Biodegradability and higher environmental compatibility further strengthen the use of marine bio-pigments over artificially acquired colored molecules. Besides that, hazardous effects associated with the consumption of synthetic colors further substantiated the use of marine dyes as color additives in industries as well. This review sheds light on marine bacterial sources of pigmented compounds along with their industrial applicability and therapeutic insights based on the data available in the literature. It also encompasses the need for introducing bacterial bio-pigments in global pigment industry, highlighting their future potential, aiming to contribute to the worldwide economy.

Cultivation-Independent Analysis of the Bacterial Community Associated With the Calcareous Sponge Clathrina clathrus and Isolation of Poriferisphaera corsica Gen. Nov., Sp. Nov., Belonging to the Barely Studied Class Phycisphaerae in the Phylum Planctomycetes

Marine ecosystems serve as global carbon sinks and nutrient source or breeding ground for aquatic animals. Sponges are ancient parts of these important ecosystems and can be found in caves, the deep-sea, clear waters, or more turbid environments. Here, we studied the bacterial community composition of the calcareous sponge Clathrina clathrus sampled close to the island Corsica in the Mediterranean Sea with an emphasis on planctomycetes. We show that the phylum Planctomycetes accounts for 9% of the C. clathrus-associated bacterial community, a 5-fold enrichment compared to the surrounding seawater. Indeed, the use of C. clathrus as a yet untapped source of novel planctomycetal strains led to the isolation of strain KS4^T. The strain represents a novel genus and species within the class Phycisphaerae in the phylum Planctomycetes and displays interesting cell biological features, such as formation of outer membrane vesicles and an unexpected mode of cell division.