Heterologous production of novel and rare C30-carotenoids using Planococcus carotenoid biosynthesis genes

Background Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus maritimus strain iso-3 was isolated from an intertidal sediment that looked industrially polluted, from the Clyde estuary in the UK. This bacterium was found to produce a yellow acyclic carotenoid with a basic carbon 30 (C30) structure, which was determined to be methyl 5-glucosyl-5,6-dihydro-4,4′-diapolycopenoate. In the present study, we tried to isolate and identify genes involved in carotenoid biosynthesis from this marine bacterium, and to produce novel or rare C30-carotenoids with anti-oxidative activity in Escherichia coli by combinations of the isolated genes. Results A carotenoid biosynthesis gene cluster was found out through sequence analysis of the P. maritimus genomic DNA. This cluster consisted of seven carotenoid biosynthesis candidate genes (orf1–7). Then, we isolated the individual genes and analyzed the functions of these genes by expressing them in E. coli. The results indicated that orf2 and orf1 encoded 4,4′-diapophytoene synthase (CrtM) and 4,4′-diapophytoene desaturase (CrtNa), respectively. Furthermore, orf4 and orf5 were revealed to code for hydroxydiaponeurosporene desaturase (CrtNb) and glucosyltransferase (GT), respectively. By utilizing these carotenoid biosynthesis genes, we produced five intermediate C30-carotenoids. Their structural determination showed that two of them were novel compounds, 5-hydroxy-5,6-dihydro-4,4′-diaponeurosporene and 5-glucosyl-5,6-dihydro-4,4′-diapolycopene, and that one rare carotenoid 5-hydroxy-5,6-dihydro-4,4′-diapolycopene is included there. Moderate singlet oxygen-quenching activities were observed in the five C30-carotenoids including the two novel and one rare compounds. Conclusions The carotenoid biosynthesis genes from P. maritimus strain iso-3, were isolated and functionally identified. Furthermore, we were able to produce two novel and one rare C30-carotenoids in E. coli, followed by positive evaluations of their singlet oxygen-quenching activities.

Two new species of nematodes from shallow and deep-water sediments in the South China Sea

Two new species of free-living marine nematodes from the South China Sea are described: Gomphionema setiforme sp. nov. from intertidal sediment and Paracomesoma longissimum sp. nov. from upper continental slope sediment. Gomphionema setiforme sp. nov. is characterized by the punctated cuticle without lateral differentiation and cuticular pores; short cephalic setiform sensilla; spiral amphideal fovea with 4 turns close to the anterior body extremity; large cuticularized buccal cavity with a massive dorsal tooth; pharynx with a large posterior bulb; short, curved spicules; knife-like gubernaculum without apophyses and 11 cup-shaped precloacal supplements. Paracomesoma longissimum sp. nov. is characterized by cuticle with transverse rows of fine punctuations without lateral differentiation; buccal cavity with three teeth; lateral outer labial setiform sensilla 1.5 times as long as the other four outer labial setiform sensilla; spiral amphideal fovea with 2.5 turns; spicules 350–360 μm long or 15.7–16 times cloacal body diameter; plate-like gubernaculum without apophyses and 25–28 papilliform precloacal supplements.

Study of the plastisphere: biofilm development and presence of faecal indicator bacteria on microplastics from the Río de la Plata estuary

Microplastics (MPs) are considered emerging pollutants and often enter aquatic ecosystems carried by currents and tides until they accumulate on the shorelines. In many cases they may be colonized by diverse microorganisms forming a community called plastisphere, which can even act as a reservoir for pathogenic microorganisms. This study carried out in the Río de la Plata estuary (southern coastal fringe, Argentina) focused on two main objectives, the analysis of the biofilm colonizing MPs under laboratory conditions, and the detection of bacteria indicating faecal contamination (Escherichia coli and Enterococci), in MPs from the intertidal sediment at coastal sites with different land uses, in the freshwater sector of the Río de la Plata estuary. The colonization experiment was carried out in the laboratory with water from the estuary for a period of 35 days (residence time of the water in the freshwater sector of the estuary). The results revealed a remarkable development and diversity of biofilm organisms from the second week of colonization on, covering the surface of the microplastic and thus masking this pollutant. On the other hand, the presence of faecal indicator bacteria in the MPs of the intertidal sediment was confirmed in all the studied sites, being proportionally higher on MPs found in areas influenced by sewage discharges.

Draft Genome Sequence of Psychrotolerant Shewanella sp. Strain VB17, Isolated from Marine Intertidal Sediment near Virginia Beach, Virginia

ABSTRACT We present the draft genome sequence of Shewanella sp. strain VB17, which was isolated from Virginia Beach, Virginia, intertidal sediment. The 5.2-Mb genome sequence of VB17 will be useful for studying the basis for seasonal low-temperature growth and eventual taxonomic classification of the species.

Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov.

A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41T, was isolated from Antarctic intertidal sediment. The isolate grew at 0–37 °C and with 0.5–10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related with some species in the genera Ruegeria , Phaeobacter , Pseudopuniceibacterium , Sulfitobacter , Puniceibacterium and Poseidonocella with 98.6–95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C18 : 0 and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41T was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41T is considered to represent a novel species in a new genus within the family Rhodobacteraceae , for which the name Antarcticimicrobium sediminis gen. nov., sp. nov. is proposed. The type strain is S4J41T (=MCCC 1K03508T=KCTC 62793T). Moreover, the transfer of Ruegeria lutea Kim et al. 2019 to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. (type strain 318-1T=JCM 30927T=KCTC 72105T) is also proposed.

Laboratory- and field-based investigation on macrofaunal control of microbial community structure and activity in intertidal sediment

<p>Benthic macrofauna occupy most of the oxygenated seafloor, where they have a strong influence on microbial activity and are major regulators of carbon and other elemental cycles. To explore the yet-elusive relationships between faunal sediment alteration (bioturbation), microbial community structure, and microbial activity, we conducted aquarium incubations of Abarenicola pacifica and Nereis vexillosa in a seawater flow system and field manipulation experiments in a sandy intertidal zone. Microsensor and geochemical profiling show strong impacts of both worms on the pore-water concentrations of electron acceptors (O<sub>2</sub>, NO<sub>3</sub><sup>-</sup>, and SO<sub>4</sub><sup>-</sup>) and metabolites (NH<sub>4</sub><sup>+</sup>, HS<sup>-</sup>, and Fe<sub>2</sub><sup>+</sup>), and suggest the distinctly different advective and diffusive type of bioirrigations generated by A. pacifica and N. vexillosa, respectively, in sediment. Comprehensive analyses on microbial community structure and activity using amplicon sequencing and quantitative-(Reverse Transcription)-PCR of 16S rRNA and functional genes suggest that the metabolically active microbial community structure in intertidal sandy sediments is highly resilient to macrofaunal disturbance. This resilience likely stems from metabolic versatility that enables dominant microorganisms to switch between (micro)aerobic and anaerobic lifestyles under the fluctuating redox conditions in these environments. Significant changes of microbial community structure were only locally observed in the fecal pellet and feeding funnel of A. pacifica and mucus of N. vexillosa, likely due to the distinct organic matter composition and/or higher exposure time to oxygen in these microenvironments. Results from the field-based manipulation experiments further suggest that, in addition to macrofaunal bioturbation, conditions of temperature, tidal movement, and supply of photosynthetic organic matter also play important roles in controlling microbial activity and community structure in intertidal sediment.</p>