Marinicella sediminis sp. nov., isolated from marine sediment

Initial Characterization of the Viridisins' Biological Properties

Viridisin A1 and A2 were previously heterologously expressed, purified, and characterized as ribosomally produced and post-translationally modified lanthipeptides. Such lanthipeptide operons are surprisingly common in Gram-negative bacteria, although their expression seems to be predominantly cryptic under laboratory conditions. However, the bioactivity and biological role of most lanthipeptide operons originating from marine-associated Pseudomonadota, such asThalassomonas viridans XOM25T, have not been described. Therefore, marine-associated Gram-negative lanthipeptide operons represent an untapped resource for novel structures, biochemistries, and bioactivities. Here, the upscaled production of viridisin A1 and A2 was performed for (methyl)lanthionine stereochemistry characterization, antibacterial, antifungal, and larval zebrafish behavioral screening. While antimicrobial activity was not observed, the VirBC modification machinery was found to install both dl- and ll-lanthionine stereoisomers. The VdsA1 and VdsA2 peptides induced sedative and stimulatory effects in zebrafish larvae, respectively, which is a bioactivity not previously reported from lanthipeptides. When combined, VdsA1 and VdsA2 counteracted the sedative and stimulatory effects observed when used individually.

Marinicella meishanensis sp. nov., a novel Marinicella member isolated from coastal mudflat sediment of Meishan Islandin the East China Sea

A Gram-negative, rod-shaped, non-motile and strictly aerobic strain, designated NBU2979T, was isolated from a coastal mudflat located on Meishan Island in the East China Sea. Strain NBU2979T grew optimally at 32 °C, with 2.0 % NaCl (w/v) and at pH 7.0-7.5. The predominant fatty acid (>10 %) was iso-C15 : 0. The major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified glycolipid, two unidentified aminophospholipids, an unidentified phospholipid and an unidentified lipid. The only respiratory quinone was ubiquinone-8. Comparative analysis of 16S rRNA gene sequences showed that strain NBU2979T exhibited highest similarity to Marinicella sediminis F2T (98.0 %), Marinicella marina S1101T (97.5 %), Marinicella litoralis KMM 3900T (96.6 %), Marinicella rhabdoformis 3539T (95.5 %), Marinicella pacifica sw153T (95.2 %) and Marinicella gelatinilytica S6413T (94.9 %). Phylogenetic analyses indicated that strain NBU2979T clustered with the genus Marinicella and was closely related to strain M. sediminis F2T. The average nucleotide identity and digital DNA-DNA hybridization values between strain NBU2979T and related species of genus Marinicella were well below the threshold limit for prokaryotic species delineation. The DNA G+C content of strain NBU2979T was 51.6 mol%. Based on its phenotypic, chemotaxonomic and genotypic data, strain NBU2979T (=KCTC 82911T=MCCC 1K06402T) is considered to be a representative of a novel species in the genus Marinicella, for which the name Marinicella meishanensis sp. nov. is proposed.

Marinicella marina sp. nov. and Marinicella gelatinilytica sp. nov., isolated from coastal sediment, and genome analysis and habitat distribution of the genus Marinicella

Three Marinicella strains, X102, S1101T and S6413T, were isolated from sediment samples from different coasts of Weihai, PR China. All strains were Gram-stain-negative, rod-shaped and non-motile. The predominant fatty acids of all strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and the major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strains X102 and S1101T shared 100 % 16S rRNA gene sequence similarity, and strains S1101T/X102 and S6413T had 95.4 % similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains S1101T and X102 were 99.9 and 99.2 %, respectively. Strain S1101T had ANI values of 69.1-72.9% and dDDH values of 17.9-20.5 % to members of the genus Marinicella. Strain S6413T had ANI values of 69.1-77.5% and dDDH values of 17.6-21.5 % to members of the genus Marinicella. The results of phylogenetic and comparative genomic analysis showed that the three strains belong to two novel species in the genus Marinicella, and strains X102 and S1101T represented one novel species, and strain S6413T represented another novel species. The result of BOX-PCR and genomic analysis showed that X102 and S1101T were not the same strain. The phylogenetic analyses and genomic comparisons, combined with phylogenetic, phenotypic and chemotaxonomic features, strongly supported that the three strains should be classified as representing two novel species of the genus Marinicella, for which the names Marinicella marina sp. nov. and Marinicella gelatinilytica sp. nov. are proposed, respectively. The type strains of the two novel species are S1101T (=KCTC 92642T=MCCC 1H01359T) and S6413T (=KCTC 92641T=MCCC 1H01362T), respectively. In addition, all previously described isolates of Marinicella were isolated from marine environments, but our study showed that Marinicella is also distributed in non-/low-saline habitats (e.g. animal gut, soil and indoor surface), which broadened our perception of the environmental distribution of Marinicella.

Long-term immersion of compostable plastics in marine aquarium: Microbial biofilm evolution and polymer degradation

The best-selling compostable plastics, polylactic acid (PLA) and polybutylene adipate-co-terephthalate (PBAT), can accidentally end up in the marine environment due to plastic waste mismanagement. Their degradation and colonization by microbial communities are poorly documented in marine conditions. To better understand their degradation, as well as the dynamics of bacterial colonization after a long immersion time (99, 160, and 260 days), PBAT, semicrystalline, and amorphous PLA films were immersed in a marine aquarium. Sequencing and chemical analyses were used in parallel to characterize these samples. Despite the variation in the chemical intrinsic parameters of these plastics, their degradation remains very slow. Microbial community structure varied according to the immersion time with a high proportion of Archaea. Moreover, the plastisphere structure of PBAT was specific. A better understanding of compostable plastic degradability is crucial to evaluate their impact on ecosystems and to eco-design new recyclable plastics with optimal degradation properties.

Red, Gold and Green: Microbial Contribution of Rhodophyta and Other Algae to Green Turtle (Chelonia mydas) Gut Microbiome

The fitness of the endangered green sea turtle (Chelonia mydas) may be strongly affected by its gut microbiome, as microbes play important roles in host nutrition and health. This study aimed at establishing environmental microbial baselines that can be used to assess turtle health under altered future conditions. We characterized the microbiome associated with the gastrointestinal tract of green turtles from Guinea Bissau in different life stages and associated with their food items, using 16S rRNA metabarcoding. We found that the most abundant (% relative abundance) bacterial phyla across the gastrointestinal sections were Proteobacteria (68.1 ± 13.9% “amplicon sequence variants”, ASVs), Bacteroidetes (15.1 ± 10.1%) and Firmicutes (14.7 ± 21.7%). Additionally, we found the presence of two red algae bacterial indicator ASVs (the Alphaproteobacteria Brucella pinnipedialis with 75 ± 0% and a Gammaproteobacteria identified as methanotrophic endosymbiont of Bathymodiolus, with <1%) in cloacal compartments, along with six bacterial ASVs shared only between cloacal and local environmental red algae samples. We corroborate previous results demonstrating that green turtles fed on red algae (but, to a lower extent, also seagrass and brown algae), thus, acquiring microbial components that potentially aid them digest these food items. This study is a foundation for better understanding the microbial composition of sea turtle digestive tracts.

Discovery and Characterization of Marinsedin, a New Class II Lanthipeptide Derived from Marine Bacterium Marinicella sediminis F2T

Microbial natural products provide a large number of drug leads. It is believed that abundant unexploited marine microorganisms also exhibit great potential for discovering compounds with novel chemical scaffolds and bioactivities. Lanthipeptides are a group of ribosomally synthesized and post-translationally modified peptides exhibiting a variety of biological functionalities. They are characterized by the presence of the thioether-containing bis-amino acids lanthionine and methyllanthionine. However, marine-derived lanthipeptides remain underexplored. Here we identified, heterologously expressed, and structurally characterized the unprecedented class II lanthipeptide marinsedin from the rare marine bacterium Marinicella sediminis F2^T. Marinsedin consists of 19 amino acids and contains a rare 2-oxobutyryl group blocking the N-terminus of the peptide chain and two overlapping intramolecular thioether rings including an unusual 12-membered macro-thioether ring. Furthermore, we also evaluated the biological activity of marinsedin, demonstrating that it exhibits moderate cytotoxicity against HeLa cells and weak cytotoxicity against HCT-116 cell lines.

Marinicella rhabdoformis sp. nov., isolated from coastal sediment

A Gram-stain-negative, rod-shaped, facultative anaerobic bacterium, designated strain 3539^T, was isolated from coastal sediment of Weihai, PR China. Optimal growth occurred at 28 °C, pH 7.5-8.0 and in the presence of 3.0 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 3539^T formed a robust clade with members of the genus Marinicella and was closely related to Marinicella litoralis JCM 16154^T, Marinicella sediminis F2^T and Marinicella pacifica sw153^T with 97.7, 96.2 and 95.4 % sequence similarity, respectively. The average amino acid identity, percentage of conserved proteins, average nucleotide identity and digital DNA-DNA hybridization values between strain 3539^T and M. litoralis JCM 16154^T were 64.9, 68.3, 72.8 and 18.9 %, respectively. The genomic DNA G+C content of strain 3539^T was 42.0 mol%. The dominant respiratory quinone was ubiquinone-8, and the major fatty acids were iso-C_15 : 0 and summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c). The polar lipids of strain 3539^T consisted of phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified lipid and three unidentified phospholipids. Based on the combination of phylogenetic, phenotypic and chemotaxonomic data, strain 3539^T is considered to represent a novel species within the genus Marinicella in he family Alcanivoracaceae, for which the name Marinicella rhabdoformis sp. nov. is proposed. The type strain of the new species is 3539^T (=KCTC 72414^T=MCCC 1H00388^T).

Dynamics of a methanol-fed marine denitrifying biofilm: 2-impact of environmental changes on the microbial community

BACKGROUND

The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of H. nitrativorans strain NL23 and M. nitratireducenticrescens in the biofilm cultures. Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm.

METHODS

The original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures. The OB was also cultivated in the commercial Instant Ocean seawater (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences. Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans strain NL23 and M. nitratireducenticrescens strain GP59.

RESULTS

High proportions of M. nitratireducenticrescens occurred in the biofilm cultures. H. nitrativorans strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl. It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0-1% NaCl and in the IO biofilm cultures. Denitrifying bacterial isolates affiliated to Marinobacter spp. and Paracoccus spp. were isolated. Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the Stappia spp. were metabolically active in the biofilm cultures.

CONCLUSIONS

These results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures. Up regulation of the denitrification genes of M. nitratireducenticrescens strain GP59 and H. nitrativorans strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm. Other denitrifying heterotrophic bacteria are present in low proportions, suggesting that the biofilm has the potential to adapt to heterotrophic, non-methylotrophic environments.