Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat

Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.

Spatio-temporal variation of the microbial community of the coast of Lebanon in response to petroleum hydrocarbon pollution

In this study, the coast of Lebanon was analyzed for the dynamic changes in sediment microbial communities in response to a major petroleum oil spill and tar contamination that occurred in the summer of 2021. Spatio-temporal variations in the microbial structure along the shores of Lebanon were assessed in comparison to baseline microbial structure determined in 2017. Microbial community structure and diversity were determined using Illumina MiSeq technology and DADA2 pipeline. The results show a significant diversity of microbial populations along the Lebanese shore, and a significant change in the sediment microbial structure within four years. Namely, Woeseia, Blastopirellula, and Muriicola were identified in sediment samples collected in year 2017, while a higher microbial diversity was observed in 2021 with Woeseia, Halogranum, Bacillus, and Vibrio prevailing in beach sediments. In addition, the results demonstrate a significant correlation between certain hydrocarbon degraders, such as Marinobacter and Vibrio, and measured hydrocarbon concentrations.

Muriicola soli sp. nov., isolated from soil

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002^T was isolated from island soil. The isolate grew at 20-37 °C (optimum, 30 °C), at pH 6.0-9.5 (optimum, pH 7) and in the presence of 0.5-4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002^T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8^T and Muriicola jejuensis EM44^T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C_15 : 1 G and iso-C_15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002^T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002^T and M. jejuensis and that between the strain and M. marianensis A6B8^T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002^T should be recognized as a novel species of the genus Muriicola, for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002^T (=KCTC 62790^T=JCM 32370^T).

Poritiphilus flavus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coral Porites lutea

A novel Gram-stain-negative, non-endospore-forming, non-motile, aerobic bacterium (strain R33^T) was isolated from coral Porites lutea and subjected to a polyphasic taxonomic study. The G+C content was 44.5 mol%. The only detected respiratory quinone was menaquinone 6 (MK-6). The major cellular fatty acids were iso-C_15 : 0 and iso-C_15 : 1 ω6c. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Global alignment based on 16S rRNA gene sequences indicated that strain R33^T shares the highest sequence identity of 93.2 % with Muriicola marianensis A6B8^T in the family Flavobacteriaceae. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R33^T forms a distinct branch in a stable clade comprising strain R33^T and members of the genera Muriicola, Robiginitalea, Eudoraea and Zeaxanthinibacter. The phylogenomic analysis also supported this 16S rRNA gene-based phylogenetic result. Comparative genomic analysis indicated that strain R33^T is rich in AraC-type DNA-binding domain-containing protein-coding genes, which means the regulation of carbon utilization is very complex. Low 16S rRNA gene identity, different polar lipids and/or cellular fatty acid profiles could readily distinguish strain R33^T from any validly published type strains. Therefore, strain R33^T is suggested to represent a new species in a new genus, for which the name Poritiphilus flavus gen. nov., sp. nov. is proposed. The type strain is R33^T (=MCCC 1K03853^T=KCTC 72443^T).

Characterization of the microbial community diversity and composition of the coast of Lebanon: Potential for petroleum oil biodegradation

In this study, the shoreline of Lebanon, which extends over 225 km along the eastern side of the Mediterranean Sea, was characterized for its sediment microbial community diversity and composition using 16S rRNA gene sequencing with Illumina MiSeq technology. Non-metric multidimensional scaling (NMDS) analysis showed no clear grouping among nearby sampled sites along the shoreline. Insignificant diversion between the wet and dry season microbial communities was observed along the coast at each sampling site. A high variation at the genus level was observed, with several novel genera identified at high relative abundance in certain locations, such as JTB255 marine benthic groups OTU_4 (5.4%) and OTU_60 (3.2%), and BD7-8 marine group OTU_5 (2.9%).

Mangrovicoccus ximenensis gen. nov., sp. nov., isolated from mangrove forest sediment

A Gram-strain-negative, coccoid bacterium, lacking bacteriochlorophyll, designated strain T1lg56^T, was isolated from a sediment sample collected from Ximen island mangrove forest, Zhejiang province, China. Cells were halotolerant, and catalase- and oxidase-positive. Growth was observed at 18-42 °C (optimum, 35 °C), at pH 6.0-9.5 (optimum, pH 6.5) and in the presence of 0-15 % (w/v) NaCl (optimum, 2-5 %). The major cellular fatty acids were C18 : 1ω7c and C16 : 0. The polar lipid profile of strain T1lg56^T consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified phospholipids and five unidentified lipids. Ubiquinone-10 was the predominant respiratory quinone. The assimilation of the substrates in the API 20NE kit was positive in strain T1lg56^T. The DNA G+C content of strain T1lg56^T was 67.2 mol%. 16S rRNA gene sequence analysis indicated that strain T1lg56^T was a member of family Rhodobacteraceae and was closely related to Poseidonocella pacifica KMM 9010^T, with 95.7 % similarity to the type strain. Phylogenetic analysis showed that strain T1lg56^T formed a separate evolutionary branch, and was parallel to other related genera of Rhodobacteraceae. Its phylogenetic distinctiveness and distinguishing phenotypic characteristics supported that strain T1lg56^T represents a novel genus of the family Rhodobacteraceae, for which the name Mangrovicoccus ximenensis gen. nov., sp. nov. is proposed. The type strain is T1lg56^T (=CCTCC AB 2016238^T=KCTC 52623^T).