Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae

Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral

The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989T, was isolated from the reef-building coral Favia sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with Parasphingorhabdus litoris DSM 22379T (95.9%) and Altererythrobacter ishigakiensis ATCC BAA-2084T (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family Sphingomonadaceae. The predominant fatty acids were C18 : 1  ω7c and/or C18 : 1  ω6c and C16 : 0. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between SCSIO 66989T and the type strains of P. litoris DSM 22379T and A. ishigakiensis ATCC BAA-2084T were 69.2-70.0%, 58.6-61.2% and 19.2-19.7%, respectively. These results indicate that strain SCSIO 66989T represents a new species of a novel genus in the family Sphingomonadaceae, for which the name Alterisphingorhabdus coralli gen. nov. sp. nov. is proposed.

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.

Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma

A novel bacterium, designated strain JHSY0214T, was isolated from the gut of a Korean limpet, Cellana toreuma. Cells of strain JHSY0214T were Gram-stain-negative, strictly aerobic, yellow-pigmented, non-spore-forming, non-motile and showed a rod–coccus growth cycle. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Parasphingorhabdus , and was most closely related to Parasphingorhabdus litoris KCTC 12764T (98.71 %). Strain JHSY0214T had two fluoroquinolone-resistance genes and seven multidrug-resistance efflux pump genes, but did not have beta-lactamase genes and zinc resistance genes compared with P. litoris KCTC 12764T. Strain JHSY0214T grew optimally at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. The predominant cellular fatty acids of strain JHSY0214T were summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c; 41.2 %), summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c; 21 %) and C16 : 0 (18.9 %). The major isoprenoid quinone was ubiquinone-10. The major polar lipids were sphingoglycolipid and phosphatidylethanolamine. The genomic DNA G+C content was 52.8 mol%. Based on phylogenetic, genotypic and phenotypic data, strain JHSY0214T represents a novel species of the genus Parasphingorhabdus , for which the name Parasphingorhabdus cellanae is proposed. The type strain is JHSY0214T (=KCTC 82387T=DSM 112279T).

Description of Novosphingopyxis iocasae sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus Novosphingopyxis

In this study, we reported a Gram-stain-negative, orange-coloured, rod-shaped, motile and faculatively anaerobic bacterium named strain PB63^T, which was isolated from the deep-sea sediment from the Mariana Trench. Growth of PB63^T occurred at 10-35 °C (optimum, 28 °C), pH 5.0-8.0 (optimum, 5.0-6.0) and with 0-7 % (w/v) NaCl (optimum, 2-3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PB63^T represented a member of the genus Novosphingopyxis and was closely related to Novosphingopyxis baekryungensis DSM 16222^T (97.9 % sequence similarity). PB63^T showed tolerance to a variety of heavy metals, including Co²⁺, Zn²⁺, Mn²⁺ and Cu²⁺. The complete genome of PB63^T was obtained, and many genes involved in heavy metal resistance were found. The genomic DNA G+C content of PB63^T was 62.8 mol%. The predominant respiratory quinone of PB63^T was ubiquinone-10 (Q-10). The polar lipids of PB63^T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, glycolipid, phosphatidylcholines and three unidentified lipids. The major fatty acids of PB63^T included summed feature 8 (C_{18 : 1}ω7c or/and C_{18 : 1}ω6c), C_{14 : 0} 2-OH, 11-methyl C_{18 : 1}ω7c, C_{16 : 0}, summed feature 3 (C_{16 : 1}ω7c and/or C_{16 : 1}ω6c) and C_{17 : 1}ω6c. The results of phylogenetic, physiological, biochemical and morphological analyses indicated that strain PB63^T represents a novel species of the genus Novosphingopyxis, and the name Novosphingopyxis iocasae sp. nov. is proposed with the type species PB63^T (=CCTCC AB 2019195^T=JCM 34178^T).

Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island

A Gram-stain-negative, catalase- and oxidase-positive, rod-shaped bacterium, designated as JK6^T was isolated from a coastal marine sediment in Jeju Island. Strain JK6^T was characterized by polyphasic investigation including genome features. It grew at pH 5.0-9.0 (optimum 7.5), 18-30 °C (optimum 25 °C) and 1.0-7.0% (w/v) NaCl (optimum 2.0%). Strain JK6^T utilized D-mannose, D-glucose, L-fucose, propionate and acetate as carbon and energy sources. The sole quinone was ubiquinone-10, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and sphingolipid. Strain JK6^T was closely related to Parasphingorhabdus flavimaris SW-151^T (98.2%), Parasphingorhabdus marina DSM 22363^T (97.6%) and Parasphingorhabdus litoris FR1093^T (97.6%) based on 16S rRNA gene sequence similarity. Genome length and GC content were 3.29 Mbp and 53.0%, respectively. Digital DNA-DNA relatedness, average nucleotide identity, and average amino acid identity between strain JK6^T and P. flavimaris SW-151^T were 16.6%, 73.9%, and 77.6%, respectively. These results showed that the strain can be recognized as a novel bacterium named Parasphingorhabdus halotolerans. The type strain of Parasphingorhabdus halotolerans sp. nov. is JK6^T (= KCTC 72818^T = VTCC 910111^T).

The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review

The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.

Sphingorhabdus lacus sp. nov. and Sphingorhabdus profundilacus sp. nov., isolated from freshwater environments

Two Gram-stain-negative, aerobic, non-motile bacteria, designated IMCC1753^T and IMCC26285^T, were isolated from a shallow eutrophic pond and a deep oligotrophic lake, respectively. Results of 16S rRNA gene sequence analysis indicated that the two strains shared 99.8 % sequence similarity and were most closely related to Sphingorhabdus contaminans JC216^T(98.7-98.8 %). The whole genome sequences of strains IMCC1753^T and IMCC26285^T were 3.5 and 2.9 Mbp in size with 56.6 and 55.5 mol% DNA G+C content, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 82.2 and 25.8 %, respectively, indicating that they are separate species. The two strains showed ≤98.8 % 16S rRNA gene sequence similarities and ≤82.2 % ANI and ≤28.7 % dDDH values to closely related species of the genus Sphingorhabdus, indicating that the two strains each represent novel species. Major fatty acid constituents of strain IMCC1753^T were C_17 : 1  ω6c, C_17 : 1  ω8c and summed features 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c) and 8 (C_18 : 1  ω6c and/or C_18 : 1  ω7c); those of strain IMCC26285^T were summed features 3 and 8. The predominant isoprenoid quinone detected in both strains was ubiquinone-10 and the most abundant polyamine was spermidine. Both strains contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid as major polar lipids. On the basis of the phylogenetic and phenotypic characteristics, strains IMCC1753^T and IMCC26285^T were considered to represent two distinct novel species in the genus Sphingorhabdus, for which the names Sphingorhabdus lacus (IMCC1753^T=KCTC 52480^T=KACC 18985^T=NBRC 112442^T) and Sphingorhabdus profundilacus (IMCC26285^T=KCTC 52479^T=KACC 18986^T=NBRC 112454^T) are proposed, respectively.