Beach sand plastispheres are hotspots for antibiotic resistance genes and potentially pathogenic bacteria even in beaches with good water quality

Massive amounts of microplastics are transported daily from the oceans and rivers onto beaches. The ocean plastisphere is a hotspot and a vector for antibiotic resistance genes (ARGs) and potentially pathogenic bacteria. However, very little is known about the plastisphere in beach sand. Thus, to describe whether the microplastics from beach sand represent a risk to human health, we evaluated the bacteriome and abundance of ARGs on microplastic and sand sampled at the drift line and supralittoral zones of four beaches of poor and good water quality. The bacteriome was evaluated by sequencing of 16S rRNA gene, and the ARGs and bacterial abundances were evaluated by high-throughput real-time PCR. The results revealed that the microplastic harbored a bacterial community that is more abundant and distinct from that of beach sand, as well as a greater abundance of potential human and marine pathogens, especially the microplastics deposited closer to seawater. Microplastics also harbored a greater number and abundance of ARGs. All antibiotic classes evaluated were found in the microplastic samples, but not in the beach sand ones. Additionally, 16 ARGs were found on the microplastic alone, including genes related to multidrug resistance (blaKPC, blaCTX-M, tetM, mdtE and acrB_1), genes that have the potential to rapidly and horizontally spread (blaKPC, blaCTX-M, and tetM), and the gene that confers resistance to antibiotics that are typically regarded as the ultimate line of defense against severe multi-resistant bacterial infections (blaKPC). Lastly, microplastic harbored a similar bacterial community and ARGs regardless of beach water quality. Our findings suggest that the accumulation of microplastics in beach sand worldwide may constitute a potential threat to human health, even in beaches where the water quality is deemed satisfactory. This phenomenon may facilitate the emergence and dissemination of bacteria that are resistant to multiple drugs.

Alteriqipengyuania flavescens sp. nov., isolated from Pearl River Estuary sediment

Two Gram-stain-negative, aerobic, rod-shaped, non-motile and golden yellow pigmented bacteria, designated as SCSIO 75105T and SCSIO 75732, were isolated from sediment in the Pearl River Estuary, Guangdong Province, PR China. Cells were positive for catalase and oxidase. Growth occurred at 10-37 °C (optimum, 28 °C), pH 6.0-10.0 (optimum, pH 7.0) and 0-5.0 % (w/v) NaCl (optimum, 2.0-3.0 %). The 16S rRNA gene analysis indicated that these two isolates shared a similarity of 100 % each other. The 16S rRNA gene sequence analysis indicated that these two isolates showed highest similarity to Altererythrobacter ishigakiensis CGMCC 1.14979T (97.3 %). However, a phylogenetic tree based on 288 orthologous clusters indicated that these two isolates were closely related to Alteriqipengyuania halimionae CPA5T. The average nucleotide identity, average amino acid identity, digital DNA-DNA hybridization and evolutionary distance values between the two isolates and Alteriqipengyuania halimionae CPA5T were 73.7-74.0 %, 65.2 %, 19.5 % and 0.24, respectively. The genomic DNA G+C content of both isolates was 65.2 mol%. The major cellular fatty acids were C18 : 1  ω7c, C17 : 1  ω6c and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), and Q-10 was the respiratory quinone. The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and one unidentified glycolipid. On the basis of the results of phenotypic, physiological, chemotaxonomic and genotypic characterization, strains SCSIO 75105T and SCSIO 75732 are considered to represent a novel species in the genus Alteriqipengyuania, for which the name Alteriqipengyuania flavescens sp. nov. is proposed. The type strain is SCSIO 75105T (=KCTC 92502T=MCCC 1K07993T).

Alteriqipengyuania abyssalis sp. nov., a Novel Member of the Class Alphaproteobacteria Isolated from Sponge, and Emended Description of the Genus Alteriqipengyuania

A novel Gram-negative, aerobic, motile, lemon-yellow-colored, and non-spore-forming rod-shaped bacterium designated strain NZ-12BT was isolated in February 2021 from a sponge species (Crateromorpha) collected at the southern Kermadec Ridge, Pacific Ocean, New Zealand. Comparative 16S rRNA gene-based analyses indicated that strain NZ-12BT shared 98.58%, 96.44%, 96.23%, and 94.78% 16S rRNA sequence similarity to Alteriqipengyuania lutimaris S-5T, Qipengyuania pelagi UST081027-248T, Qipengyuania citreus RE35F/1T, and Alteriqipengyuania halimionae CPA5T, respectively. The major respiratory quinone was ubiquinone-10(Q-10). The polar lipid profile of NZ-12BT was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methyl-ethanolamine, phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, three unknown phospholipids, and three unknown glycolipids. The major fatty acids of strain NZ-12BT were C18:1ω12t, C16:0, C17:1ω6c, and C14:02-OH. Carotenoids were present. Genome mining analysis revealed a biosynthetic gene cluster encoding for the terpene biosynthesis. Pairwise ANI and dDDH values of strain NZ-12BT and closely related phylogenetic neighbors were below the threshold values of 95% and 70%, respectively. The DNA G+C content was 65.4 mol% (by genome). Based on data obtained by a polyphasic approach, type strain NZ-12BT (=DSM 112810T = NCCB 100841T) represents a novel species of the genus Alteriqipengyuania, for which the name Alteriqipengyuania abyssalis sp. nov. is proposed.

Genomic-based taxonomic classification of the family Erythrobacteraceae

The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.

Description of Erythrobacter mangrovi sp. nov., an aerobic bacterium from rhizosphere soil of mangrove plant (Kandelia candel)

A novel Gram-stain negative, aerobic, non-motile, rod-shaped bacterium, designated as strain EB310^T, was isolated from rhizosphere soil of mangrove plant Kandelia candel in Fugong village, Zhangzhou, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EB310^T belonged to the genus Erythrobacter, clustering with Erythrobacter pelagi JCM 17468^T, Erythrobacter lutimaris KCTC 42109^T and Erythrobacter marisflavi KCTC 62896^T, and showed the highest 16S rRNA gene sequence similarity of 97.5% to Erythrobacter pelagi JCM 17468^T. The genomic average nucleotide identity and in silico DNA-DNA hybridization values between strain EB310^T and the reference strains were 71.0-75.5% and 19.8-20.0%, respectively. Growth ranges of the isolate occurred at 10-45 °C (optimum 28-30 °C), pH 5.5-9.5 (optimum pH 7.5) and 0-9.0% NaCl concentrations (optimum 2.0%, w/v). The strain did not produce bacteriochlorophyll a and flexirubin, but produced carotenoids. The strain contained Q-10 as the predominant ubiquinone and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and summed feature 8 (C_18:1 ω6c/C_18:1 ω7c) as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylcholine. Differential phenotypic characteristics, together with chemotaxonomic, phylogenetic and genomic distinctiveness, indicated that strain EB310^T is distinguishable from other members of the genus Erythrobacter. On the basis of the data exhibited, strain EB310^T is considered to represent a novel species of the genus Erythrobacter, for which the name Erythrobacter mangrovi sp. nov., is proposed. The type strain is EB310^T (= KCTC 72109^T = MCCC 1K03690^T). The genomic DNA G + C content is 62.9 mol%.

Erythrobacter insulae sp. nov., isolated from a tidal flat

A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a tidal flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus Erythrobacter . JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of Erythrobacter longus , Erythrobacter aquimaris , Erythrobacter nanhaisediminis , Erythrobacter vulgaris , Erythrobacter seohaensis , Erythrobacter litoralis and Erythrobacter citreus and 93.7–96.6 % to the type strains of the other species of the genus Erythrobacter . The ANI and dDDH values between JBTF-M21T and the type strains of E. longus , E. nanhaisediminis , E. seohaensis and E. litoralis were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of E. aquimaris , E. vulgaris and E. citreus were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus Erythrobacter with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).

Sulfur-Containing Carotenoids from A Marine Coral Symbiont Erythrobacter flavus Strain KJ5

Erythrobacter flavus strain KJ5 (formerly called Erythrobacter sp. strain KJ5) is a yellowish marine bacterium that was isolated from a hard coral Acropora nasuta in the Karimunjawa Islands, Indonesia. The complete genome sequence of the bacterium has been reported recently. In this study, we examined the carotenoid composition of this bacterium using high-performance liquid chromatography coupled with ESI-MS/MS. We found that the bacterium produced sulfur-containing carotenoids, i.e., caloxanthin sulfate and nostoxanthin sulfate, as the most abundant carotenoids. A new carotenoid zeaxanthin sulfate was detected based on its ESI-MS/MS spectrum. The unique presence of sulfated carotenoids found among the currently known species of the Erythrobacter genus were discussed.

Erythrobacter nanhaiensis sp. nov., A Novel Member of the Genus Erythrobacter Isolated from the South China Sea

A Gram-negative, motile, rod-shaped, aerobic bacterial strain with tufty polar flagella, JLT1363^T, was isolated from the South China Sea. The bacteria formed yellow colonies on rich organic medium. The major cellular fatty acids present in JLT1363^T were C_18:1 ω7c and/or C_18:1 ω6c (36.06%), C_17:1 ω6c (17.04%), C_14:0 2-OH (9.85%), and C_16:0 (8.09%). The genome size was ~3.12 Mbps with a G+C content of 64.9%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JLT1363^T fell within the genus Erythrobacter. The 16S rRNA gene sequence similarity between strain JLT1363^T and the type strains of Erythrobacter species ranged from 95.0% (with Erythromicrobium ramosum) to 98.7% (with Erythrobacter lutimaris). The Average Nucleotide Identity (ANI) value between genome sequences of strain JLT1363^T and Erythrobacter lutimaris KCTC 42109^T was 82.2%. Strain JLT1363^T lacked bacteriochlorophyll a, and the major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylcholine, and phosphatidylglycerol. Phylogenetic and phenotypic properties indicated that strain JLT1363^T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter nanhaiensis sp. nov. is proposed. The type strain is JLT1363^T (=CGMCC 1.7293^T = LMG 24872^T).

Complete genome sequence of Erythrobacter seohaensis SW-135T sheds light on the ecological role of the genus Erythrobacter for phosphorus cycle in the marine environment

Erythrobacter seohaensis SW-135^T was isolated from inter sediments collected from an intertidal zone of the Yellow Sea in Korea. The genome of E. seohaensis SW-135^T was sequenced and comprised of one circular chromosome with the size of 2,942,673 bp and DNA G + C content of 61.7%. It was reported that E. seohaensis SW-135^T was positive for alkaline phosphatase activity by enzymatic test. Genomic annotation indicated that the genome of E. seohaensis SW-135^T had two alkaline phosphatase-encoding genes, phoD and phoX, which products can dephosphorylate phosphoesters to more bioavailable dissolved inorganic phosphorus for microorganisms in the phosphorus limited condition. Comparative genomic analysis of marine Erythrobacter strains revealed that phoD and phoX were widely distributed in these strains, indicating the genus Erythrobacter may play an important role in the marine phosphorus cycle. This study broadens our understandings about ecological roles of the genus Erythrobacter participating in the marine phosphorus cycle, which is rarely investigated previously.

Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons

A Gram-stain-negative, motile, rod-shaped, orange-pigmented bacterium able to degrade polycyclic aromatic hydrocarbons was isolated from deep-sea sediment of the Atlantic Ocean and subjected to a polyphasic taxonomic study. The strain, designated s21-N3T, could grow at 4–37 °C (optimum 28 °C), at pH 5–10 (optimum pH 7–8) and with 1–7 % (w/v) NaCl (optimum 2–3 %). Strain s21-N3T was positive for nitrate reduction, denitrification, aesculin hydrolysis, oxidase and catalase, but negative for indole production and urease. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain s21-N3T formed a distinct branch within the genus Erythrobacter, sharing high similarities with three closely related strains, Erythrobacter marinus HWDM-33T (98.67 %), ‘Erythrobacter luteus’ KA37 (97.80 %) and Erythrobacter gangjinensis K7-2T (97.59 %). The similarities between strain s21-N3T and other type strains of recognized species within the genus Erythrobacter ranged from 95.00 to 96.47 %. The digital DNA–DNA hybridization values and average nucleotide identity (ANI) values between strain s21-N3T and the three closely related strains Erythrobacter marinus HWDM-33T, ‘Erythrobacter luteus’ KA37 and Erythrobacter gangjinensis K7-2T were 18.60, 18.00 and 18.50 % and 74.24, 72.49 and 72.54 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and summed feature 3 (C16 : 1ω7c/ω6c). The respiratory lipoquinone was identified as Q-10. The major polar lipids comprised sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The G+C content of the chromosomal DNA was determined to be 58.18 mol%. The combined genotypic and phenotypic distinctiveness demonstrated that strain s21-N3T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter atlanticus sp. nov. is proposed, with the type strain s21-N3T ( = MCCC 1A00519T = KCTC 42697T).

Erythrobacter luteus sp. nov., isolated from mangrove sediment

A Gram-staining-negative, orange-pigmented, aerobic bacterial strain, designated KA37T, was isolated from a mangrove sediment sample collected from Yunxiao mangrove National Nature Reserve, Fujian Province, China. Growth was observed at 4-37 °C, 0-3% (w/v) NaCl and pH 5-10. Mg2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Erythrobacter, which belongs to the family Erythrobacteraceae. Strain KA37T was most closely related to Erythrobacter gangjinensis KCTC 22330T (96.9% sequence similarity), followed by Erythrobacter marinus KCTC 23554T (96.8%); similarity to other members of the genus was below 96.6%. The major fatty acids were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain KA37T did not produce bacteriochlorophyll a. The predominant respiratory quinone was ubiquinone 10 (Q-10). The polar lipids of strain KA37T were sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unknown lipids and one unidentified phospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence, the novel strain most appropriately belongs to the genus Erythrobacter, but can be distinguished readily from species of the genus Erythrobacter with validly published names. The name Erythrobacter luteus sp. nov. is proposed, with strain KA37T ( = MCCC 1F01227T = KCTC 42179T) as the type strain.