Search

As the closest living relatives of animals, choanoflagellates offer insights into the ancestry of animal cell physiology. Here, we report the isolation and characterization of a colonial choanoflagellate from Mono Lake, California. The choanoflagellate forms large spherical colonies that are an order of magnitude larger than those formed by the closely related choanoflagellate Salpingoeca rosetta . In cultures maintained in the laboratory, the lumen of the spherical colony is filled with a branched network of extracellular matrix and colonized by bacteria, including diverse Gammaproteobacteria and Alphaproteobacteria. We propose to erect Barroeca monosierra gen. nov., sp. nov. Hake, Burkhardt, Richter, and King to accommodate this extremophile choanoflagellate. The physical association between bacteria and B. monosierra in culture presents a new experimental model for investigating interactions among bacteria and eukaryotes. Future work will investigate the nature of these interactions in wild populations and the mechanisms underpinning the colonization of B. monosierra spheres by bacteria., Importance: The diversity of organisms that live in the extreme environment of Mono Lake (California, USA) is limited. We sought to investigate whether the closest living relatives of animals, the choanoflagellates, exist in Mono Lake, a hypersaline, alkaline, arsenic-rich environment. We repeatedly isolated members of a new species of choanoflagellate, which we have named Barroeca monosierra . Characterization of B. monosierra revealed that it forms large spherical colonies containing diverse co-isolated bacteria, providing an opportunity to investigate mechanisms underlying physical associations between eukaryotes and bacteria., Competing Interests: The authors declare no conflict of interest.

A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated as FTW29 T , was isolated from surface seawater sampled in Futian district, Shenzhen, China. Growth of strain FTW29 T was observed at 15-42 ℃ (optimum, 28-30 ℃), pH 4.0-9.0 (optimum, pH 5.5-7.5) and in the presence of 0.5-10% NaCl (optimum, 3.0% NaCl). Strain FTW29 T showed 95.0-96.8% 16 S rRNA gene sequence similarity to various type strains of the genera Thioclava, Sinirhodobacter, Rhodobacter, Haematobacter and Frigidibacter of the family Paracoccaceae, and its most closely related strains were Thioclava pacifica DSM 10,166 T (96.8%) and Thioclava marina 11.10-0-13 T (96.7%). The phylogenomic tree constructed on the bac120 gene set showed that strain FTW29 T formed a clade with the genus Thioclava, with a bootstrap value of 100%. The evolutionary distance values between FTW29 T and type strains of the genus Thioclava were 0.17-0.19, which are below the recommended standard (0.21-0.23) for defining a novel genus in the family Paracoccaceae. In strain FTW29 T , the major fatty acids identified were summed feature 8 (C 18:1 ω7c) and C 16:0, and the predominant respiratory quinones were ubiquinone-10 and ubiquinone-9. The composition of polar lipids in strain FTW29 T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid, two unidentified glycolipids and an unidentified lipid. The genome of strain FTW29 T comprised one circle chromosome and six plasmids, with a G + C content of 61.4%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain FTW29 T and seven type strains of the genus Thioclava were 76.6-78.4%, 53.2-56.4% and 19.3-20.4%, respectively. Altogether, the phenotypic, phylogenetic and chemotaxonomic evidence illustrated in this study suggested that strain FTW29 T represents a novel species of the genus Thioclava, with the proposed name Thioclava litoralis sp. nov. The type strain is FTW29 T (= KCTC 82,841 T  = MCCC 1K08523 T )., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus., (© 2023. The Author(s).)

A new isolate designated as 1XM1-14 T was isolated from a tidal flat sediment of Xiamen Island. The yellow-pigmented colonies and rod-shaped cells were observed. Strain 1XM1-14 T could hydrolyze Tweens 20, 40, 60, aesculin, and skim milk, and was chemoheterotrophic and mesophilic, required NaCl for the growth. The 16S rRNA gene-based phylogenetic analysis indicated that strain 1XM1-14 T was the most closely related to Altererythrobacter epoxidivorans CGMCC 1.7731 T (97.0%), followed by other type strain of the genus Altererythrobacter with identities below 97.0%. The DNA-DNA hybridization and average nucleotide identity values between strain 1XM1-14 T and its relatives of the genus Altererythrobacter were below the respective thresholds for prokaryotic species demarcation. The phylogenomic inference further revealed that strain 1XM1-14 T formed a separate branch distinct from the type strains of the recognized species within the genus Altererythrobacter. The major cellular fatty acids of strain 1XM1-14 T were identified as summed feature 8 (C 18:1 ω6c and/or C 18:1 ω7c), C 17:1 ω6c, and C 16:0 ; the profile of polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified glycolipid, and two unidentified lipids; the respiratory quinone was determined to ubiquinone-10. The genomic size and DNA G+C content of strain 1XM1-14 T were 2.5 Mbp and 62.71%. The key carotenoid biosynthetic genes were determined in the genome of strain 1XM1-14 T and the generated carotenoids were detected. The combined genotypic and phenotypic characteristics supported the classification of strain 1XM1-14 T (= GDMCC 1.2383 T  = KCTC 82612 T ) as a novel species in the genus Altererythrobacter, for which the name Altererythrobacter litoralis sp. nov. is proposed., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 "UltraPac" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

A novel Gram-reaction-negative, aerobic, motile, rod-shaped, grey bacterium, strain P4.10X T , was isolated from plastic debris sampled from shallow waters in the Mediterranean Sea (Valencia, Spain). P4.10X T was catalase- and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA gene sequences revealed that P4.10X T was closely related to Maritalea myrionectae DSM 19524 T and Maritalea mobilis E6 T (98.25 and 98.03 % sequence similarity, respectively). The DNA G+C content of the genome sequence of P4.10X T was 53.66 %. The genomic indexes average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) confirmed its classification as representing a novel species of the genus Maritalea . The predominant fatty acids were summed feature 8 (C 18 : 1 ω7 c /C 18 : 1 ω6 c ) and C 18 : 1 ω 7c 11-methyl. The results of this polyphasic study confirm that P4.10X T represents a novel species of the genus Maritalea , for which the name Maritalea mediterranea sp. nov. is proposed (type strain P4.10X T =CECT 30306 T = DSM 112386 T ).

A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, methyl red-positive, and lipase-negative bacterium, designated A5.8 T , was isolated from beach sediment of Zhairuo Island located in the East China Sea. Growth occurred at 10-40 °C (optimum, 30 °C), pH 5.5-9.5 (optimum, 7.5), and 0-2% NaCl (optimum, 1.5%). Based on 16S rRNA gene sequence analysis, strain A5.8 T belongs to the genus Ancylobacter, sharing the highest similarity with Ancylobacter aquaticus JCM 20518 T (98.0%). Its polar lipids mainly consist of phosphatidylethanolamine (PE) and phosphatidylcholine (PC). The predominant fatty acids are summed feature 8 (C 18:1 ω7c and/or C 18:1 ω6c, 91.0%), and the major respiratory quinone is Q-10. The DNA G + C content is 67.2 mol%. Based on above analysis, as well as digital DNA-DNA hybridization (22.5-22.9%) and average nucleotide identity (83.0-83.6%) of strain A5.8 T with reference type strains of the genus Ancylobacter, strain A5.8 T was suggested to represent a novel species of the genus Ancylobacter, for which the name Ancylobacter gelatini sp. nov. is proposed. The type strain is A5.8 T (= MCCC 1K07167 T  = LMG 32566 T )., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

A novel Gram-stain-negative, non-motile, halophilic bacterium designated strain M10.9X T was isolated from the inner sediment of an aluminium can collected from the Mediterranean Sea (València, Spain). Cells of strain M10.9X T were rod-shaped and occasionally formed aggregates. The strain was oxidase-negative and catalase-positive, and showed a slightly psychrophilic, neutrophilic and slightly halophilic metabolism. The phylogenetic analyses revealed that strain M10.9X T was closely related to Sagittula stellata E-37 T and Sagittula marina F028-2 T . The genomic G+C content of strain M10.9X T was 65.2 mol%. The average nucleotide identity and digital DNA-DNA hybridization values were 76.6 and 20.9 %, respectively, confirming its adscription to a new species within the genus Sagittula . The major cellular fatty acids were C 18 : 1   ω7 c /C 18 : 1   ω6 c and C 16 : 0 . The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. According to the resuts of a polyphasic study, strain M10.9X T represents a novel species of the genus Sagittula for which the name Sagittula salina sp. nov. (type strain M10.9X T =DSM 112301 T =CECT 30307 T ) is proposed.

Microbial community metabolism and functionality play a key role modulating global biogeochemical processes. However, the metabolic activities and contribution of actively growing prokaryotes to ecosystem energy fluxes remain underexplored. Here we describe the temporal and spatial dynamics of active prokaryotes in the different water masses of the Mediterranean Sea using a combination of bromodeoxyuridine labelling and 16S rRNA gene Illumina sequencing. Bulk and actively dividing prokaryotic communities were drastically different and depth stratified. Alteromonadales were rare in bulk communities (contributing 0.1% on average) but dominated the actively dividing community throughout the overall water column (28% on average). Moreover, temporal variability of actively dividing Alteromonadales oligotypes was evinced. SAR86, Actinomarinales and Rhodobacterales contributed on average 3-3.4% each to the bulk and 11, 8.4 and 8.5% to the actively dividing communities in the epipelagic zone, respectively. SAR11 and Nitrosopumilales contributed less to the actively dividing than to the bulk communities during all the study period. Noticeably, the large contribution of these two taxa to the total prokaryotic communities (23% SAR11 and 26% Nitrosopumilales), especially in the meso- and bathypelagic zones, results in important contributions to actively dividing communities (11% SAR11 and 12% Nitrosopumilales). The intense temporal and spatial variability of actively dividing communities revealed in this study strengthen the view of a highly dynamic deep ocean. Our results suggest that some rare or low abundant phylotypes from surface layers down to the deep sea can disproportionally contribute to the activity of the prokaryotic communities, exhibiting a more dynamic response to environmental changes than other abundant phylotypes, emphasizing the role they might have in community metabolism and biogeochemical processes., (© 2022. The Author(s).)

A novel bacterium, designated CAU 1612 T , was isolated from coastal sediment sampled in the Republic of Korea. Cells of the strain were Gram-stain-negative, rod-shaped and motile. Optimum growth occurred at 30 °C, at pH 7.0 and with 1.0 % (w/v) NaCl. Based on 16S rRNA gene sequences, phylogenetic analysis revealed that strain CAU 1612 T belonged to the genus Sneathiella and showed highest similarity to ' Sneathiella litorea ' JCM 33810 T (98.5 %), followed by Sneathiella chungangensis KCTC 32476 T (97.7 %), Sneathiella aquimaris KCTC 12842 T (96.0 %), Sneathiella chinensis LMG 23452 T (95.5 %), Sneathiella limimaris KCTC 52846 T (95.5 %) and Sneathiella glossodoripedis KCTC 12842 T (95.4 %). The average nucleotide identity and digital DNA-DNA hybridization values of strain CAU 1612 T were estimated to be 68.5-81.7 % and ≤23.7 %, respectively, to members of the genus Sneathiella . The DNA G+C content was 54.1 mol%. The major cellular fatty acids (>10 %) were C 16:0 , C 19 : 0 cyclo ω 8 c and summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ). The major menaquinone was Q-10 and the predominant polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. On the basis of taxonomic evidence, strain CAU 1612 T represents a novel species, for which the name Sneathiella sedimenti sp. nov. is proposed. The type strain is CAU 1612 T (=KCTC 82427 T =MCCC 1K06082 T ).

A light pink coloured bacterium, designated strain BN140002 T , was isolated from a soil sample collected in Goesan-gun, Chungcheongbuk-do, Republic of Korea. Cells of strain BN140002 T were Gram-stain-negative, aerobic, motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed 94.7, 94.7, 93.9, 93.3, 93.4 and 93.0% similarities to Salinarimonas rosea KCTC 22346 T , Salinarimonas ramus DSM 22962 T , Saliniramus fredricksonii HL-109 T , Microvirga soli R491 T , Chelatococcus caeni EBR-4-1 T and Chelatococcus composti PC-2 T , respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. The major cellular fatty acids were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6c) and summed feature 1 (C 12 : 0 aldehyde and/or unknown 10.98) and the predominant ubiquinone was Q-10. The genomic DNA G+C content of strain BN140002 T was 70.1 mol%. The genomic orthoANI values between strain BN140002 T and Salinarimonas rosea KCTC 22346 T and Salinarimonas ramus DSM 22962 T were 75.0 and 74.8 %, respectively. Strain BN140002 T had a class I-C type CRISPR-Cas system (CRISPR-associated helicase Cas3, CRISPR-associated protein Cas8c, CRISPR-associated protein Cas7, CRISPR-associated RecB family exonuclease Cas4, CRISPR-associated protein 1, 2). Based on phenotypic, chemotaxonomic and phylogenetic data, strain BN140002 T should be assigned as a novel species of the genus Salinarimonas , for which the name Salinarimonas soli sp. nov. is proposed. The type strain is BN140002 T (=KCTC 42643 T =CCTCC AB 2017173 T ).

Two Gram-reaction-negative strains, designated as B13 T and MA2-2, were isolated from two different aromatic hydrocarbon-degrading enrichment cultures and characterized using a polyphasic approach to determine their taxonomic position. The two strains had identical 16S rRNA gene sequences and were most closely related to Pinisolibacter ravus E9 T (97.36 %) and Siculibacillus lacustris SA-279 T (96.33 %). Cells were facultatively aerobic rods and motile with a single polar flagellum. The strains were able to degrade ethylbenzene as sole source of carbon and energy. The assembled genome of strain B13 T had a total length of 4.91 Mb and the DNA G+C content was 68.8 mol%. The predominant fatty acids (>5 % of the total) of strains B13 T and MA2-2 were C 18 : 1  ω 7 c /C 18 : 1  ω 6 c , C 16 : 1  ω 7 c /C 16 : 1  ω 6 c and C 16 : 0 . The major ubiquinone of strain B13 T was Q10, while the major polar lipids were phosphatidyl- N -methylethanolamine, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and a phospholipid. Based on phenotypic characteristics and phylogenetic data, it is concluded that strains B13 T and MA2-2 are members of the genus Pinisolibacter and represent a novel species for which the name Pinisolibacter aquiterrae sp. nov. is proposed. The type strain of the species is strain B13 T (=LMG 32346 T =NCAIM B.02665 T ).

Three Gram-staining-negative, aerobic and rod-shaped strains, designated as T40-1 T , T40-3 T and JL-62 T , were isolated from the deep-sea water in the southwest Indian ridge. For strain T40-1 T , growth occurred at 15-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0.5-5.0 % NaCl (w/v; optimum, 2.0 %). Strain T40-3 T could grow at 15-40 °C (optimum, 28 °C), with 0.5-11.0 % NaCl (optimum, 2.0 %, w/v) at pH 6.0-9.5 (optimum, 8.0). The temperature, pH and salinity ranges for growth of strain JL-62 T were 15-40 °C (optimum, 30 °C), pH 5.5-9.0 (optimum, pH 7.5-8.0) and 0.5-9.0 % NaCl (w/v; optimum, 4.0 %). Ubiquinone-10 was the sole ubiquinone in all strains, the major fatty acids (>20 %) were summed feature 8 (C 18 : 1  ω 7 c / C 18 : 1  ω 6 c ). The major polar lipids of strains T40-1 T and T40-3 T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain JL-62 T contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sulfoquinovosyldiacylglycerol as major polar lipids. Phylogenetic trees based on 16S rRNA gene and core-genomic sequences revealed affiliation of strains T40-1 T and T40-3 T to the family Roseobacteraceae and formed two independent clades from other Roseobacteraceae genera, and those two strains had average nucleotide identities of 62.0-72.0 % to their phylogenetically related species which fell into to the genus boundary range, indicating that they represent two novel genera. While strain JL-62 T represents a novel species in the genus Oricola belonging to the family Phyllobacteriaceae , which was supported by overall genomic relatedness index calculations. The DNA G+C contents of strains T40-1 T , T40-3 T and JL-62 T were 66.5, 60.1 and 62.1 mol %, respectively. Based on the polyphasic taxonomic data, strains T40-1 T (=MCCC M24557 T =KCTC 82975 T ) and T40-3 T (=MCCC 1K05135 T =KCTC 82976 T ) are classified as representing two novel genera belonging to the family Roseobacteraceae with the names Mesobacterium pallidum gen. nov., sp. nov. and Heliomarina baculiformis gen. nov., sp. nov. are proposed, and strain JL-62 T (=MCCC M24579 T =KCTC 82974 T ) is proposed to represent a novel species within the genus Oricola with the name Oricola indica sp. nov. is proposed.

A Gram-negative, aerobic, non-flagellated and rod-shaped bacterium, strain ASW11-22 T , was isolated from an intertidal sediment collected from a coastal area of Qingdao, PR China. The strain grew at 15-40 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0.5-10 % (w/v) NaCl (optimum, 1.0 %). It hydrolysed gelatin and aesculin but did not reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ASW11-22 T belonged to the genus Celeribacter , showing the highest sequence similarity to the type strains of Celeribacter halophilus MCCC 1A06432 T (98.20 %) and Celeribacter ethanolicus NH195 T (97.84 %). The genomic DNA G+C content was 59.1 mol%. The major cellular fatty acid (>10 %) of the strain was summed feature 8 (C 18 : 1  ω7 c and/or C 18 : 1  ω6 c ) and its main polar lipids were phosphatidylglycerol and one unidentified aminolipid. The sole respiratory quinone of strain ASW11-22 T was ubiquinone-10. On the basis of the polyphasic evidence presented in this paper, strain ASW11-22 T represents a novel Celeribacter species, for which the name Celeribacter litoreus sp. nov. is proposed. The type strain is ASW11-22 T (=KCTC 82495 T =MCCC 1K05584 T ).

A yellow-coloured bacterium, designated strain JGD-16 T , was isolated from a tidal flat in Janggu-do, Garorim Bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-flagellated and short ovoid to coccoid-shaped. Growth was observed at 10-37 °C (optimum, 30 °C), pH 6.0-9.0 (pH 8.0) and with 1-5% (w/v) NaCl (2%). Results of 16S rRNA gene sequence analysis indicated that strain JGD-16 T was closely related to Altererythrobacter xiamenensis LY02 T (97.1 %), Altererythrobacter aurantiacus O30 T (96.3 %), Altererythrobacter ishigakiensis JPCCMB0017 T (95.8 %), Altererythrobacter epoxidivorans JCS350 T (95.7 %) and Altererythrobacter insulae BPTF-M16 T (95.3%). Phylogenomic analysis using the maximum-likelihood algorithm showed that strain JGD-16 T formed a clade with the genus Altererythrobacter . The genomic DNA G+C content was 57.8 mol%. The predominant respiratory quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, a sphingoglycolipid, an unidentified glycolipid and an unidentified lipid. The major fatty acids were C 18:1 ω 7 c (31.5 %) and C 18:3 ω 6 c (19.6 %). On the basis of its phylogenomic, physiological and chemotaxonomical characteristics, strain JGD-16 T represents a novel species within the genus Altererythrobacter , for which the name Altererythrobacter lutimaris JGD-16 T sp. nov. is proposed. The type strain is JGD-16 T (=KCTC 72632 T =KACC 21405 T =JCM 33750 T ). We also propose the reclassification of Altererythrobacter deserti as Tsuneonella deserti comb. nov., Altererythrobacter estronivorus as Croceicoccus estronivorus comb. nov. and Altererythrobacter muriae as Alteripontixanthobacter muriae comb. nov.

A Gram-stain-negative, aerobic, milky white bacterium, designated B2012 T , was isolated from mangrove sediment collected at Beibu Gulf, South China Sea. Antimicrobial activity assay revealed that the isolate possesses the capability of producing antibacterial compounds. Strain B2012 T shared the highest 16S rRNA gene sequence relatedness (96.9-95.5 %) with members of the genus Acuticoccus . The isolate and all known Acuticoccus species contain Q-10 as the main respiratory quinone and have the same polar lipid components (phosphatidylcholine, unidentified glycolipid, unidentified lipid, unidentified amino lipid and phosphatidylglycerol). However, genomic relatedness referred by values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and the percentage of conserved proteins between strain B2012 T and other type strains of the genus Acuticoccus were below the proposed thresholds for species discrimination. The genome of strain B2012 T was assembled into 65 scaffolds with an N50 size of 244239 bp, resulting in a 5.5 Mb genome size. Eight secondary metabolite biosynthetic gene clusters were detected in this genome, including three non-ribosomal peptide biosynthetic loci encoding yet unknown natural products. Strain B2012 T displayed moderately halophilic and alkaliphilic properties, growing optimally at 2-3 % (w/v) NaCl concentration and at pH 8-9. The major cellular fatty acids (>10 %) were anteiso-C 15 : 0 , C 16 : 0 dimethyl aldehyde (DMA) and C 16 : 0 . Combined data from phenotypic, genotypic and chemotaxonomic analyses suggested that strain B2012 T represents a novel species of the genus Acuticoccus , for which the name Acuticoccus mangrovi sp. nov. is proposed. The type strain of the type species is B2012 T (=MCCC 1K04418 T =KCTC 72962 T ).

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640 T , isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640 T were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °С and pH 7. Strain CC-CFT640 T showed highest 16S rRNA gene sequence similarity to members of the genus Enhydrobacter (90.0 %, n =1) followed by Hypericibacter (89.4-90.0 %, n =2), Reyranella (88.8-89.8 %, n =5) and Nitrospirillum (89.2-89.4 %, n =2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated Reynerella species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % ( n =1), 74.0-74.6 % ( n =2), 67.5-68.3 % ( n =2) when compared within the type strains of the genera Enhydrobacter , Reyranella and Niveispirillum , respectively. The dominant cellular fatty acids (>5 %) included C 16 : 0 , iso-C 17 : 1  ω 10 c , C 19 : 0 cyclo ω 8 c , C 18 : 1 2-OH and C 18 : 1  ω 7 c /C 18 : 1  ω 6 c . The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA-DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640 T is considered to represent a novel genus and species of the family Rhodospirillaceae , for which the name Vineibacter terrae gen. nov., sp. nov. is proposed. The type strain is CC-CFT640 T (=BCRC 81219 T =JCM 33507 T ).

Magnetotactic bacteria (MTB) are prokaryotes that form intracellular magnetite (Fe 3 O 4 ) or greigite (Fe 3 S 4 ) nanocrystals with tailored sizes, often in chain configurations. Such magnetic particles are each surrounded by a lipid bilayer membrane, called a magnetosome, and provide a model system for studying the formation and function of specialized internal structures in prokaryotes. Using fluorescence-coupled scanning electron microscopy, we identified a novel magnetotactic spirillum, XQGS-1, from freshwater Xingqinggong Lake, Xi'an City, Shaanxi Province, China. Phylogenetic analyses based on 16S rRNA gene sequences indicate that strain XQGS-1 represents a novel genus of the Alphaproteobacteria class in the Proteobacteria phylum. Transmission electron microscopy analyses reveal that strain XQGS-1 forms on average 17 ± 3 magnetite magnetosome particles with an ideal truncated octahedral morphology, with an average length and width of 88.3 ± 11.7 nm and 83.3 ± 11.0 nm, respectively. They are tightly organized into a single chain along the cell long axis close to the concave side of the cell. Intrachain magnetic interactions likely result in these large equidimensional magnetite crystals behaving as magnetically stable single-domain particles that enable bacterial magnetotaxis. Combined structural and chemical analyses demonstrate that XQGS-1 cells also biomineralize intracellular amorphous calcium phosphate (2 to 3 granules per cell; 90.5- ± 19.3-nm average size) and weakly crystalline calcium carbonate (2 to 3 granules per cell; 100.4- ± 21.4-nm average size) in addition to magnetite. Our results expand the taxonomic diversity of MTB and provide evidence for intracellular calcium phosphate biomineralization in MTB. IMPORTANCE Biomineralization is a widespread process in eukaryotes that form shells, teeth, or bones. It also occurs commonly in prokaryotes, resulting in more than 60 known minerals formed by different bacteria under wide-ranging conditions. Among them, magnetotactic bacteria (MTB) are remarkable because they might represent the earliest organisms that biomineralize intracellular magnetic iron minerals (i.e., magnetite [Fe 3 O 4 ] or greigite [Fe 3 S 4 ]). Here, we report a novel magnetotactic spirillum (XQGS-1) that is phylogenetically affiliated with the Alphaproteobacteria class. In addition to magnetite crystals, XQGS-1 cells form intracellular submicrometer calcium carbonate and calcium phosphate granules. This finding supports the view that MTB are also an important microbial group for intracellular calcium carbonate and calcium phosphate biomineralization.

A novel bacterium, designated strain CAU 1637 T , was isolated from a tidal mudflat. Cells of strain CAU 1637 T were Gram-stain-negative, aerobic, motile with single flagellum and rod-shaped. The optimum conditions for growth were observed at 30 °C, pH 6.0 and in the presence of 2 % (w/v) NaCl. The respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1637 T was closely related to the genus Roseibium , with the highest similarity to Roseibium aestuarii NRBC 112946 T (97.4 %), followed by Roseibium hamelinense NRBC 16783 T (96.8 %), Roseibium aquae JCM 19310 T (96.4 %), Roseibium sediminis KCTC 52373 T (95.8 %) and Roseibium denhamense JCM 10543 T (95.3 %). The predominant cellular fatty acids were C 18 : 1  ω 7 c 11-methyl and summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity values between the novel isolate and related strains ranged from 71.0 to 76.4 %, and the DNA-DNA hybridization values ranged from 19.3 to 20.3 %. The G+C content was 58.4 mol% and the whole-genome size was 4.6 Mb, which included 17 contigs and 3931 protein-coding genes. Based on the taxonomic data, strain CAU 1637 T represents a novel species of the genus Roseibium , for which the name Roseibium limicola sp. nov. is proposed. The type strain is CAU 1637 T (=KCTC 82429 T =MCCC 1K06080 T ).

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79 T and A. flavus D11M-2 T , they showed 97.9 % sequence identity, much higher than the sequence identities 92.7-94.3 % between P. flava NH6-79 T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79 T and A. flavus D11M-2 T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79 T and A. flavus D11M-2 T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79 T and other closely related type strains (54.3 %-58.1 % and 68.6-70.4 %, respectively). P. flava NH6-79 T and A. flavus D11M-2 T also contained summed feature 8 (C 18 : 1  ω 6 c and/or C 18 : 1  ω 7c) and C 16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

An aerobic, Gram-stain-negative, rod-shaped bacterium with flagellum, designated L22 T , was isolated from sediment of Hulun Lake, Inner Mongolia, China. The organism was found to grow optimally at 30° C in a medium containing 0-0.75% (w/v) NaCl at pH 7.5. The major fatty acid identified was summed feature 8 (C 18:1 ω7c). The dominant polar lipids were phosphomonoester, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The main respiratory quinone was Q-10. The draft genome sequence of strain L22 T consisted of 4354,788 bp. The G + C content of genomic DNA was 69.8 mol %. The 16S rRNA gene sequences indicated that strain L22 T was affiliated with the genus Methylobrevis within the family Pleomorphomonadaceae, being most closely related to Methylobrevis pamukkalensis JCM 30229 T with 95.9% 16S rRNA gene sequences similarity. The AAI, ANI and dDDH values between strain L22 T and M. pamukkalensis JCM 30229 T were 72.5%, 80.7% and 22.7%. Based on taxonomic results in this study, we proposed that strain L22 T a novel species in the genus Methylobrevis of the family Pleomorphomonadaceae, for which the name Methylobrevis albus sp. nov. is proposed. The type strain is L22 T (=KCTC 72858 T =MCCC 1H00432 T )., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The prospection of new degrading enzymes of the plant cell wall has been the subject of many studies and is fundamental for industries, due to the great biotechnological importance of achieving a more efficient depolymerization conversion from plant polysaccharides to fermentable sugars, which are useful not only for biofuel production but also for various bioproducts. Thus, we explored the shotgun metagenome data of a bacterial community (CB10) isolated from sugarcane bagasse and recovered three metagenome-assembled genomes (MAGs). The genomic distance analyses, along with phylogenetic analysis, revealed the presence of a putative novel Chitinophaga species, a Pandoraea nosoerga, and Labrys sp. isolate. The isolation process for each one of these bacterial lineages from the community was carried out in order to relate them with the MAGs. The recovered draft genomes have reasonable completeness (72.67-100%) and contamination (0.26-2.66%) considering the respective marker lineage for Chitinophaga (Bacteroidetes), Pandoraea (Burkholderiales), and Labrys (Rhizobiales). The in-vitro assay detected cellulolytic activity (endoglucanases) only for the isolate Chitinophaga, and its genome analysis revealed 319 CAZymes, of which 115 are classified as plant cell wall degrading enzymes, which can act in fractions of hemicellulose and pectin. Our study highlights the potential of this Chitinophaga isolate provides several plant-polysaccharide-degrading enzymes., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

Microbial proton-pumping rhodopsins are considered the simplest strategy among phototrophs to conserve energy from light. Proteorhodopsins are the most studied rhodopsins thus far because of their ubiquitous presence in the ocean, except in Antarctica, where they remain understudied. We analyzed proteorhodopsin abundance and transcriptional activity in the Western Antarctic coastal seawaters. Combining quantitative PCR (qPCR) and metagenomics, the relative abundance of proteorhodopsin-bearing bacteria accounted on average for 17, 3.5, and 29.7% of the bacterial community in Chile Bay (South Shetland Islands) during 2014, 2016, and 2017 summer-autumn, respectively. The abundance of proteorhodopsin-bearing bacteria changed in relation to environmental conditions such as chlorophyll a and temperature. Alphaproteobacteria , Gammaproteobacteria , and Flavobacteriia were the main bacteria that transcribed the proteorhodopsin gene during day and night. Although green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones, the latter were transcribed more intensely, resulting in >50% of the proteorhodopsin transcripts during the day and night. Flavobacteriia were the most abundant proteorhodopsin-bearing bacteria in the metagenomes; however, Alphaproteobacteria and Gammaproteobacteria were more represented in the metatranscriptomes, with qPCR quantification suggesting the dominance of the active SAR11 clade. Our results show that proteorhodopsin-bearing bacteria are prevalent in Antarctic coastal waters in late austral summer and early autumn, and their ecological relevance needs to be elucidated to better understand how sunlight energy is used in this marine ecosystem. IMPORTANCE Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula's coastal waters. This information is crucial to understand better how sunlight enters this marine environment through alternative ways unrelated to chlorophyll-based strategies. The relative abundance of proteorhodopsin-bearing bacteria seems to be related to environmental parameters (e.g., chlorophyll a , temperature) that change yearly at the coastal water of the West Antarctic Peninsula during the austral late summers and early autumns. Proteorhodopsin-bearing bacteria from Antarctic coastal waters are potentially able to exploit both the green and blue spectrum of sunlight and are a prevalent group during the summer in this polar environment.

A novel bacterial strain, designated SW136 T , was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW136 T represented a novel member of the genus Aurantimonas , forming a distinct cluster with ' Aurantimonas litoralis ', Aurantimonas coralicida and Aurantimonas manganoxydans (98.2, 98.1 and 97.9% sequence similarity, respectively). The predominant cellular fatty acid of strain SW136 T was C 18 : 1  ω 7 c . Strain SW136 T contained ubiquinone-10 as the dominant respiratory quinone, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content was 64.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values of strain SW136 T with A. coralicida CGMCC 1.12222 T and A. manganoxydans CGMCC 1.12225 T were 78.8 and 78.6 % and 21.5 and 25.5 %, respectively. On the basis of phylogenetic inference and phenotypic characteristics, we propose that strain SW136 T represents a novel species of the genus Aurantimonas , with the name Aurantimonas marina sp. nov. The type strain is SW136 T (=CGMCC 1.17725 T =KCTC 82366 T ).

A Gram-stain-negative, strictly aerobic, motile bacterium, designated strain RKSG073 T , was isolated from the sea sponge Aplysina fistularis , collected off the west coast of San Salvador, The Bahamas. Cells were curved-to-spiral rods with single, bipolar (amphitrichous) flagella, oxidase- and catalase-positive, non-nitrate-reducing and required salt for growth. RKSG073 T grew optimally at 30-37 °C, pH 6-7, and with 2-3 % (w/v) NaCl. The predominant fatty acids of RKSG073 T were summed feature 8 (C 18 : 1 ω6 c and/or C 18 : 1 ω7 c ) and C 16 : 0 . Major isoprenoid quinones were identified as Q-10 and Q-9. Phylogenetic analyses of nearly complete 16S rRNA genes and genome sequences positioned strain RKSG073 T in a clade with its closest relative Aestuariispira insulae AH-MY2 T (92.1 % 16S rRNA gene sequence similarity), which subsequently clustered with Hwanghaeella grinnelliae Gri0909 T , Marivibrio halodurans ZC80 T and type species of the genera Kiloniella , Thalassospira and Terasakiella . The DNA G+C content calculated from the genome of RKSG073 T was 42.2 mol%. On the basis of phylogenetic distinctiveness and polyphasic analysis, here we propose that RKSG073 T (culture deposit numbers: ATCC collection = TSD-74 T , BCCM collection = LMG 29869 T ) represents the type strain of a novel genus and species within the family Kiloniellaceae , order Rhodospirillales and class Alphaproteobacteria , for which the name Curvivirga aplysinae gen. nov., sp. nov. is proposed.

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain designated as 6D45A T was isolated from mangrove soil and characterized using a polyphasic taxonomic approach. Strain 6D45A T was found to grow at 10-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.0) and in 0-5 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D45A T fell into the genus Salipiger and shared 99.1 % identity with the closest type strain Salipiger pacificus CGMCC 1.3455 T and less than 97.2 % identity with other type strains of this genus. The 34.8 % digital DNA-DNA hybridization (dDDH) and 88.3 % average nucleotide identity (ANI) values between strain 6D45A T and the closest relative above were well below recognized thresholds of 70 % DDH and 95-96 % ANI for species definition, implying that strain 6D45A T should represent a novel genospecies. The phylogenomic analysis indicated that strain 6D45A T formed an independent branch distinct from reference strains. The predominant cellular fatty acid of strain 6D45A T was summed feature 8 (C 18 : 1  ω6 c and/or C 18 : 1  ω7 c, 66.9 %); the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, two unidentified glycolipids and an unknown lipid; the respiratory quinone was Q-10. The genomic DNA G+C content was 66.5 mol %. Based on the phenotypic and genotypic characteristics, strain 6D45A T is concluded to represent a novel species of the genus Salipiger , for which the name Salipiger mangrovisoli sp. nov., is proposed. The type strain of the species is 6D45A T (=GDMCC 1.1960 T =KCTC 82334 T ). We also propose the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov. and ' Pelagibaca abyssi ' as a species of the genus Salipiger .

Two bacterial strains, designated as 1-4-3 T and 1-4-4, were isolated from a mangrove sediment cultured with coastal seawater. The cells were Gram-stain-negative, motile, short, rod-shaped bacteria with flagella. Growth occurred at 4-37 °C, pH 7.0-9.0, and 0-7% NaCl. The predominant fatty acids of the novel strains were C 18 : 1  ω7 c, C 19 : 0 cyclo ω 8c, C 18 : 0 , and C 16 : 0 . A phylogenetic analysis based on 16S rRNA gene sequences and whole genome phylogeny analysis based on distance matrix revealed an affiliation between the two strains and the genus Aureimonas , with closest sequence similarity to A. populi 4M3-2 T (96.41 and 96.64% similarity, respectively) and A. glaciistagni (96.01 and 96.23% similarity, respectively). The DNA G+C content of strain 1-4-3 T was 66.80 mol%. Strain 1-4-3 T displayed low DNA-DNA relatedness to A. populi 4M3-2 T , with an average nucleotide identity value of 77.47 % and digital DNA-DNA hybridization value of 22.83 %. Genotypic, chemotaxonomic, and phenotypic data indicate that strains 1-4-3 T and 1-4-4 represent a novel species of the genus Aureimonas , for which we propose the name Aureimonas mangrovi sp. nov. The type strain is 1-4-3 T (=LMG 31693 T =CGMCC 1.18507 T ).

Strains M65 T , M69 and JN25 were isolated from seawater of the West Pacific Ocean. Cells of the three strains were Gram-stain-negative, aerobic and rod-shaped. Cells were motile by means of flagella. On the basis of the results of 16S rRNA gene sequence analysis, strains M65 T , M69 and JN25 showed the highest 16S rRNA gene sequence similarity to Henriciella algicola MCS27 T (98.8 %), followed by Henriciella marina DSM 19595 T (98.4 %), Henriciella barbarensis MCS23 T (98.4 %), Henriciella pelagia LA220 T (98.3 %), Henriciella aquimarina P38 T (98.1 %) and Henriciella litoralis SD10 T (97.8 %). The 16S rRNA gene sequence similarities among the isolates were 100 %. Phylogenetic analyses revealed that the isolates fell within a cluster comprising the Henriciella species and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between strain M65 T and the type strains of Henriciella species were 73.9-85.8 % and 19.9-22.4 %, respectively. The sole respiratory quinone detected in the three isolates was ubiquinone 10. The principal fatty acids were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ) and C 16 : 0 . The major polar lipids were glucuronopyranosyldiglyceride, monoglycosyldiglyceride and one unidentified glycolipid. The DNA G+C content was 61.3-61.4 mol%. Phylogenetic distinctiveness, chemotaxonomic differences, together with phenotypic properties, revealed that the isolates could be differentiated from the Henriciella species with validly published names. Therefore, it is proposed that strains M65 T , M69 and JN25 represent a novel species of the genus Henriciella , for which the name Henriciella mobilis sp. nov. (type strain, M65 T =CGMCC 1.15927 T =KCTC 52576 T ) is proposed.

A novel Gram-stain-negative, rod-shaped, yellow bacterium, designated as LB1R16 T , was isolated from the Laigu glacier on the Tibetan Plateau, PR China. Strain LB1R16 T was catalase-positive, oxidase-negative and grew at 0-28 °C, pH 6.0-8.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LB1R16 T belongs to the family Sphingosinicellaceae but formed an independent lineage. The highest level of 16S rRNA gene sequence similarities were found to Polymorphobacter arshaanensis DJ1R-1 T (95.24 %), Sphingoaurantiacus capsulatus YLT33 T (94.78 %) and Sandarakinorhabdus limnophila DSM 17366 T (94.67 %). The genomic DNA G+C content was 68.8 mol%. The main cellular fatty acids were summed feature 8 (C 18 : 1  ω 7 c /C 18 : 1  ω 6 c ), summed feature 3 (C 16 : 1  ω 7 c /C 16 : 1  ω 6 c ), C 16 : 0 and C 12 : 0 -OH. The respiratory quinone was ubiquinone-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid, one unidentified phospholipid and two unidentified polar lipids, which were different from the type strains of Polymorphobacter arshaanensis , Sphingoaurantiacus capsulatus and Sandarakinorhabdus limnophila . Based on a polyphasic approach, a novel species of a new genus, Glacieibacterium frigidum gen. nov., sp. nov., within the family Sphingosinicellaceae is proposed. The type strain is LB1R16 T (=CGMCC 1.11941 T =NBRC 113873 T ).

Elucidating the timescale of the evolution of Alphaproteobacteria, one of the most prevalent microbial lineages in marine and terrestrial ecosystems, is key to testing hypotheses on their co-evolution with eukaryotic hosts and Earth's systems, which, however, is largely limited by the scarcity of bacterial fossils. Here, we incorporate eukaryotic fossils to date the divergence times of Alphaproteobacteria, based on the mitochondrial endosymbiosis that mitochondria evolved from an alphaproteobacterial lineage. We estimate that Alphaproteobacteria arose ~1900 million years (Ma) ago, followed by rapid divergence of their major clades. We show that the origin of Rickettsiales, an order of obligate intracellular bacteria whose hosts are mostly animals, predates the emergence of animals for ~700 Ma but coincides with that of eukaryotes. This, together with reconstruction of ancestral hosts, strongly suggests that early Rickettsiales lineages had established previously underappreciated interactions with unicellular eukaryotes. Moreover, the mitochondria-based approach displays higher robustness to uncertainties in calibrations compared with the traditional strategy using cyanobacterial fossils. Further, our analyses imply the potential of dating the (bacterial) tree of life based on endosymbiosis events, and suggest that previous applications using divergence times of the modern hosts of symbiotic bacteria to date bacterial evolution might need to be revisited.

Strain BGMRC 2036 T was isolated from rhizosphere soil of Bruguiear gymnorrhiza collected from the Beibu Gulf of China. Optimum growth occurred at 28 °C, pH 7.0, and under the conditions of 3-5% (w/v) NaCl. The phylogenetic comparisons of 16S rRNA gene sequences displayed that strain BGMRC 2036 T was closely related to Martelella limonii NBRC109441 T (96.6% sequence similarity), M. mediterranea CGMCC 1.12224 T (96.5%), M. lutilitoris GH2-6 T (96.5%), M. radicis BM5-7 T (96.2%), and M. mangrove BM9-1 T (95.9%), M. suaedae NBRC109440 T (95.8%). The phylogenomic tree based on the up-to-date bacterial core gene set indicated that the strain BGMRC 2036 T form a clade formed with members of the genera Martelella. The major polar lipids include phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphotidylinositol, two unidentified phospholipids, and three unidentified ninhydrin positive phospholipids. The major respiratory quinone is Q-10, which is similar to those of genera Martelella. The main cellular fatty acids are C 18:1 ω7c, C 16:0 , and C 12:0 aldehyde. Genome sequencing revealed a genome size of 4.99 Mbp and a G + C content of 62.3 mol%. Pairwise comparison of the genomes of the new strain BGMRC 2036 T and the three reference strains M. endophytica YC 6887 T , M. mediterranea CGMCC 1.12224 T , and M. mangrovi USBA-857 indicated that gANI value was lower than 81% and a digital DNA-DNA hybridization value was lower than 27%. The strain BGMRC 2036 T possessed genes putatively encoding riboflavin synthesis and flavodoxin A polyphasic taxonomic study suggested that strain BGMRC 2036 T represented a novel species belonging to the genus Martelella, and it was named Martelella alba sp. nov. The type strain is BGMRC 2036 T (=KCTC 52121 T  =NBRC 111908 T ).

We isolated a novel strain, R1DC25 T , described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25 T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25 T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria . R1DC25 T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer , Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii , respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C 19 : 0 cyclo ω 8 c , a combination of C 18 : 1 ω 7 c and/or C 18 : 1 ω 6 c and C 16 : 0 . On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25 T (=KCTC 72348 T ;=JCM 33619 T ;=NCCB 100699 T ) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. ( Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi , of a mangrove).

We described the bacterial diversity of walnut grove soils under organic and conventional farming. The bacterial communities of rhizospheric and nonrhizospheric soils of pecan tree (Carya illinoensis K. Koch) were compared considering two phenological stages (sprouting and ripening). Sixteen operational taxonomic units (OTUs) were identified significantly more abundant according to the plant development, only one according to the farming condition, and none according to the soil origin. The OTUs specificaly abundant according to plant development included Actinobateria (2) and Betaproteobacteria (1) related OTUs more abundant at the sprouting stage, while at the fruit ripening (FR) stage the more abundant OTUs were related to Actinobacteria (6), Alphaproteobacteria (6), and unclassified Bacteria (1). The Gaiellaceae OTU18 (Actinobacteria) was more abundant under conventional farming. Thus, our study revealed that the plant development stage was the main factor shaping the bacterial community structure, while less influence was noticed for the farming condition. The bacterial communities exhibited specific metabolic capacities, a large range of carbon sources being used at the FR stage. The identified OTUs specifically more abundant represent indicators providing useful information on soil condition, potential tools for the management of soil bacterial communities., (© 2021 The Society for Applied Microbiology.)

A bacterial strain designated RZ02 T was isolated from surface seawater collected from the Yellow Sea in PR China and characterized by polyphasic taxonomy. Cells of strain RZ02 T were Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive rods forming ochre-pigmented colonies. Growth occurred at 7-36 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 1-5 % (optimum, 2 %) NaCl. The major cellular fatty acids (>10 %) of strain RZ02 T were summed feature 8 (C 18 : 1  ω 6 c and/or C 18 : 1  ω 7 c ), summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ) and C 16 : 0 . The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and sphingoglycolipid. The genome size of strain RZ02 T was 2.79 Mbp with a G+C content of 55.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RZ02 T was mostly related to Pontixanthobacter luteolus SW-109 T and Pontixanthobacter aestiaquae HDW-31 T (97.3 and 97.1% sequence similarity, respectively), and formed a phyletic lineage with members of the genus Pontixanthobacter . The phylogenetic analysis based on the up-to-date bacterial core gene sequences confirmed that strain RZ02 T clustered within the genus Pontixanthobacter . The average nucleotide identity and in silico DNA-DNA hybridization values between strain RZ02 T and P. luteolus SW-109 T and P. aestiaquae HDW-31 T were 72.8 and 72.9 % and 18.7 and 18.5%, respectively. Based on these evidences, strain RZ02 T is proposed to represent a novel species of the genus Pontixanthobacter under the name Pontixanthobacter rizhaonensis sp. nov. The type strain is RZ02 T (=KCTC 62828 T =MCCC 1K04521 T ). In addition, based on the results of whole genome analyses, proposals of Pseudopontixanthobacter gen. nov., Pseudopontixanthobacter confluentis comb. nov. and Pseudopontixanthobacter sediminis comb. nov. are also included.

The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades., (Copyright © 2021 Elsevier GmbH. All rights reserved.)

Magnetotactic bacteria (MTB) are diverse prokaryotes that produce magnetic nanocrystals within intracellular membranes (magnetosomes). Here, we present a large-scale analysis of diversity and magnetosome biomineralization in modern magnetotactic cocci, which are the most abundant MTB morphotypes in nature. Nineteen novel magnetotactic cocci species are identified phylogenetically and structurally at the single-cell level. Phylogenetic analysis demonstrates that the cocci cluster into an independent branch from other Alphaproteobacteria MTB, that is, within the Etaproteobacteria class in the Proteobacteria phylum. Statistical analysis reveals species-specific biomineralization of magnetosomal magnetite morphologies. This further confirms that magnetosome biomineralization is controlled strictly by the MTB cell and differs among species or strains. The post-mortem remains of MTB are often preserved as magnetofossils within sediments or sedimentary rocks, yet paleobiological and geological interpretation of their fossil record remains challenging. Our results indicate that magnetofossil morphology could be a promising proxy for retrieving paleobiological information about ancient MTB., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

A bisphenol A-degrading bacterium, designated as strain H4 T , was isolated from surface seawater, which was sampled from the Jiulong River estuary in southeast PR China. Strain H4 T is Gram-stain-negative, aerobic, short rod-shaped, lacking bacteriochlorophyll a, motile with multifibrillar stalklike fascicle structures and capable of degrading bisphenol A. Growth of strain H4 T was observed at 24-45 °C (optimum, 32 °C), at pH 5.5-9 (optimum, pH 7.0) and in 0-7 % NaCl (optimum, 2 %; w/v) . The 16S rRNA gene sequence of strain H4 T showed highest similarity to Croceicoccus pelagius Ery9 T (98.7 %), Croceicoccus sediminis (98.3 %), Croceicoccus naphthovorans PQ-2 T (98.1 %) and Croceicoccus ponticola GM-16 T (97.6 %), followed by Croceicoccus marinus E4A9 T (96.7 %) and Croceicoccus mobilis Ery22 T (96.0 %). Phylogenetic analysis revealed that strain H4 T fell within a clade comprising the type strains of Croceicoccus species and formed a phyletic line with them that was distinct from other members of the family Erythrobacteraceae . The sole respiratory quinone was quinone 10 (Q-10). The predominant fatty acids (>5 % of the total fatty acids) of strain H4 T were summed feature 8 (C 18 : 1  ω 6 c and/or C 18 : 1  ω 7 c ), summed feature 3 (C 16 : 1  ω 6 c and/or C 16 : 1  ω 7 c ), C 17 : 1  ω 6 c and C 14 : 0 2-OH. The genomic DNA G+C content was 62.8 mol%. In the polar lipid profile, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, two sphingoglycolipids and three unknown lipids were the major compounds. Based on the genotypic and phenotypic data, strain H4 T represents a novel species of the genus Croceicoccus , for which the name Croceicoccus bisphenolivorans sp. nov. is proposed. The type strain is H4 T (=DSM 102182 T =MCCC1 K02301 T ).

A prosthecate bacterial strain, designated G-192 T , was isolated from decaying biomass of a haloalkaliphilic cyanobacterium Geitlerinema sp. Z-T0701. The cells were aerobic, Gram-negative, non-endospore-forming and dimorphic, occurring either as sessile bacteria with a characteristic stalk or as motile flagellated cells. The strain utilized a limited range of substrates, mostly peptonaceous, but was able to degrade whole proteins. Growth occurred at 5-46 °C (optimum, 35-40 °C), pH 7.3-10.3 (optimum, pH 8.0-9.0), 0-14 % NaCl (v/w; optimum, 2.0-6.0 %, v/w). The G+C content of the genomic DNA of strain G-192 T was 66.8%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain G-192 T formed a distinct evolutionary lineage within the family Hyphomonadaceae . Strain G-192 T showed the highest 16S rRNA sequence similarity to Glycocaulis profundi ZYF765 T (95.2%), Oceanicaulis stylophorae GISW-4 T (94.2%) and Marinicauda salina WD6-1 T (95.5%). The major cellular fatty acids (>5% of the total) were C 18:1 ω 9 c , C 18:0 and 11-methyl-C 18:1 ω7 c . The major polar lipids were glycolipids and phospholipids. The only respiratory quinone was ubiquinone-10 (Q-10). Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain G-192 T represents a novel species of a new genus, for which the name Alkalicaulis satelles gen. nov., sp. nov. is proposed. The type strain is G-192 T (=VKM B-3306 T =KCTC 72746 T ). The strain is the first representative of the stalked bacteria associated with a haloalkaliphilic cyanobacterium. Based on phylogenomic indices and phenotypic data, it is proposed to evolve two novel families Maricaulaceae fam. nov. and Robiginitomaculaceae fam. nov. out of the current family Hyphomonadaceae . In addition, it is proposed to place the first two families in the novel order Maricaulales ord. nov. and novel order Hyphomonadales ord. nov. is proposed to accommodate the family Hyphomonadaceae .

A Gram-negative, dark orange-pigmented, aerobic, non-spore-forming, coccoid-shaped bacterium designated as ZS-1/3 T was isolated from a floating plastic litter (polypropylene straw) sample, collected from shallow seawater near the public beach of Laganas on Zakynthos island, Greece. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate is affiliated with the genus Parvularcula in the family Parvularculaceae . Its closest relatives are Parvularcula lutaonensis (98.09  %) and Parvularcula oceanus (95.89  %). The pH and temperature ranges for growth are pH 5-10 and 20-38 °C (optima, pH 7.0 and 28 °C). The predominant fatty acids are C 18 : 1  ω 7 c (56.84  %), C 16 : 0 (27.51  %), C 18 : 0 (2.25  %) and C 12 : 0 (1.42  %). The predominant respiratory quinone detected in strain ZS-1/3 T is quinone-10 (Q10); the majority of detected polar lipids are glycolipid. The DNA G+C content is 62.5  mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain ZS-1/3 T from other members of the genus Parvularcula . Thus, strain ZS-1/3 T is considered to represent a novel species of the genus, for which the name Parvularcula mediterranea . sp. nov. is proposed. The type strain is ZS-1/3 T (=NCAIM B 02654 T =CCM 9032 T ).

The elevated NH 3 -N and NO 2 -N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation ( p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio . Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

A Gram stain-negative, aerobic, non-motile, short, rod-shaped bacterial strain CAU 1482 T was isolated from coal mine wastewater in Hongcheon, Korea. It grew well at 30 °C, pH 8.5, 2% NaCl (w/v). 16S rRNA-based phylogeny indicated that CAU 1482 T forms a distinct lineage within Aureimonas with high similarity to Aureimonas frigidaquae CW5 T (98.2%), Aureimonas altamirensis S21B T (98.0%), and Aureimonas glaciei B5-2 T (96.3%). The predominant cellular fatty acids were C 18:1 2-OH, C 16:0 , C 18:1 ω7c, and/or C 18:1 ω6c (summed feature 8), with Q-10 as the major isoprenoid quinone. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified aminolipids, and three unidentified lipids. The 3.9-Mb genome included 8 contigs and 3599 protein-coding genes with a 56.7 mol% G + C content. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CAU 1482 T and closely related strains of A. frigidaquae CW5 T and A. altamirensis S21B T were 72.2‒72.4% and 18.7‒18.8%, respectively. These phenotypic, chemotaxonomic, and phylogenetic data support CAU 1482 T as a novel Aureimonas species, for which the name Aureimonas fodinaquatilis sp. nov. is proposed. The type strain is CAU 1482 T (= KCTC 62995 T  = NBRC 113692 T ).

A marine alphaproteobacterium, designated as strain GH3-10 T , was isolated from the rhizosphere mud of a halophyte ( Suaeda japonica ) collected at the seashore of Gangwha Island, Republic of Korea. The isolate was found to be Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive, non-motile, short rods and produced orange-coloured colonies. The 16S rRNA gene- and whole genome-based phylogenetic analyses exhibited that strain GH3-10 T belonged to the genus Aurantiacibacter and was most closely related to Aurantiacibacter atlanticus s21-N3 T (98.7 % 16S rRNA gene sequence similarity) and Aurantiacibacter marinus KCTC 23554 T (98.4 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unidentified lipid. The major fatty acids were C 18 : 1  ω 7 c , summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ) and C 18 : 1  ω 7 c 10-methyl. The DNA G+C content was 61.3 mol% (by genome). Average nucleotide identity and DNA-DNA relatedness values between the isolate and its phylogenetically closest relatives, together with phenotypic distinctness warranted the taxonomic description of a new species. On the basis of data obtained by a polyphasic approach, strain GH3-10 T (=KCTC 62379 T =JCM 32444 T ) represents a novel species of the genus Aurantiacibacter , for which the name Aurantiacibacter rhizosphaerae sp. nov. is proposed. According to phylogenetic coherence based on 16S rRNA genes and core genomes, it is also proposed that Erythrobacter suaedae Lee et al . 2019. and Erythrobacter flavus Yoon et al . 2003 be transferred to Aurantiacibacter suaedae comb. nov. and Qipengyuania flava comb. nov., respectively.

A Gram-stain-negative and aerobic bacterial strain, designated as JL3514 T , was isolated from surface water of the hydrothermal system around Kueishan Island. The isolate formed red colonies and cells were non-flagellated, rod-shaped and contained methanol-soluble pigments. Growth was observed at 10-50 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and in the presence of 0-9 % (w/v) NaCl (optimum, 2 %). Strain JL3514 T was positive for catalase and weakly positive for oxidase. Results of 16S rRNA gene sequence analyses showed highest similarities to species in the family Erythrobacteraceae , namely Croceibacterium atlanticum (96.1 %), Pelagerythrobacter marensis (96.0 %), Tsuneonella rigui (96.0 %) and Altericroceibacterium xinjiangense (96.0 %). Phylogenetic analysis based on core gene sequences revealed that the isolate formed a distinct branch with the related species and it had a lower average amino acid identity value than the suggested threshold for genera boundaries. The major fatty acids (>5 %) were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ), summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ), C 16 : 0 , C 17 : 1  ω 6 c , C 14 : 0 2-OH and C 12 : 0 . The dominant polar lipids comprised diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, two unidentified lipids and one unidentified phospholipid. The main respiratory quinones were ubiquinone-10 (95.7 %) and ubiquinone-9 (4.3 %). The DNA G+C content from the genome was 63.0 mol%. Based on the presented data, we consider strain JL3514 T to represent a novel genus of the family Erythrobacteraceae , with the name Pseudopontixanthobacter vadosimaris gen. nov., sp. nov. The type strain is JL3514 T (=KCTC 62623 T =MCCC 1K03561 T ).

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.

One motile strain designated, YIM DR1026 T was isolated from the roots of Psammosilene tunicoides collected from Gejiu, Yunnan province, China. The cells of strain YIM DR1026 T were Gram-negative and short-rod shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM DR1026 T was a member of the genus Aureimonas and closely related to Aureimonas rubiginis (96.7%). DNA-DNA relatedness values between strain YIM 1026 T and Aureimonas rubiginis BCRC 80440 T was 38.2 ± 1.5%. The ANI value between YIM DR1026 T and other Aureimonas members were below the cut-off level (95-96%) recommended as the average nucleotide identity (ANI) criterion for interspecies identity. Strain YIM DR1026 T grew at 4-30 °C (optimum 28 °C), pH 4.0-9.0 (optimum pH 6.0-7.0) and tolerated NaCl (w/v) up to 1% (optimum 0%). Q-10 was sole the respiratory ubiquinone present in YIM DR1026 T . Polar lipids of strain YIM DR1026 T were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, sulfoquinovosyldiacylglycerol, unidentified aminolipid and unidentified polar lipid. The genomic G + C content was 64.6 mol%. The major fatty acids were C 18:1 ω7c, C 16:0 and summed feature 3 (C 16:1ω 7c/C 16:1ω 6c). Based on phenotypic, phylogenetic, chemotaxonomic and genome comparison, strain YIM DR1026 T represents a novel species of the genus Aureimonas, for which the name Aureimonas psammosilene sp. nov. is proposed. The type strain is YIM DR1026 T (= KCTC 42691 T  = NBRC 112412 T ).

Strain MEBiC09520 T , which was isolated from a tidal sediment in Incheon, Korea, is a pale yellow, rod-shaped bacterium, cells of which are 0.4-0.5 µm in width and 1.5-2 µm in length. Strain MEBiC09520 T shared 95.17 and 92.57% 16S rRNA gene sequence similarity with Emcibacter nanhaiensis and E. congregatus , respectively. It grew optimally at pH 6.0, at 55 °C and with 2.5-3.5% (w/v) NaCl. Its polar lipid components included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), an unidentified phospholipid (PL), three unidentified aminolipids (ALs) and two unidentified lipids (L). The fatty acids C 16:0 , C 19:0 cyclo ω8 c , C 14:0 2-OH and summed feature 8 (C 18:1 ω7 c and/or C 18:1 ω6 c ) were predominantly present in its cell wall. Strain MEBiC09520 T was thermophilic, while E. nanhaiensis and E. congregatus were mesophilic. Although E. nanhaiensis showed no nitrate reduction activity, MEBiC09520 T and E. congregatus showed a positive reaction. These strains differed in carbohydrate utilization. In particular, E. congregatus was able to thrive on various carbohydrate substrates as compared to the other strains. The average nucleotide identity value was 69.92% between strain MEBiC09520 T and E. congregatus ZYL T , 70.38% between E. congregatus ZYL T and E. nanhaiensis HTCJW17 T , and 72.83% between strain MEBiC09520 and E. nanhaiensis HTCJW17 T . Considering these differences, strain MEBiC09520 T (=KCCM 43320 T =MCCC 1K03920 T ) is suggested to represent and novel species of a new genus, Luteithermobacter gelatinilyticus gen. nov., sp. nov., and E. congregatus should be reclassified as Paremcibacter congregatus gen. nov., comb. nov.

We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

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.

Priority pollutants such as polyethylene (PE) microplastic, lead (Pb 2+ ), and cadmium (Cd 2+ ) have attracted the interest of environmentalists due to their ubiquitous nature and toxicity to all forms of life. In this study, periphytic biofilms (epiphyton and epixylon) were used to bioremediate heavy metals (HMs) and to biodegrade PE under high (120,000 ppm) methane (CH 4 ) doses. Both periphytic biofilms were actively involved in methane oxidation, HMs accumulation and PE degradation. Epiphyton and epixylon both completely removed Pb 2+ and Cd 2+ at concentrations of 2 mg L -1 and 50 mg L -1 , respectively, but only partially removed these HMs at a relatively higher concentration (100 mg L -1 ). Treatment containing 12% 13 CH 4 proved to be most effective for biodegradation of PE. A synergistic effect of HMs and PE drastically changed microbial biota and methanotrophic communities. High-throughput 16S rRNA gene sequencing revealed that Cyanobacteria was the most abundant class, followed by Gammaproteobacteria and Alphaproteobacteria in all high-methane-dose treatments. DNA stable-isotope probing was used to label 13 C in a methanotrophic community. A biomarker for methane-oxidizing bacteria, pmoA gene sequence of a 13 C-labeled fraction, revealed that Methylobacter was most abundant in all high-methane-dose treatments compared to near atmospheric methane (NAM) treatment, followed by Methylococcus . Methylomonas , Methylocystis , Methylosinus, and Methylocella were also found to be increased by high doses of methane compared to NAM treatment. Overall, Cd +2 had a more determinantal effect on methanotrophic activity than Pb 2+ . Epiphyton proved to be more effective than epixylon in HMs removal and PE biodegradation. The findings proved that both epiphyton and epixylon can be used to bioremediate HMs and biodegrade PE as an efficient ecofriendly technique under high methane concentrations.