Acuticoccus yangtzensis gen. nov., sp. nov., a Novel Member in the Family Rhodobacteraceae, Isolated from the Surface Water of the Yangtze Estuary

Taklimakanibacter albus sp. nov., an Endophytic Bacterial Species Isolated from the Root of Paris polyphylla var. yunnanensis

A Gram-negative, white-pigment, rod-shaped bacterial strain YIM B02566T was isolated from the root of Paris polyphylla var. yunnanensis in China. Strain YIM B02566T exhibited optimal growth at 28 °C and pH 7.0 on Reasoner's 2A agar without NaCl supplementation. Phylogenetic analyses based on the 16S rRNA gene sequences and the concatenation of 433 single-copy orthologous genes revealed that strain YIM B02566T formed a distinct lineage in the genus Taklimakanibacter. The sequence similarity of the 16S rRNA gene between YIM B02566T and two known species of genus Taklimakanibacter were 99.12% (T. deserti SYSU D60010T) and 99.05% (T. lacteus SYSU D60012T), respectively. The principal fatty acids were C19:0 cyclo ω8c, C16:0, and summed feature 8. Strain YIM B02566T contained UQ-10 as the sole respiratory quinone. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, two unidentified aminolipids, and an unidentified polar lipid. The whole-genome analysis indicated that the genome size was 7.2 Mbp, and the genomic DNA G + C content was 62.9%. The digital DNA-DNA hybridization values between strain YIM B02566T and two Taklimakanibacter species were 24.50% (T. deserti SYSU D60010T) and 25.40% (T. lacteus SYSU D60012T). Meanwhile, the ANI and AAI values between strain YIM B02566T and its closest neighbours are well below the proposed thresholds for species determination. Therefore, based on polyphasic analysis, the isolate represents a novel species, for which the name Taklimakanibacter albus is proposed. The type strain is YIM B02566T (= CGMCC 1.18656T = JCM 34643T).

Long-term nitrogen fertilization and sweetpotato cultivation in the wheat-sweetpotato rotation system decrease alkaline phosphomonoesterase activity by regulating soil phoD-harboring bacteria communities

The alkaline phosphomonoesterase (ALP)-harboring community (phoD-harboring community) plays a crucial role in the conversion of organic phosphorus (P) into available P (AP). However, the response mechanisms of phoD-harboring communities to fertilization strategies, crop types, and their interactions within the wheat-sweetpotato rotation are poorly understood. A nine-year field experiment of different fertilization strategies was established under the wheat-sweetpotato rotation. After harvesting the crop, we collected soil samples without fertilization (CK), inorganic NK fertilization (NK), inorganic NPK fertilization (NPK), and a combined application of inorganic NPK and organic fertilizer (NPKM). We employed high-throughput sequencing and enzymology techniques to analyze the composition and functional activity of phoD-harboring bacterial communities as well as their correlation with soil physicochemical properties. The results showed that long-term nitrogen (N) fertilization, especially inorganic N, significantly reduced soil pH and ALP activity while increasing AP compared with CK. The AP content in sweetpotato season was significantly higher than that in wheat season. Inorganic N fertilization dramatically reshaped the communities of phoD-harboring bacteria and decreased diversity. The phoD-harboring bacterial communities in sweetpotato season were significantly different from those in wheat season. The N fertilization significantly reduced the relative abundance of Acuticoccus, Methylibium, Rhizobacter, and Roseivivax, which was positively correlated with ALP activity. These groups in sweetpotato season decreased significantly compared with wheat season. A structural equation model indicates that pH and AP play a significant role in regulating the phoD-harboring bacteria communities, ALP activity, and their interactions. We demonstrate that fertilization strategies and crop types have a substantial impact on the phoD-harboring bacteria communities and functions, which are closely linked to soil pH and AP levels. Our study highlights the detrimental effects of soil acidification resulting from inorganic N fertilization on P-cycling bacterial communities and functions. However, the combination of inorganic and organic fertilizer can mitigate these adverse effects.

Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench

A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.0-3.8 µm in size, designated as 960558^T, was isolated from sediment sampled in the Mariana Trench. Strain 960558^T grows at 4-37 °C (optimum, 28 °C), pH 6-7 (optimum, pH 7) and in the presence of 1-5 % (w/v) NaCl (optimum, 3 %). Strain 960558^T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558^T and members of the family Rhodobacteraceae by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558^T is Planktotalea lamellibrachiae JAM 119^T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C_16 : 0, 11-methyl C_18 : 1  ω7c and C_18 : 1  ω7c and/or C_18 : 1  ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558^T is 61 %. Average nucleotide identity and digital DNA-DNA hybridization results of strain 960558^T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558^T is considered to represent a novel genus and species within the family Rhodobacteraceae, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558^T (=KCTC 82619^T=MCCC 1K04727^T).

Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum

A 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing, Gram-stain-negative, strictly aerobic, non-motile, yellow-reddish, oval-shaped bacterial strain, designated M5D2P5^T, was isolated from a root of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, PR China. M5D2P5^T grew at 10-40 °C (optimum 30-35 °C), pH 5.0-10.0 (optimum pH 8.0) and with 0-7% NaCl (optimum 3.0 %). The strain was positive for catalase and oxidase. The phylogenetic trees based on 16S rRNA gene sequences indicated that M5D2P5^T clustered with Acuticoccus yangtzensis JL1095^T, and shared 98.0, 97.3, 97.2, 96.9 and less than 96.9 % 16S rRNA gene similarities to A. yangtzensis JL1095^T, Acuticoccus mangrovi B2012^T, Acuticoccus sediminis PTG4-2^T, Acuticoccus kandeliae J103^T, and all the other type strains, respectively. However, the phylogenomic tree showed it clustered with A. kandeliae J103^T. M5D2P5^T contained Q-10 as the major respiratory quinone, as well as two minor respiratory quinones, Q-7 and Q-8. Its major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified glycolipid, and four unidentified lipids. The genomic DNA G+C content was 66.5 %. The digital DNA-DNA hybridization score and the average nucleotide identity based on blast values of M5D2P5^T to A. yangtzensis JL1095^T, A. kandeliae J103^T, A. mangrovi B2012^T, and A. sediminis PTG4-2^T, were 20.8, 23.7, 20.7, and 21.5 %, and 73.3, 79.5, 74.4, and 73.7 %, respectively. The phylogenetic and phenotypic characteristics allowed the discrimination of M5D2P5^T from its phylogenetic relatives. The novel species Acuticoccus kalidii sp. nov. is therefore proposed, and the type strain is M5D2P5^T (=CGMCC 1.19149^T=KCTC 92132^T).

Acuticoccus mangrovi sp. nov., with an antibacterial property, isolated from mangrove sediment

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).

Propylenella binzhouense gen. nov., sp. nov. isolated from activated sludge, and proposal of Propylenellaceae fam. nov

A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped, and aerobic bacterial strain (designated L72^T) was isolated from propylene oxide saponification wastewater activated sludge obtained from a wastewater treatment facility in Binzhou (Shandong Province, PR China). Strain L72^T grew between 25 and 40 °C (optimum growth at 30 °C). The pH range for growth was between 6.0 and 8.0 (optimum growth at pH 7.0). The range of NaCl concentrations for the growth of strain L72^T was 0-3.0 % (w/v), with optimum growth at 1.0-2.0 % (w/v). The major cellular fatty acids of strain L72^T were C_19:0cyclo ω8c, C_18:1ω7c, iso-C_15:0, and anteiso-C_15:0. Strain L72^T contained Q-10 as the predominant respiratory quinone. The polar lipid profile was composed of Phosphatidylcholine, Glycolipid, Aminophospholipid, Phosphatidylethanolamine, Phosphatidylserine, Phosphatidyldimethylethanolamine, one unknown lipid (L) and two unidentified Phospholipids (PL). Genome sequencing revealed a genome size of 4,703,686 bp and a G + C content of 69.0 mol%. The 16S rRNA gene sequence similarities of strain L72^T with other species were less than 94%. Phylogenetic analyses based on 16S rRNA gene sequences and genome data, revealed that strain L72^T formed a distinct phylogenetic lineage within the order Hyphomicrobiales, separating them from members of all families. Strain L72^T showed 70.7% average nucleotide identity and 18.6% digital DNA-DNA hybridization identity with the closely related species Rhodoligotrophos defluvii. Based on the phenotypic, phylogenetic and chemotaxonomic data, a new family Propylenellaceae fam. nov. comprising the genus Propylenella gen. nov. and species Propylenella binzhouense sp. nov. is proposed. The type strain is L72^T (=  CCTCC AB 2019081^T  =  KCTC 72254^T).

Pseudopontixanthobacter vadosimaris gen. nov., sp. nov., isolated from shallow sea near Kueishan Island

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  ω7c and/or C_18 : 1  ω6c), summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_16 : 0, C_17 : 1  ω6c, 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).

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Acuticoccus sediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean and proposal of Acuticoccaceae fam. nov

A Gram-staining negative, aerobic, oval-shaped bacterium, designated strain PTG4-2^T, was isolated from deep-sea sediment of the Indian Ocean. Growth was observed with 1-9 % (w/v) NaCl with optimal growth with 3 %, at pH 6.0-10.0 with an optimum of pH 7.0, and at 4-40 °C with an optimum of 30 °C. Positive for catalase and oxidase. The results of a 16S rRNA gene sequence comparison indicated that PTG4-2^T was most closely related to Acuticoccus yangtzensis JL1095^T (97.3 %), followed by Acuticoccus kandeliae J103^T (96.5 %), all other species shared <93 % sequence similarity. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PTG4-2^T forms a distinct lineage within the genus Acuticoccus, and revealed that the genus Acuticoccus forms a novel family-level clade in the order Rhizobiales. The ANI and the DNA-DNA hybridization estimate values between PTG4-2^T and two type strains (A. yangtzensis JL1095^T and A. kandeliae J103^T) were 79.9-76.2 % and 23.1-20.8 %, respectively. PTG4-2^T contained Q-10 as the predominant ubiquinone. The principal fatty acids (>5 %) were summed feature 8 [C18 : 1ω7c/ω6c (72.2 %)], C18 : 0 (8.4 %), C20 : 1ω7c (6.4 %) and C16 : 0 (6.3 %). The polar lipids consisted of phosphatidylglycerol, three unidentified phospholipids, two unidentified glycolipids, one unidentified aminolipid and one unknown lipid. The DNA G+C content of PTG4-2^T is 69.2 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, PTG4-2^T should be classified as representing a novel species of the genus Acuticoccus, for which the name Acuticoccus sediminis sp. nov. is proposed, with the type strain PTG4-2^T (=MCCC 1A01274^T=KCTC 52323^T). In addition, a novel family, Acuticoccaceae fam. nov., is proposed to accommodate the genus Acuticoccus.

Aestuariivirga litoralis gen. nov., sp. nov., a proteobacterium isolated from a water sample, and proposal of Aestuariivirgaceae fam. nov

A Gram-stain-negative, non-motile, short rod and aerobic bacterium, designated strain SYSU M10001^T, was isolated from a water sample collected from the coastal region of Pearl River Estuary, Guangdong Province, PR China. Strain SYSU M10001^T showed optimal growth at 28 °C, pH 7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and concatenation of 20 protein markers revealed a distinct lineage for strain SYSU M10001^T in the order Rhizobiales. Strain SYSU M10001^T showed highest 16S rRNA gene sequence similarities to Hyphomicrobium nitrativorans NL23^T (91.1 %) and Hyphomicrobium hollandicum IFAM KB-677^T (91.1 %). The respiratory ubiquinone was Q-8. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and three unidentified lipids. The predominant cellular fatty acids identified were C19 : 0cyclo ω8c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content was determined to be 65.5 % (genome). On the basis of differences in the phenotypic, physiological and biochemical characteristics, and results of the phylogenetic analyses, strain SYSU M10001^T is proposed to represent a novel species in a novel genus for which the name Aestuariivirga litoralis gen. nov., sp. nov. The type strain of the type species Aestuariivirga litoralis is SYSU M10001^T (=NBRC 112960^T=KCTC 52945^T). Besides, the distinct phylogenetic lineage and the distinct chemotaxonomic profile among the families in the order Rhizobiales indicated that strain SYSU M10001^T should represent a new family for which the name Aestuariivirgaceae fam. nov. is proposed.

Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary

Acuticoccus yangtzensis JL1095^T is a proteobacterium from a genus belonging to the family Rhodobacteraceae; it was isolated from surface waters of the Yangtze Estuary, China. This strain displays the capability to utilize aromatic and simple carbon compounds. Here, we present the genome sequence, annotations, and features of A. yangtzensis JL1095^T. This strain has a genome size of 5,043,263 bp with a G + C content of 68.63%. The genome contains 4286 protein-coding genes, 56 RNA genes, and 83 pseudo genes. Many of the protein-coding genes were predicted to encode proteins involved in carbon metabolism pathways, such as aromatic degradation and methane metabolism. Notably, a total of 31 genes were predicted to encode form II carbon monoxide dehydrogenases, suggesting potential for carbon monoxide oxidation. The genome analysis helps better understand the major carbon metabolic pathways of this strain and its role in carbon cycling in coastal marine ecosystems.