Genotypic Variation of Endophytic Nitrogen-Fixing Activity and Bacterial Flora in Rice Stem Based on Sugar Content

Enhancement of the nitrogen-fixing ability of endophytic bacteria in rice is expected to result in improved nitrogen use under low-nitrogen conditions. Endophytic nitrogen-fixing bacteria require a large amount of energy to fix atmospheric nitrogen. However, it is unknown which carbon source and bacteria would affect nitrogen-fixing activity in rice. Therefore, this study examined genotypic variations in the nitrogen-fixing ability of rice plant stem as affected by non-structural carbohydrates and endophytic bacterial flora in field-grown rice. In the field experiments, six varieties and 10 genotypes of rice were grown in 2017 and 2018 to compare the acetylene reduction activity (nitrogen-fixing activity) and non-structural carbohydrates (glucose, sucrose, and starch) concentration in their stems at the heading stage. For the bacterial flora analysis, two genes were amplified using a primer set of 16S rRNA and nitrogenase (NifH) gene-specific primers. Next, acetylene reduction activity was correlated with sugar concentration among genotypes in both years, suggesting that the levels of soluble sugars influenced stem nitrogen-fixing activity. Bacterial flora analysis also suggested the presence of common and genotype-specific bacterial flora in both 16S rRNA and nifH genes. Similarly, bacteria classified as rhizobia, such as Bradyrhizobium sp. (Alphaproteobacteria) and Paraburkholderia sp. (Betaproteobacteria), were highly abundant in all rice genotypes, suggesting that these bacteria make major contributions to the nitrogen fixation process in rice stems. Gammaproteobacteria were more abundant in CG14 as well, which showed the highest acetylene reduction activity and sugar concentration among genotypes and is also proposed to contribute to the higher amount of nitrogen-fixing activity.

Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from oil reservoir water

A novel Gram-staining-negative, spiral-shaped bacterium, designated strain 64-1^T, was isolated from oil reservoir water collected from Liaohe oilfield, north-eastern China. Growth occurred at 15-55 °C and pH 6.0-10.0. The sole respiratory quinone was Q-10. The predominant cellular fatty acids were summed feature 8 (C_18 : 1  ω7c /C_18 : 1  ω6c), C_16 : 0 and C_19 : 0 cyclo ω8c. The polar lipids consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), an unidentified aminophospholipid (UAPL), an unidentified aminolipid (UAL) and two unidentified polar lipids (UPL). The genomic DNA G+C content of strain 64-1^T was 64.5 mol%. Strain 64-1^T shared the highest 16S rRNA gene sequence similarities with Phaeospirillum chandramohanii JA145^T (92.0 %) and Telmatospirillum siberiense 26-4b1^T (91.8 %). In the phylogenetic trees, the strain constituted a sub-cluster within the family Rhodospirillaceae. Based on the results of morphological, physiological, biochemical and phylogenetic analysis, strain 64-1^T represents a new species of a novel genus within the family Rhodospirillaceae, for which the name Oleiliquidispirillum nitrogeniifigens gen. nov., sp. nov. is proposed. The type strain is 64-1^T (=CGMCC 1.16798^T=LMG 31399^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.

Hypericibacter terrae gen. nov., sp. nov. and Hypericibacter adhaerens sp. nov., two new members of the family Rhodospirillaceae isolated from the rhizosphere of Hypericum perforatum

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum. Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913^T and R5959^T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C_19 : 0 cyclo ω8c and C_16 : 0; in addition, C_18 : 1ω7c was also found as a predominant fatty acid in strain R5913^T. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913^T and R5959^T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656^T, Dongia mobilis CGMCC 1.7660^T, Dongia soli D78^T and Dongia rigui 04SU4-P^T. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae, for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913^T=DSM 109816^T=CECT 9472^T) and Hypericibacter adhaerens sp. nov. (type strain R5959^T=DSM 109817^T=CECT 9620^T).

Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family

BACKGROUND

Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive.

RESULTS

We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, iron homeostasis and DNA repair system genes. Lastly, phylogenomic analysis showed that MTB cluster closely with phototrophic bacteria in this family. One photoheterotrophic genus, Phaeospirillum, clustered within and displays high genomic similarity with Magnetospirillum. Moreover, the phylogenetic tree topologies of magnetosome synthesis genes in MTB and photosynthesis genes in phototrophic bacteria from the Rhodospirillaceae family were reasonably congruent with the phylogenomic tree, suggesting that these two traits were most likely vertically transferred during the evolution of their lineages.

CONCLUSION

Our new genomic data indicate that MTB and phototrophic bacteria within the family Rhodospirillaceae possess diversified photoreceptors that may be responsible for phototaxis. Their genomes also contain comprehensive stress response genes to mediate the negative effects caused by illumination. Based on phylogenetic studies, most of MTB and phototrophic bacteria in the Rhodospirillaceae family evolved vertically with magnetosome synthesis and photosynthesis genes. The ancestor of Rhodospirillaceae was likely a magnetotactic phototrophic bacteria, however, gain or loss of magnetotaxis and phototrophic abilities might have occurred during the evolution of ancestral Rhodospirillaceae lineages.

Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake

A bacterial strain designated LTC-2T was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2T were Gram-reaction-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2T forms a distinct lineage with respect to closely related genera in the family Rhodospirillaceae , most closely related to the genera Elstera and Dongia , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94 %. On the basis of the genotypic and phenotypic data, strain LTC-2T represents a novel genus and species of the family Rhodospirillaceae , for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2T ( = BCRC 80445T = LMG 26999T = KCTC 32017T).

Ciceribacter lividus gen. nov., sp. nov., isolated from rhizosphere soil of chick pea (Cicer arietinum L.)

The taxonomic position of strain MSSRFBL1(T), isolated from chickpea rhizosphere soil from Kannivadi, India, was determined. Strain MSSRFBL1(T) formed bluish black colonies, stained Gram-negative and was motile, aerobic, capable of fixing dinitrogen, oxidase-negative and catalase-positive. Q-10 was the major respiratory quinone. Major fatty acids of strain MSSRFBL1(T) were C18 : 1ω7c and C19 : 0cycloω8c. Minor amounts of C18 : 0, C12 : 0, C14 : 0 3-OH, C18 : 0 3-OH, C16 : 0, C16 : 1ω6c/C16 : 1ω7c, C17 : 0 3-OH and C20 : 1ω7c were also present. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine and two unidentified glycolipids. Bacteriohopane derivatives (BHD1 and 2), diplopterol, diploptene, bishomohopanediol, adenosylhopane and 2β-methyl bacteriohopanetetrol were the major hopanoids of strain MSSRFBL1(T). The genomic DNA G+C content was 71 mol%. EzTaxon-e-based blast analysis of the 16S rRNA gene indicated the highest similarity of strain MSSRFBL1(T) to Ensifer adhaerens LMG 20216(T) (97.3 %) and other members of the genus Ensifer (<96.9 %) in the family Rhizobiaceae of the class Alphaproteobacteria. However, phylogenetic analysis based on 16S rRNA, recA, thrC and dnaK gene sequences showed distinct out-grouping from the recognized genera of the family Rhizobiaceae. Based on phenotypic, genotypic and chemotaxonomic characters, strain MSSRFBL1(T) represents a novel species in a new genus in the family Rhizobiaceae for which the name Ciceribacter lividus gen. nov., sp. nov. is proposed. The type strain of Ciceribacter lividus is MSSRFBL1(T) ( = DSM 25528(T) = KCTC 32403(T)).