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- Monthly distribution of ammonia-oxidizing microbes in a tropical bay
- Tie-Qiang Mao , Yan-Qun Li , Hong-Po Dong , Wen-Na Yang , Li-Jun Hou
- J. Microbiol. 2021;59(1):10-19. Published online November 17, 2020
- DOI: https://doi.org/10.1007/s12275-021-0287-5
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Abstract
- Ammonia oxidation, performed by ammonia-oxidizing archaea
(AOA) and bacteria (AOB), plays a critical role in the cycle
of nitrogen in the ocean. For now, environmental variables
controlling distribution of ammonia-oxidizing microbes are
still largely unknown in oceanic environments. In this study,
we used real-time quantitative PCR and high-throughput sequencing
methods
to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17– 20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17–20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.
- Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum)
- Shin Ae Lee , Tae-Wan Kim , Mee-Kyung Sang , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon
- J. Microbiol. 2020;58(10):832-840. Published online September 29, 2020
- DOI: https://doi.org/10.1007/s12275-020-0258-2
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Abstract
- Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15–40°C, pH 6.0–9.0, and 0–3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10–37°C, pH 6.0– 8.0, and 0–1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso- C15:0, and iso-C16:0. The polar lipids of strain 12200R- 189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R- 189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).
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