Jae-Ho Joa

Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices

The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.

Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea

Two bacterial strains isolated from air samples, 5317S-33(T) and 5413S-11(T), were characterized by determining their phenotypic characteristics, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these isolates belonged to the genus Methylobacterium. Strain 5317S-33(T) was most closely related to Methylobacterium adhaesivum AR27(T) (97.9% sequence similarity). Strain 5413S-11(T) was most closely related to Methylobacterium fujisawaense DSM 5686(T) (97.3% sequence similarity), Methylobacterium oryzae CBMB20(T) (97.1% similarity) and Methylobacterium radiotolerans JCM 2831(T) (97.0% similarity). Cells of both strains were strictly aerobic, Gram-negative, motile and rod-shaped. The major fatty acid was C(18:1)omega7c. The G+C contents of the genomic DNA were 68.0 mol% for strain 5317S-33(T) and 73.2 mol% for strain 5413S-11(T). According to DNA-DNA hybridization data, strain 5317S-33(T) showed a level of DNA-DNA relatedness of 33 % with M. adhaesivum DSM 17169(T), and strain 5413S-11(T) showed low levels of DNA-DNA relatedness (<35%) with M. fujisawaense DSM 5686(T), M. oryzae CBMB20(T) and M. radiotolerans DSM 1819(T). On the basis of this polyphasic analysis, it was concluded that strains 5317S-33(T) and 5413S-11(T) represent two novel species within the genus Methylobacterium, for which the names Methylobacterium iners sp. nov. (type strain 5317S-33(T) =KACC 11765(T) =DSM 19015(T)) and Methylobacterium aerolatum sp. nov. (type strain 5413S-11(T) =KACC 11766(T) =DSM 19013(T)) are proposed.

Niabella soli sp. nov., isolated from soil from Jeju Island, Korea

A dark yellow-coloured bacterium, JS13-8(T), was isolated from a soil sample from Jeju Island, Republic of Korea. The cells were aerobic, Gram-negative, non-motile, short rods (0.5-0.7 x 0.8-1.4 microm). Growth occurred at 15-35 degrees C (optimally at 30 degrees C), at pH 5.0-8.0 (optimally at pH 6.0-7.0) and at 0-1 % NaCl (w/v). Flexirubin pigment was produced. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JS13-8(T) was closely related to Niabella aurantiaca KACC 11698(T) (95.0 % sequence similarity). The major respiratory quinone system was MK-7 and the predominant cellular fatty acids were iso-C(15 : 0), iso-C(15 : 1) G, iso-C(17 : 0) 3-OH and summed feature 3. The DNA G+C content was 45 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic data, strain JS13-8(T) represents a novel species of the genus Niabella, for which the name Niabella soli sp. nov. is proposed. The type strain is strain JS13-8(T) (=KACC 12604(T)=DSM 19437(T)).

Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea

Soil microorganisms play an essential role in soil ecosystem processes such as organic matter decomposition, nutrient cycling, and plant nutrient availability. The land use for greenhouse cultivation has been increasing continuously, which involves an intensive input of agricultural materials to enhance productivity; however, relatively little is known about bacterial communities in greenhouse soils. To assess the effects of environmental factors on the soil bacterial diversity and community composition, a total of 187 greenhouse soil samples collected across Korea were subjected to bacterial 16S rRNA gene pyrosequencing analysis. A total of 11,865 operational taxonomic units at a 97% similarity cutoff level were detected from 847,560 sequences. Among nine soil factors evaluated; pH, electrical conductivity (EC), exchangeable cations (Ca2+, Mg2+, Na+, and K+), available P2O5, organic matter, and NO3-N, soil pH was most strongly correlated with bacterial richness (polynomial regression, pH: R2 = 0.1683, P < 0.001) and diversity (pH: R2 = 0.1765, P < 0.001). Community dissimilarities (Bray-Curtis distance) were positively correlated with Euclidean distance for pH and EC (Mantel test, pH: r = 0.2672, P < 0.001; EC: r = 0.1473, P < 0.001). Among dominant phyla (> 1%), the relative abundances of Proteobacteria, Gemmatimonadetes, Acidobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were also more strongly correlated with pH and EC values, compared with other soil cation contents, such as Ca2+, Mg2+, Na+, and K+. Our results suggest that, despite the heterogeneity of various environmental variables, the bacterial communities of the intensively cultivated greenhouse soils were particularly influenced by soil pH and EC. These findings therefore shed light on the soil microbial ecology of greenhouse cultivation, which should be helpful for devising effective management strategies to enhance soil microbial diversity and improving crop productivity.

Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches

The microbiome in the rhizosphere–the region surrounding plant roots–plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner’s 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These results showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.

Mucilaginibacter ginsengisoli sp. nov. isolated from a ginseng-cultivated soil.

A dark-pink-coloured bacterial strain, B4Y-8T, was isolated from a soil cultivated with ginseng. The 16S rRNA gene sequence of this strain showed highest similarity with Mucilaginibacter litoreus BR-18T (96.8 %), Mucilaginibacter lutimaris BR-3T (96.6 %) and Mucilaginibacter defluvii A5T (96.2 %) among the type strains of species of the genus Mucilaginibacter. Strain B4Y-8T was a strictly aerobic, Gram-stain-negative, non-motile, short-rod-shaped bacterium producing a large amount of extracellular polymeric substance. The strain grew at 10-35 °C (optimum, 25 °C), at pH 3.0-11.0 (optimum, pH 7.0) and in the presence of 0-1 % (w/v) NaCl (optimum, 0 %). The DNA G+C content of strain B4Y-8T was 49.0 mol%. It contained menaquinone 7 (MK-7) as the major isoprenoid quinone, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0 as the major fatty acids. On the basis of evidence from the present polyphasic taxonomic study, strain B4Y-8T should be classified as representing a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter ginsengisoli sp. nov. is proposed. The type strain is B4Y-8T ( = KACC 18152T = JCM 30759T).

Chitinophaga rhizosphaerae sp. nov., isolated from rhizosphere soil of a tomato plant

An aerobic, Gram-stain-negative, non-spore-forming, non-flagellated, rod-shaped or filamentous bacterial strain, T16R-86T, was isolated from rhizosphere of a tomato plant collected from a farm on Buyeo-gun, Chungcheongnam-do, South Korea. It grew at the temperature range 10-37 °C (optimum, 28 °C) and pH range 6.0-9.0 (optimum, pH 7.0), and tolerated up to 2 % (w/v) NaCl. According to 16S rRNA gene sequence analysis, strain T16R-86T shared the highest similarity with Chitinophaga barathri YLT18T (96.8 %) and C. pinensis DSM 2588T (96.7 %), forming a subcluster with C. barathri YLT18T, C. cymbidii R156-2T and C. niabensis JS13-10T in the phylogenetic tree. The major fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone MK-7. Polar lipids were phosphatidylethanolamine, five unknown aminolipids, an unknown aminophospholipid, one unknown phospholipid and two unknown lipids. The DNA G+C content was 53.6 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain T16R-86T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga rhizosphaerae sp. nov. is proposed. The type strain is T16R-86T (=KACC 18790T=JCM 31600T).

Soil Dehydrogenase Activity and Microbial Biomass C in Croplands of JeJu Province

This study was carried out to evaluate the soil dehydrogenase activity and microbial biomass C with soil type and land use in cropland of JeJu region. Soil chemical properties, dehydrogenase activity, and microbial biomass C were analyzed after sampling from upland (50 sites), orchard (50 sites), paddy (30 sites), horticultural facility (30 sites) in March. Average pH values was at 6.3 in upland soil, however soil chemical properties showed a large spatial variations in both orchard and horticultural facility soil. The Zn and Cu contents increased by the continuous application of pig manure compost in some citrus orchard soil. Soil dehydrogenase activity and microbial biomass C were higher in non-volcanic ash than in volcanic ash soil regardless of land use type. Soil dehydrogenase activity was two to four times higher in upland than in the others. It was at 38.7 ug TPF in non-volcanic ash of upland soil. Microbial biomass C content was very high in horticultural facility soil and it showed at 216.8 in non-volcanic ash. Soil dehydrogenase activity showed a positive correlation with organic matter (=0.59), Zn (=0.65), and Cu (=0.66) in non-volcanic ash horticultural facility soil. There was a negative correlation (=0.57) between soil organic matter and dehydrogenase activity in volcanic ash upland soil.

Effect of Temperature Condition on Nitrogen Mineralization and Soil Microbial Community Shift in Volcanic Ash Soil

This study was carried out to evaluate effect of temperature condition on nitrogen mineralization of organic matter, distribution of microbial group by PLFA profiles, and soil microbial community structure in volcanic ash soil. Dried soil 30 g mixed well each 2 g of pellet (OFPE) organic fertilizers, pig manure compost (PMC), and food waste compost (FWC). And then had incubated at , , and , respectively. Nitrogen mineralization rate increased with increasing temperature and that was in the order of FWC>OFPE>PMC. Distribution ratio of microbial group by PLFA profiles were different significantly caused by incubation temperature and the type of organic matter. As incubating time passed, density of microbial group decreased gradually. The Gram-bacteria PLFA/Gram+ bacteria PLFA, Fungi PLFA/Bacteria PLFA, and Unsaturated PLFA/saturated PLFA ratios were decreased according to the increasing temperature gradually. But cy19:0/ ratio increased both FWC and PMC treatment. Principal component analysis using PLFA profiles showed that microbial community structure made up clearly at both 75 days () and 270 days () by temperature factor. As incubating time passed, microbial community structure shifted gradually.

Plant growth and fruit quality as affected by canopy locations in ‘Shiranuhi’ mandarin

Fruit quality (soluble solids and acidity) and growth properties of fruiting branches in different canopy positions (upper, middle, and lower) of ‘Shiranuhi’ mandarin [(C. unshiu × C. sinensis) × C. reticulate] trees were determined during fruit maturation. Length, diameter, and number of leaves per fruiting branch increased in order from the upper, through the middle, to the lower parts of the canopy. Fruit diameter, fruit weight, pulp weight and pulp thickness were also highest in the upper part. Transverse sections of stem end protrusions in fruit from the upper, middle, and lower parts of the tree canopy were 37.3 ± 2.3 mm, 33.2 ± 0.2 mm and 32.1 ± 0.4 mm, respectively. Soluble solid content increased during fruit maturation at all locations within the canopy and was highest in the upper part. Likewise, acid content decreased with fruit maturity and was lowest in the lower part. These results suggested that harvesting be staggered starting with fruit from the upper part of the canopy as part of crop management in ‘Shiranuhi’ mandarin for direct effect on fruit quality.