- Effects of diet type, developmental stage, and gut compartment in the gut bacterial communities of two Cerambycidae species (Coleoptera)
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Jeong Myeong Kim , Min-Young Choi , Jae-Woo Kim , Shin Ae Lee , Jae-Hyung Ahn , Jaekyeong Song , Seong-Hyun Kim , Hang-Yeon Weon
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J. Microbiol. 2017;55(1):21-30. Published online December 30, 2016
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DOI: https://doi.org/10.1007/s12275-017-6561-x
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The gut bacterial community of wood-feeding beetles has
been examined for its role on plant digestion and biocontrol
method development. Monochamus alternatus and Psacothea
hilaris, both belonging to the subfamily Lamiinae, are woodfeeding
beetles found in eastern Asia and Europe and generally
considered as destructive pests for pine and mulberry
trees, respectively. However, limited reports exist on the gut
bacterial communities in these species. Here, we characterized
gut bacterial community compositions in larva and imago of
each insect species reared with host tree logs and artificial
diets as food sources. High-throughput 454 pyrosequencing
of bacterial 16S rRNA gene revealed 225 operational taxonomic
units (OTUs) based on a 97% sequences similarity cutoff
from 138,279 sequence reads, the majority of which were
derived from Proteobacteria (48.2%), Firmicutes (45.5%), and
Actinobacteria (5.2%). The OTU network analysis revealed
7 modules with densely connected OTUs in specific gut samples,
in which the distributions of Lactococcus-, Kluyvera-,
Serratia-, and Enterococcus-related OTUs were distinct between
diet types or developmental stages of the host insects.
The gut bacterial communities were separated on a detrended
correspondence analysis (DCA) plot and by c-means fuzzy
clustering analysis, according to diet type. The results from
this study suggest that diet was the main determinant for gut
bacterial community composition in the two beetles.
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- Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea
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Jeong Myeong Kim , An-Sung Roh , Seung-Chul Choi , Eun-Jeong Kim , Moon-Tae Choi , Byung-Koo Ahn , Sun-Kuk Kim , Young-Han Lee , Jae-Ho Joa , Seong-Soo Kang , Shin Ae Lee , Jae-Hyung Ahn , Jaekyeong Song , Hang-Yeon Weon
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J. Microbiol. 2016;54(12):838-845. Published online November 26, 2016
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DOI: https://doi.org/10.1007/s12275-016-6526-5
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Abstract
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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.
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- Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches
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Shin Ae Lee , Jiyoung Park , Bora Chu , Jeong Myeong Kim , Jae-Ho Joa , Mee Kyung Sang , Jaekyeong Song , Hang-Yeon Weon
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J. Microbiol. 2016;54(12):823-831. Published online November 26, 2016
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DOI: https://doi.org/10.1007/s12275-016-6410-3
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Abstract
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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 culturedependent
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.
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International Journal of Systematic and Evolutionary Microbiology
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- Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices
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Jae-Hyung Ahn , Shin Ae Lee , Jeong Myeong Kim , Myung-Sook Kim , Jaekyeong Song , Hang-Yeon Weon
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J. Microbiol. 2016;54(11):724-731. Published online October 29, 2016
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DOI: https://doi.org/10.1007/s12275-016-6463-3
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1,003
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Abstract
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Fertilization and the response of the soil microbial community
to the process significantly affect crop yield and the environment.
In this study, the seasonal variation in the bacterial
communities in rice field soil subjected to different
fertilization treatments for more than 50 years was investigated
using 16S rRNA sequencing. The simultaneous application
of inorganic fertilizers and rice straw compost (CAPK)
maintained the species richness of the bacterial communities
at levels higher than that in the case of non-fertilization (NF)
and application of inorganic fertilizers only (APK) in the initial
period of rice growth. The seasonal variation in the bacterial
community structure in the NF and APK plots showed
cyclic behavior, suggesting that the effect of season was important;
however, no such trend was observed in the CAPK
plot. In the CAPK plot, the relative abundances of putative
copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria
were higher and those of putative oligotrophs such
as Acidobacteria and Plactomycetes were lower than those in
the other plots. The relative abundances of organotrophs with
respiratory metabolism, such as Actinobacteria, were lower
and those of chemoautotrophs that oxidize reduced iron and
sulfur compounds were higher in the CAPK plot, suggesting
greater carbon storage in this plot. Increased methane emission
and nitrogen deficiency, which were inferred from the
higher abundances of Methylocystis and Bradyrhizobium in
the CAPK plot, may be a negative effect of rice straw application;
thus, a solution for these should be considered to increase
the use of renewable resources in agricultural lands.
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- Siphonobacter intestinalis sp. nov., a bacterium isolated from the feces of Pseudorhynchus japonicus
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Shin Ae Lee , Jeong Myeong Kim , Jae-Hyung Ahn , Jae-Ho Joa , Soo-Jin Kim , Mee-Kyung Sang , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon
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J. Microbiol. 2016;54(11):709-712. Published online October 29, 2016
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DOI: https://doi.org/10.1007/s12275-016-6451-7
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934
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3
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Abstract
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Strain 63MJ-2T was isolated from the feces of broad-winged
katydid (Pseudorhynchus japonicus) collected in Korea. The
16S rRNA gene sequence of this strain showed the highest
sequence similarity with that of Siphonobacter aquaeclarae
P2T (96.1%) and had low similarities (below 86.3%) with those
of other members of family ‘Flexibacteraceae’. The strain
63MJ-2T is a strictly aerobic, Gram-stain-negative, non-motile,
rod-shaped bacterium. The strain grew at 4–35°C (optimum,
25–30°C), pH of 5.0–9.0 (optimum, 6.0–7.0), and
0–2.0% (optimum, 1.0–2.0) (w/v) NaCl. The DNA G+C content
of strain 63MJ-2T was 43.5 mol%. The major fatty acids
were C16:1 ω5c (42.5%), iso-C17:0 3-OH (18.7%), and summed
feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c, 18.0%). The major
menaquinone was MK-7 and polar lipids were phosphatidylethanolamine,
six unknown aminolipids, and five unknown
lipids. Based on the evidence from our polyphasic
taxonomic study, we conclude that strain 63MJ-2T should be
classified as a novel species of the genus Siphonobacter, and
propose the name Siphonobacter intestinalis sp. nov. The
type strain is 63MJ-2T (=KACC 18663T =NBRC 111883T).
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Citations
Citations to this article as recorded by 
- Notification of changes in taxonomic opinion previously published outside the IJSEM: List of Changes in Taxonomic Opinion no. 43
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2026;[Epub] CrossRef - Validation List no. 227: valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2026;[Epub] CrossRef -
Siphonobacter curvatus sp. nov., isolated from a freshwater river
Yunho Lee, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology
.2018; 68(6): 1925. CrossRef
- Virgibacillus xinjiangensis sp. nov., Isolated from a Salt Lake of Xin-jiang Province in China
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Che Ok Jeon , Jeong Myeong Kim , Dong-Jin Park , Li-Hua Xu , Cheng-Lin Jiang , Chang-Jin Kim
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J. Microbiol. 2009;47(6):705-709. Published online February 4, 2010
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DOI: https://doi.org/10.1007/s12275-009-0107-9
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793
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8
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A strictly aerobic Gram-positive, moderately halophilic spore forming bacterium, designated strain SL6-1T, was isolated from a salt lake in Xin-jiang province, China. Growth of strain SL6-1T was observed at NaCl concentrations of 0~20% (w/v) (the optimum being 5~7%, w/v). The peptidoglycan type of strain SL6-1T was A1γ-meso-diaminopimelic acid and its major cellular fatty acids were iso-C14:0 and iso-C16:0 and anteiso-C15:0. The major respiratory isoprenoid quinone was MK-7 and the G+C content of the genomic DNA was 44.5 mol%. The major cellular phospholipids were phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL6-1T formed a phylogenetic lineage within the genus Virgibacillus. Based on 16S rRNA gene sequence similarity, the strain was most closely related to Virgibacillus olivae E308T, Virgibacillus kekensis YIM kkny16T, Virgibacillus marismortui DSM 12325T with 97.1%, 97.1%, and 97.0% gene sequence similarities, respectively and the sequence similarities to other related taxa were less than 96.7%. The DNA relatedness values between strain SL6-1T and V. olivae E308T, V. kekensis YIM kkny16T, V. marismortui DSM 12325T were 16.7%, 51.0%, and 22.8%, respectively. On the basis of physiological, biochemical and phylogenetic properties, strain SL6-1T represents a novel species, for which the name Virgibacillus xinjiangensis sp. nov. is proposed. The type strain is SL6-1T (=KCTC 13128T =DSM 19031T).
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International Journal of Systematic and Evolutionary Microbiology
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Francisco J. Deive, Ana Rodríguez, Adélia Varela, Cátia Rodrígues, Maria C. Leitão, Jos A. M. P. Houbraken, Ana B. Pereiro, María A. Longo, M. Ángeles Sanromán, Robert A. Samson, Luís Paulo N. Rebelo, Cristina Silva Pereira Green Chemistry.2011; 13(3): 687. CrossRef - List of new names and new combinations previously effectively, but not validly, published
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