• Asian-Australasian Journal of Animal Sciences
• /
• v.22 no.6
• /
• pp.900-905
• /
• 2009

We analyzed succession of the bacterial communities during composting of animal manure in three individual facilities. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) targeting for the bacterial 16S rRNA gene were used to clarify the changes of bacterial community throughout each composting process. Our study revealed that the bacterial community structures differed during the composting process. The bacterial community in composting of facility A showed little change throughout the process. In the compost sample from facility B, its community had a small shift as the temperature increased. In compost from facility C, the temperature dynamically changed; it was shown that various bacterial communities appeared and disappeared as follows: in the initial phase, the members of phylum Bacteroidetes dominated; in the thermophilic phase, some bacteria belonging to phylum Firmicutes increased; towards the end, the community structure consisted of three phyla, Bacteroidetes, Firmicutes, and Proteobacteria. This study provides some information about the bacterial community actually present in field-scale composting with animal manure.

• The Plant Pathology Journal
• /
• v.34 no.4
• /
• pp.341-346
• /
• 2018

The microbiome makes a significant contribution to plant health and endophytes may generate positive effects for the host. However, there is a limited knowledge available concerning the kiwifruit endophyte. Therefore, we discuss endophyte microbiome community structures among the kiwifruit cultivars. Total reads numbered 17620 in cv. Hayward, 11515 in cv. Haegeum and 13613 in cv. Jecygold. The number of OTUs was follows: 112 in cv. Hageum; and 87 in cvs. Hayward and Jecygold. Most of the identified OTUs were phylum Proteobacteria and it emerged that Actinobacteria, Firmicute and Bacteroidetes were mainly present. While the largest difference in Proteobacteria content is between cv. Haegeum and cv. Jecygold, they shared more OTUs than cv. Hayward. As well, this study revealed the presence of remarkably dominated OTU of Pseudomonas spp. in kiwifruit sap regardless of cultivars. To the best of our knowledge, this study is the first tone to investigate the kiwifruit endophyte-microbiome community.

• The Plant Pathology Journal
• /
• v.35 no.4
• /
• pp.362-371
• /
• 2019

Plant phenotype is affected by a community of associated microorganisms which requires dissection of the functional fraction. In this study, we aimed to culture the functionally active fraction of an upland soil microbiome, which can suppress tomato bacterial wilt. The microbiome fraction (MF) from the rhizosphere of Hawaii 7996 treated with an upland soil or forest soil MF was successively cultured in a designed modified M9 (MM9) medium partially mimicking the nutrient composition of tomato root exudates. Bacterial cells were harvested to amplify V3 and V4 regions of 16S rRNA gene for QIIME based sequence analysis and were also treated to Hawaii 7996 prior to Ralstonia solanacearum inoculation. The disease progress indicated that the upland MM9 $1^{st}$ transfer suppressed the bacterial wilt. Community analysis revealed that species richness was declined by successive cultivation of the MF. The upland MM9 $1^{st}$ transfer harbored population of phylum Proteobacteria (98.12%), Bacteriodetes (0.69%), Firmicutes (0.51%), Actinobacteria (0.08%), unidentified (0.54%), Cyanobacteria (0.01%), FBP (0.001%), OD1 (0.001%), Acidobacteria (0.005%). The family Enterobacteriaceae of Proteobacteria was the dominant member (86.76%) of the total population of which genus Enterobacter composed 86.76% making it a potential candidate to suppress bacterial wilt. The results suggest that this mixed culture approach is feasible to harvest microorganisms which may function as biocontrol agents.

• Weed & Turfgrass Science
• /
• v.4 no.2
• /
• pp.124-128
• /
• 2015

Large patch, caused by Rhizoctonia solani AG2-2 IV, is a soil-born disease that is the most important of warm season turfgrass such as zoysia and Bermuda grass. This study was conducted to analysis of the soil microbial community structure on large patch. Center of the large patch (CLC), edge (CLE) and healthy (CLH) part of microbial communities were examined using metagenomics in Phylum level. Distribution trends of the rhizosphere microorganisms were similar to the order Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes, Gemmatimonadetes, Nitrospira, Cyanobactria and Verrucomicrobia in soil collections. Contrastively Actinobacteria was more 56% abundant in healthy part soil (16%) than in the center (9.28%) or edge (10.84%) parts. Taxonomic distributions were compared among the CLC, CLE and CLH, total 6,948 OTUs were detected in the CLC, 6,505 OTUs for the CLE and 5,537 OTUs were detected in the CLE. Distributions of Actinobacteria OTUs were appeared 615 OTUs in the CLC, 709 OTUs in the CLE and 891 OTUs in the CLH. Among Actinobacteria, 382 OTUs were overlapped in the all soils. Not matched OTUs of CLH (286 OTUs) was detected 23 times higher than CLC (91 OTUs) and CLE (126 OTUs).

• International Journal of Industrial Entomology and Biomaterials
• /
• v.39 no.2
• /
• pp.45-53
• /
• 2019

The popularity of keeping stag beetles (Dorcus titanus castanicolor Motschulsky 1861, Coleoptera: Lucanidae) as pets has increased. Consistent with the rise in the number of insect farms using these beetles, the number of contaminated or diseased D. titanus castanicolor has also increased. This investigation was conducted to analyze the cause of D. titanus castanicolor disease. The contaminated larvae of D. titanus castanicolor showed Allomyrina nudivirus infection symptoms similar to those of Allomyrina nudivirus infection. However, the disease carried by of D. titanus castanicolor is not derived from the virus infecting Allomyrina, as determined by PCR. Our study revealed that the major gut microbes of infectious D. titanus castanicolor belonged to the phylum Proteobacteria, and specifically, Pseudomonas knackmussi (Symptom 1 - 39.62% to Symptom 2 - 41.50% to Symptom 3 - 76.76% as the disease progressed severely) and Citrobacter koseri (Symptom 1 - 1.48% to Symptom 2 - 6.04% to Symptom 3 - 6.16% as the disease progressed severely) were detected. Additionally, a high proportion of larvae from the uninfected group were found to harbor bacteria belonging to the phylum Firmicutes (72%). However, as the disease progressed severely in these beetles, the proportion of Firmicutes decreased (Symptom 1 - 72.03% to Symptom 2 - 44.7% to Symptom 3 - 26.3%). These findings imply that colonization by Firmicutes was inversely proportional to Proteobacteria colonization in the gut. This was found to be true for both the normal and disease conditions of D. titanus castanicolor. In this study, we examined the distribution of intestinal microbial communities in normal and contaminated larvae. We observed a correlation between these contaminated microbes and the overall health of the beetle, and our findings suggest that there may be a link between disease progression and the gut microbiome.

• Korean Journal of Microbiology
• /
• v.47 no.1
• /
• pp.56-65
• /
• 2011

Culture-independent microscopic observations and 16S rDNA analyses were applied to describe the bacterial community inherent to the biofilm structure of the RABC (Rotating Activated Bacillus Contactors) process for swine butchery wastewater treatment. The ratios of Gram-positive bacterial counts to total bacterial counts of the RABC process were significantly increased in the last aeration tank as well as returned sludge, while those of the existing A2O (Anaerobic-Anoxic-Oxic) process maintained constant from aeration tanks to returned sludge. Totally nine phyla were recovered by 16S rDNA analysis, two of which were major groups: the Proteobacteria (64.1%) and the Actinobacteria (18.4%). The third major group was the endospore-forming Firmicutes (5.4%). The remaining six minor groups are the Bacteroidetes (3.3%), the Chlorobi (2.2%), the Nitrospirae (1.1%), the Chlorofleix (1.1%), the Acidobacteria (1.1%), and the Fusobacteria (1.1%). The ratio of endospore-forming bacteria was 19.4%, which was composed of the members of the Firmicutes phylum (5.4%) and the Intrasporangiaceae family (14.0%) of the Actinobacteria phylum. Nitrifying and denitrifying related- and phosphorus accumulating related-sequences were composed of 6.5% and 5.4% of total community, respectively, these could mean the high capacity of the RABC process to remove odor compounds and reduce eutrophication by efficient removing inorganic nutrients.

• Korean Journal of Organic Agriculture
• /
• v.28 no.2
• /
• pp.235-250
• /
• 2020

Agricultural practices are known to have a crucial influence not only on soil physico-chemical properties but also on microbial communities. To investigate the effect of farming practices on soil microbial communities, a total of 10 soil samples were collected, including five conventional and five organic farming soils cultivated with peppers in plastic greenhouse. We conducted barcorded-pyrosequencing of V1-V3 regions of 16S rRNA genes to examine soil microbial communities of two different farming practices. Taxonomic classification of the microbial communities at the phylum level indicated that a total of 22 bacterial phyla were present across all samples. Among them, seven abundant phyla (>3%) including Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes were found, and Proteobacteria (33.0 ± 5.7%), Actinobacteria (19.9 ± 9.7%), and Firmicutes (13.6 ± 5.0%) comprised more than 66% of the relative abundance of the microbial communities. Organic farming soils showed higher relative abundances of Proteobacteria and Firmicutes, while Actinobacteria and Chloroflexi were more abundant in conventional farming soils. Notably, the genera Bacillus (higher in organic farming soils) and Streptomyces (higher in conventional farming soils) exhibited significant variation in relative abundance between organic and conventional farming soils. Finally, correlation analysis identified significant relationships (p<0.05) between soil chemical properties, in particular, pH and organic matter content and microbial communities. Taken together, this study demonstrated that the changes of soil physico-chemical properties by agricultural farming practices effected significantly (p<0.05) on soil microbial communities.

• Journal of Life Science
• /
• v.23 no.6
• /
• pp.770-778
• /
• 2013

To determine the seasonal variation of bacterial community in the seawater of Gwangyang Bay, three hundred thirty six bacterial strains were isolated on February, May, July and October 2011. Amplified Ribosomal DNA Restriction Analysis (ARDRA) was used to construct the phylotyes of the isolates using the restriction endonuclease, Hae III. Diversity indices of ARDRA patterns were calculated. One hundred and one phylotypes including 40 unique pylotypes were found at the 80% similarity level. Partial 16S rRNA genes of one hundred thirty nine strains representing each phylotypes were sequenced and compared. Bacterial community composed of 4 different phyla which include Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. Proteobacteria was the prevailing phylum in all seasons, followed by Bacteroidetes in winter, spring and autumn while Actinobacteria in summer. At the family level, Flavobacteriaceae dominated in winter and spring and Pseudoalteromonadaceae did in summer and autumn. Genera Altererythrobacter, Loktanella, Pseudoalteromonas and Vibrio were encountered in all seasons. The most diverse bacterial community was found in autumn followed by the order of spring, winter and summer.

• Journal of Korean Society of Forest Science
• /
• v.106 no.2
• /
• pp.121-129
• /
• 2017

The soil microbiome plays important roles in material cycling and plant growth in forest ecosystem. Although a lot of researches on forest soil fungi in Korea have been performed, the studies on forest soil bacterial communities have been limited. In this study, we conducted next generation sequencing (NGS) targeting 16S rRNA gene to investigate the soil bacterial communities from natural red pine (Pinus densiflora) forest in Mt. Janggunbong, Bonghwa-gun, Gyeongbuk, Korea. Our results showed that the entire bacterial communities in the study sites include the phyla Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, which have been typically observed in forest soils. The composition ratio of Proteobacteria was the highest in the soil bacteria community. The results reflect that Proteobacteria is copiotroph, which generally favors relatively nutrient-rich conditions with abundant organic matter. Some rhizobia species such as Burkholderia, Bradyrhizobium, Rhizobium, which are known to contribute to soil nitrogen-fixation, exist in the study sites. As a result of correlation analysis between soil physicochemical characteristics and bacteria communities, the soil pH was significantly correlated with the soil bacteria compositions.

• Korean Journal of Microbiology
• /
• v.46 no.4
• /
• pp.366-374
• /
• 2010

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Spirastrella abata. A total of 164 bacterial strains associated with the sponge were cultivated using Zobell and Natural sea salt media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 95% similarities compared with known bacterial species, and the isolates belonged to four phyla, Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteriodetes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge- derived total gDNA showed five major DGGE bands, and their sequences showed more than 96% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of four phyla, including Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Spirochetes, and Chloroflexi. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with S. abata by both RFLP and DGGE methods; however, overall bacterial community in the sponge differed depending on the analysis methods.