• The Plant Pathology Journal
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• v.38 no.4
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• pp.372-382
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• 2022

Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.

• Journal of Microbiology and Biotechnology
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• v.32 no.10
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• pp.1275-1283
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• 2022

Understanding soil microbial community structure in the Arctic is essential for predicting the impact of climate change on interactions between organisms living in polar environments. The hypothesis of the present study was that soil microbial communities and soil chemical characteristics would vary depending on their associated plant species and local environments in Arctic mature soils. We analyzed soil bacterial communities and soil chemical characteristics from soil without vegetation (bare soil) and rhizosphere soil of three Arctic plants (Cassiope tetragona [L.] D. Don, Dryas octopetala L. and Silene acaulis [L.] Jacq.) in different local environments (coal-mined site and seashore-adjacent site). We did not observe any clear differences in microbial community structure in samples belonging to different plant rhizospheres; however, samples from different environmental sites had distinct microbial community structure. The samples from coal-mined site had a relatively higher abundance of Bacteroidetes and Firmicutes. On the other hand, Acidobacteria was more prevalent in seashore-adjacent samples. The relative abundance of Proteobacteria and Acidobacteria decreased toward higher soil pH, whereas that of Bacteroidetes and Firmicutes was positively correlated with soil pH. Our results suggest that soil bacterial community dissimilarity can be driven by spatial heterogeneity in deglaciated mature soil. Furthermore, these results indicate that soil microbial composition and relative abundance are more affected by soil pH, an abiotic factor, than plant species, a biotic factor.

• The Korean Journal of Ecology
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• v.19 no.6
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• pp.543-562
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• 1996

Zooplankton community structure and the factors correlated with community differences were examined in sandusky Bay (SB) and the open water of Lake Erie (LE, U.S.A.). SB zooplankton communities differed from those in LE by having a greater rotifer density and species richness. Keratella spp., Brachionus spp., and Pompholyx complanata dominated SB rotifers; Brachionus and Pompholyx were rarely seen in LE. Of 19 rotifer species observed, nine species were found only at SB sites. Ordination of zooplankton species abundance by detrended correspondence analysis (DCA) showed an overlap between SB and LE sites, but indicated a portion of the space that was occupied by only SB communities. The seasonal trajectories of zooplankton dynamics in the ordination space at SB sites differed from that of LE. The zooplankton most important in forcing site separation along a DCA Axis I at SB sites were Brachionus angularis, Pompholyx complanata, Keratella valga, Keratella quadrata, Filinia terminalis (rotifers), and Eubosmina coregoni and Daphnia (cladocerans). These species had axis scores which were significantly correlated (p<0.01) with bacterial density and bacterial phosphorus, total phosphorus, and algal density. Very high baterial density and very abundant bacterivorous rotifers in SB suggest that the transport of bacterial carbon through rotifers may be a relatively important link to higher trophic leaels. We believe that this "microbial carbon flow" from the base of the food web may be important in determining the suitability of SB as a spawning site and nursery for larval and juvenile fish.nile fish.

• Journal of Animal Science and Technology
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• v.62 no.4
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• pp.504-520
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• 2020

Proliferation of shrubs at the expense of native forage in pastures has been associated with large changes in dry-matter intake and dietary components for grazing ruminants. These changes can also affect the animals' physiology and metabolism. However, little information is available concerning the effect of pastoral-shrub grazing on the rumen bacterial community. To explore rumen bacteria composition in grazing yaks and the response of rumen bacteria to increasing shrub coverage in alpine meadows, 48 yak steers were randomly assigned to four pastures with shrub coverage of 0%, 5.4%, 11.3%, and 20.1% (referred as control, low, middle, and high, respectively), and ruminal fluid was collected from four yaks from each pasture group after 85 days. Rumen fermentation products were measured and microbiota composition determined using Ion S5™ XL sequencing of the 16S rRNA gene. Principal coordinates analysis (PCoA) and similarity analysis indicated that the degree of shrub coverage correlated with altered rumen bacterial composition of yaks grazing in alpine shrub meadows. At the phyla level, the relative abundance of Firmicutes in rumen increased with increasing shrub coverage, whereas the proportions of Bacteroidetes, Cyanobacteria and Verrucomicrobia decreased. Yaks grazing in the high shrub-coverage pasture had decreased species of the genus Prevotellaceae UCG-001, Lachnospiraceae XPB1014 group, Lachnospiraceae AC2044 group, Lachnospiraceae FCS020 group and Fretibacterium, but increased species of Christensenellaceae R-7 group, Ruminococcaceae NK4A214 group, Ruminococcus 1, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005 and Lachnospiraceae UCG-008. These variations can enhance the animals' utilization efficiencies of cellulose and hemicellulose from native forage. Meanwhile, yaks grazed in the high shrub-coverage pasture had increased concentrations of ammonia nitrogen (NH₃-N) and branched-chain volatile fatty acids (isobutyrate and isovalerate) in rumen compared with yaks grazing in the pasture without shrubs. These results indicate that yaks grazing in a high shrub-coverage pasture may have improved dietary energy utilization and enhanced resistance to cold stress during the winter. Our findings provide evidence for the influence of shrub coverage on the rumen bacterial community of yaks grazing in alpine meadows as well as insights into the sustainable production of grazing yaks on lands with increasing shrub coverage on the Qinghai-Tibet Plateau.

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

• The Korean Journal of Pesticide Science
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• v.21 no.1
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• pp.1-8
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• 2017

Although a global ban on the use of endosulfan, an organochloline insecticide, has taken effect in mid-2012, it has been still used in several countries, including India and China, and detected in diverse environments in the world due to its relative persistence and semi-volatility. In this study, the effect of endosulfan on soil bacterial community was investigated using 16S rRNA gene pyrosequencing method. When endosulfan was applied to an upland soil at a rate of 100 mg/kg soil (ES soil), the number of operational taxonomic units (OTU) and diversity indices for bacteria initially decreased and gradually recovered to the level of the non-treated soil (NT soil) during an eight-week incubation period. At bacterial phylum level, relative abundances of Proteobacteria and Verrucomicrobia were higher while those of Chloroflexi and Spirochaetes were lower in the ES soil than in the NT soil, suggesting that an endosulfan application affects the bacterial community structure in soil. In the ES soil, the relative abundances of the OTUs affiliated to the genera Sphingomonas and Burkholderia increased in the initial period of incubation while those affiliated to the genera Pseudonocardia and Opitutus increased in the late period of incubation. Because the first three genera contain bacterial strains reported to degrade endosulfan, they are expected to be involved in the degradation of endosulfan, probably one after another.

• Journal of Life Science
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• v.24 no.4
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• pp.393-402
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• 2014

Culture-dependent and culture-independent denaturing gradient gel electrophoresis (DGGE) analyses were employed to investigate the bacterial community associated with a natural dye wastewater treatment facility. A total of 104 (influent water, 48 strains; aeration tank, 25; settling tank, 31) bacterial strains were isolated. Based on the 16S rRNA gene sequences comparison analysis, the isolates belonged to four phyla: Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes. Seventeen DGGE bands representing dominant taxa in each sample were cloned and partially sequenced. The same four phyla were detected by DGGE fingerprinting. The most dominant taxon retrieved by both methods was the member of the phylum Proteobacteria with Alphaproteobacteria as the predominant class. The bacterial community associated with the natural dye wastewater treatment facility is composed of parasites of animals and plants, decomposers of polysaccharides and dyes, and producers of extracellular polysaccharides.

• Korean Journal of Microbiology
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• v.33 no.4
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• pp.257-261
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• 1997

To scrutinize the bacterial community composition of Lake Soyang in winter, bacterial numbers belonging to Eubacteria, Proteobacteria and Cytophaga-Flavobacterium group were estimated by using 16S and 23S rRNA targeted oligonucleotide probes. Total bacterial numbers ranged from $0.7{\times}10^6$ to $1.1{\times}10^6cells{\cdot}ml^{-1}$, and vertical profile of total bacteria showed a peak at 5 m depth. The ratio of eubacteria to total bacteria were 34~90% and at 5 m and 10 m depths those were low exhibiting, 39 and 34%, respectively. The percentage of proteobacteria ${\alpha}$-group ranged 10.8~28.7%, ${\beta}$-group 4.5~53.5%, ${\gamma}$-group 4.9~35.5% and Cytophaga-Flavobacterium group 6.1~21.1%. The dominant groups were ${\beta}$-group at 0, 2 and 5 m, ${\gamma}$-group at 10 m, ${\alpha}$-group at 30 m and Cytophaga-Flavobacterium group at 50 m depth. In winter season, Lake Soyang can be divided into three layer, 0~2 m, 5~10 m and 30~50 m, by the bacteria community composition. By this method, new informations about aquatic ecosystem were developed.

• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.951-970
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• 2023

This study utilized Italian ryegrass silage (IRGS) - based total mixed ration (TMR) as feedstuff and evaluated its effects on rumen fermentation, growth performance, blood parameters, and bacterial community in growing Hanwoo heifers. Twenty-seven Hanwoo heifers (body weight [BW], 225.11 ± 10.57 kg) were randomly allocated to three experimental diets. Heifers were fed 1 of 3 treatments as follows: TMR with oat, timothy, and alfalfa hay (CON), TMR with 19% of IRGS (L-IRGS), and TMR with 36% of IRGS (H-IRGS). Feeding high levels of IRGS (H-IRGS) and CON TMR to heifers resulted in a greater molar proportion of propionate in the rumen. The impact of different TMR diets on the BW, average daily gain, dry matter intake, and feed conversion ratio of Hanwoo heifers during the growing period did not differ (p > 0.05). Furthermore, the blood metabolites, total protein, albumin, aspartate aminotransferase, glucose, and total cholesterol of the heifers were not affected by the different TMR diets (p > 0.05). In terms of rumen bacterial community composition, 264 operational taxonomic units (OTUs) were observed across the three TMR diets with 240, 239, and 220 OTUs in CON, L-IRGS, and H-IRGS, respectively. IRGS-based diets increased the relative abundances of genera belonging to phylum Bacteroidetes but decreased the abundances of genus belonging to phylum Firmicutes compared with the control. Data showed that Bacteroidetes was the most dominant phylum, while Prevotella ruminicola was the dominant species across the three TMR groups. The relative abundance of Ruminococcus bromii in the rumen increased in heifers fed with high inclusion of IRGS in the TMR (H-IRGS TMR). The relative abundance of R. bromii in the rumen significantly increased when heifers were fed H-IRGS TMR while P. ruminicola increased in both L-IRGS and H-IRGS TMR groups. Results from the current study demonstrate that the inclusion of IRGS in the TMR is comparable with the TMR containing high-quality forage (CON). Thus, a high level of IRGS can be used as a replacement forage ingredient in TMR feeding and had a beneficial effect of possibly modulating the rumen bacterial community toward mainly propionate-producing microorganisms.

• Animal Bioscience
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• v.37 no.2
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• pp.261-273
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• 2024

Objective: The objective of this study was to evaluate the growth performance, rumen fermentation parameters and bacterial community of post-weaning dairy calves in response to five diets varying in corn silage (CS) inclusion. Methods: A total of forty Holstein weaned bull calves (80±3 days of age;128.2±5.03 kg at study initiation) were randomized into five groups (8 calves/group) with each receiving one of five dietary treatments offered as total mixed ration in a 123-d feeding study. Dietary treatments were control diet (CON; 0% CS dry matter [DM]); Treatment 1 (T1; 27.2% CS DM); Treatment 2 (T2; 46.5% CS DM); Treatment 3 (T3; 54.8% CS DM); and Treatment 4 (T4; 67.2% CS DM) with all diets balanced for similar protein and energy concentration. Results: Results showed that calves offered CS had greater average daily gain, body length and chest depth growth, meanwhile altered rumen fermentation indicated by decreased rumen acetate concentrations. Principal coordinate analysis showed the rumen bacterial community structure was affected by varying CS inclusion diets. Bacteroidetes and Firmicutes were the predominant bacterial phyla in the calf rumens across all treatments. At the genus level, the abundance of Bacteroidales_RF16_group was increased, whereas Unclassified_Lachnospiraceae was decreased for calves fed CS. Furthermore, Spearman's correlation test between the rumen bacteria and rumen fermentation parameters indicated that Bacteroidales_RF16_group and Unclassified Lachnospiraceae were positively correlated with propionate and acetate, respectively. Conclusion: The results of the current study suggested that diet CS inclusion was beneficial for post-weaning dairy calf growth, with 27.2% to 46.5% CS of diet DM recommended to achieve improved growth performance. Bacteroidales_RF16_group and Unclassified Lachnospiraceae play an important role in the rumen fermentation pattern for post-weaning calves fed CS.