• Journal of Microbiology and Biotechnology
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• v.27 no.10
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• pp.1808-1819
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• 2017

Knowledge on the functional characteristics and temporal variation of anaerobic bacterial populations is important for better understanding of the microbial process of two-stage anaerobic reactors. However, owing to the high diversity of anaerobic bacteria, close attention should be prioritized to the frequently abundant bacteria that were defined as core bacteria and putatively functionally important. In this study, using MiSeq sequencing technology, the core bacterial community of 98 operational taxonomic units (OTUs) was determined in a two-stage upflow blanket filter reactor treating pharmaceutical wastewater. The core bacterial community accounted for 61.66% of the total sequences and accurately predicted the sample location in the principal coordinates analysis scatter plot as the total bacterial OTUs did. The core bacterial community in the first-stage (FS) and second-stage (SS) reactors were generally distinct, in that the FS core bacterial community was indicated to be more related to a higher-level fermentation process, and the SS core bacterial community contained more microbes in syntrophic cooperation with methanogens. Moreover, the different responses of the FS and SS core bacterial communities to the temperature shock and influent disturbance caused by solid contamination were fully investigated. Co-occurring analysis at the Order level implied that Bacteroidales, Selenomonadales, Anaerolineales, Syneristales, and Thermotogales might play key roles in anaerobic digestion due to their high abundance and tight correlation with other microbes. These findings advance our knowledge about the core bacterial community and its temporal variability for future comparative research and improvement of the two-stage anaerobic system operation.

• The Plant Pathology Journal
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• v.37 no.6
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• pp.662-672
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• 2021

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

• Ocean and Polar Research
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• v.35 no.4
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• pp.415-425
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• 2013

In order to understand phytoplankton and bacterial distribution in tropical coral reef ecosystems in relation to the mangrove community, their biomass and activities were measured in the sea waters of the Chuuk and the Kosrae lagoons located in Micronesia. Chlorophyll a and bacterial abundance showed maximal values in the seawater near the mangrove forests, and then steeply decreased as the distance increased from the mangrove forests, indicating that environmental conditions for these microorganisms changed greatly in lagoon waters. Together with chlorophyll a, abundance of Synechococcus and phototrophic picoeukaryotes and a variety of indicator pigments for dinoflagellates, diatoms, green algae and cryptophytes also showed similar spatial distribution patterns, suggesting that phytoplankton assemblages respond to the environmental gradient by changing community compositions. In addition, primary production and bacterial production were also highest in the bay surrounded by mangrove forest and lowest outside of the lagoon. These results suggest that mangrove waters play an important role in energy production and nutrient cycling in tropical coasts, undoubtedly receiving large inputs of organic matter from shore vegetation such as mangroves. However, the steep decrease of biomass and production of phytoplankton and heterotrophic bacteria within a short distance from the bay to the level of oligotrophic waters indicates that the effect of mangrove waters does not extend far away.

• Korean Journal of Exercise Nutrition
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• v.25 no.4
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• pp.24-37
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• 2021

[Purpose] To determine whether physical activity (PA), primarily the recommended 60 minutes of moderate-to-vigorous PA, is associated with gut bacterial microbiota in 10-year-old children. [Methods] The Block Physical Activity Screener, which provides minutes/day PA variables, was used to determine whether the child met the PA recommendations. 16S rRNA sequencing was performed on stool samples from the children to profile the composition of their gut bacterial microbiota. Differences in alpha diversity metrics (richness, Pielou's evenness, and Faith's phylogenetic diversity) by PA were determined using linear regression, whereas beta diversity (unweighted and weighted UniFrac) relationships were assessed using PERMANOVA. Taxon relative abundance differentials were determined using DESeq2. [Results] The analytic sample included 321 children with both PA and 16S rRNA sequencing data (mean age [SD] =10.2 [0.8] years; 54.2% male; 62.9% African American), where 189 (58.9%) met the PA recommendations. After adjusting for covariates, meeting the PA recommendations as well as minutes/day PA variables were not significantly associated with gut richness, evenness, or diversity (p ≥ 0.19). However, meeting the PA recommendations (weighted UniFrac R² = 0.014, p = 0.001) was significantly associated with distinct gut bacterial composition. These compositional differences were partly characterized by increased abundance of Megamonas and Anaerovorax as well as specific Christensenellaceae_R-7_group taxa in children with higher PA. [Conclusion] Children who met the recommendations of PA had altered gut microbiota compositions. Whether this translates to a reduced risk of obesity or associated metabolic diseases is still unclear.

• Journal of Animal Science and Technology
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• v.65 no.2
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• pp.387-400
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• 2023

Ruminal protozoa, especially entodiniomorphs, engulf other members of the rumen microbiome in large numbers; and they release oligopeptides and amino acids, which can be fermented to ammonia and volatile fatty acids (VFAs) by amino acid-fermenting bacteria (AAFB). Studies using defaunated (protozoa-free) sheep have demonstrated that ruminal protozoa considerably increase intraruminal nitrogen recycling but decrease nitrogen utilization efficiency in ruminants. However, direct interactions between ruminal protozoa and AAFB have not been demonstrated because of their inability to establish axenic cultures of any ruminal protozoan. Thus, this study was performed to evaluate the interaction between Entodinium caudatum, which is the most predominant rumen ciliate species, and an AAFB consortium in terms of feed degradation and ammonia production along with the microbial population shift of select bacterial species (Prevotella ruminicola, Clostridium aminophilum, and Peptostreptococcus anaerobius). From an Ent. caudatum culture that had been maintained by daily feeding and transfers every 3 or 4 days, the bacteria and methanogens loosely associated with Ent. caudatum cells were removed by filtration and washing. An AAFB consortium was established by repeated transfers and enrichment with casamino acids as the sole substrate. The cultures of Ent. caudatum alone (Ec) and AAFB alone (AAFB) and the co-culture of Ent. caudatum and AAFB (Ec + AAFB) were set up in three replicates and incubated at 39℃ for 72 h. The digestibility of dry matter (DM) and fiber (NDF), VFA profiles, ammonia concentrations, pH, and microscopic counts of Ent. caudatum were compared among the three cultures. The co-culture of AAFB and Ent. caudatum enhanced DM degradation, VFA production, and Ent. caudatum cell counts; conversely, it decreased acetate: propionate ratio although the total bacterial abundance was similar between Ec and the Ec + AAFB co-culture after 24 h incubation. The ammonia production and relative abundance of C. aminophilum and P. anaerobius did not differ between AAFB alone and the Ec + AAFB co-culture. Our results indicate that Ent. caudatum and AAFB could have a mutualistic interaction that benefited each other, but their interactions were complex and might not increase ammoniagenesis. Further research should examine how such interactions affect the population dynamics of AAFB.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.3 no.4
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• pp.271-275
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• 1998

Controversial observations on the effect of pre-attached bacteria on the attachment of diatoms to artificial surfaces immersed in seawater have been made. Furthermore, it is not known whether or not pre-attached bacteria on artificial surfaces influence attachment of diatoms in natural seawater. In this study, we used various surfaces to which marine bacteria were pre-attached for different incubation periods. In the first experiment, glass slides were initially attached by marine natural bacteria with different exposure time (0-133 hr) and then immersed into seawater for a certain time period. The attachment of diatoms was not affected by the abundance of pre-attached bacteria (p > 0.05). The maximum abundance of attached diatoms was found on control surfaces, and the minimum abundance on surfaces where attached bacterial abundance was highest. In the second experiment, glass slides and acryl slides, either attached by marine natural bacteria for 6 days or coated by agar, were immersed in seawater. Untreated slides were also employed. On the surfaces of acryl slides with the most abundant attached bacteria ($5.4{\pm}0.02{\times}10^5\;cells\;cm^{-2}$), abundances of attached diatoms were less than those on untreated slides. On the surfaces of glass slides with bacterial abundance of $2.5{\pm}1.0{\times}10^5\;cells\;cm^{-2}$, however, abundances of attached diatoms were not different from those of untreated slides. On the agar-coated slides, the immigration rate and immigration coefficient were on average > 2 folds compared to other surfaces, indicating high rates of diatom attachment on mucilage simulated surfaces. Therefore, it seems that pre-attachment of bacteria is not prerequisite for the attachment of diatoms on artificial surfaces.

• Journal of Microbiology and Biotechnology
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• v.32 no.4
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• pp.419-429
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• 2022

American ginseng (Panax quinquefolium L.) is a perennial herbaceous plant widely cultivated in China, Korea, the United States, and Japan due to its multifunctional properties. In northwest China, transplanting after 2-3 years has become the main mode of artificial cultivation of American ginseng. However, the effects of the cultivation process on the chemical properties of the soil and bacterial community remain poorly understood. Hence, in the present study, high-throughput sequencing and soil chemical analyses were applied to investigate the differences between bacterial communities and nutrition driver factors in the soil during the cultivation of American ginseng. The responses of soil nutrition in different ecological niches were also determined with the results indicating that the cultivation of American ginseng significantly increased the soluble nutrients in the soil. Moreover, the bacterial diversity fluctuated with cultivation years, and 4-year-old ginseng roots had low bacterial diversity and evenness. In the first two years of cultivation, the bacterial community was more sensitive to soil nutrition compared to the last two years. Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, Firmicutes, and Bacteroidetes dominated the bacterial community regardless of the cultivation year and ecological niche. With the increase of cultivation years, the assembly of bacterial communities changed from stochastic to deterministic processes. The high abundance of Sphingobium, Novosphingobium, and Rhizorhabdus enriched in 4-years-old ginseng roots was mainly associated with variations in the available potassium (AK), total phosphorus (TP), total potassium (TK), and organic matter (OM).

• Animal Bioscience
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• v.34 no.11
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• pp.1784-1793
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• 2021

Objective: An experiment was conducted to evaluate the effects of bamboo leaf extract (BLE) on the production performance, rumen fermentation parameters, and rumen bacterial communities of heat-stressed dairy cows. Methods: The experiment comprised a 14-day adaptation period and a 21-day experimental period and was conducted in a high-temperature and humidity environment (daily mean ambient temperature = 33.5℃±1.3℃; daily mean relative humidity = 64.9%±0.8%, daily mean temperature-humidity index = 86.2±0.4). Twelve Holstein dairy cows were randomly allocated into two groups. A total mixed ration supplemented with BLE at 0 (CON) and 1.3 g/kg dry matter (DM) were fed, respectively. Feed intake and milk yield were recorded daily. Milk samples were collected on 1, 11, and 21 d of the experimental period to analyze milk performance. Rumen fluid samples were collected on 21 d of the experimental period to analyze rumen fermentation parameters and rumen bacterial communities. Results: Compared with the control group, supplementation of BLE increased milk yield (p<0.01), milk fat yield (p = 0.04), 4% fat-corrected milk (p<0.01) and milk fat content (p<0.01); reduced somatic cell count (p<0.01). No differences in DM intake and milk protein or lactose content were observed between two groups. Supplementation of BLE also increased the rumen total volatile fatty acid (p<0.01), acetate (p<0.01), butyrate (p<0.01), and valerate (p = 0.05) concentrations. However, no significant effects were observed on rumen pH, ammonia nitrogen, propionate, acetate/propionate ratio, isobutyrate, or isovalerate. Furthermore, BLE increased the rumen bacterial abundance and the diversity of the rumen bacterial community. The BLE reduced the Firmicutes/Bacteroidetes abundance ratio and increased the abundances of Butyrivibrio_2 (p<0.01) and Ruminococcus_2 (p<0.01). Conclusion: The BLE supplementation at 1.3 g/kg DM could improve production performance and rumen fermentation in dairy cows during heat stress.

• Journal of Environmental Health Sciences
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• v.43 no.6
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• pp.491-498
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• 2017

Objective: Bacterial abundance and community compositions have been examined in Asian dust events, clarifying their impacts on public health. This study aims to determine the bacterial community compositions and viable bacteria in Asian dust particles in the Asian dust or non-Asian dust event of March 2016. Methods: The dust samples were collected using the high volume air sampler or high volume cascade impactor, and bacterial 16S rRNA genes were amplified using PCR, followed by pyrosequencing. Bacterial diversity index, richness estimate and community composition in the particles were analyzed from the sequencing data using Mothur software. Results: The results showed that the diversity and richness during Asian dust events were higher than them in non-Asian dust events. The total bacterial community analysis showed that at the phylum Proteobacteria, Actinobacteria and Firmicutes were the most dominant of Asian dust events and non-Asian dust events. In addition, the bacterial colony counts were higher during Asian dust event, comparing with non-Asian dust event. Conclusions: This study showed that bacterial community and richness of Asian dust samples was more complex and higher than non-Asian dust samples in Gyeonggi-do, Korea, which could affect public health and environment. Thus, the continuous monitoring of Asian dust could be an alternative for managing airborne bacteria.

• Journal of Microbiology and Biotechnology
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• v.24 no.3
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• pp.313-323
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• 2014

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.