• Journal of Microbiology and Biotechnology
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• 제32권4호
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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).

• Journal of Ecology and Environment
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• 제38권4호
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• pp.461-476
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• 2015

Global warming has accelerated glacial retreat in the high Arctic. The exposed glacier foreland is an ideal place to study chronosequential changes in ecosystems. Although vegetation succession in the glacier forelands has been studied intensively, little is known about the microbial community structure in these environments. Therefore, this study focused on how glacial retreat influences the bacterial community structure and its relationship with soil properties. This study was conducted in the foreland of the Midtre Lovénbreen glacier in Svalbard (78.9°N). Seven soil samples of different ages were collected and analyzed for moisture content, pH, soil organic carbon and total nitrogen contents, and soil organic matter fractionation. In addition, the structure of the bacterial community was determined via pyrosequencing analysis of 16S rRNA genes. The physical and chemical properties of soil varied significantly along the distance from the glacier; with increasing distance, more amounts of clay and soil organic carbon contents were observed. In addition, Cyanobacteria, Firmicutes, and Actinobacteria were dominant in soil samples taken close to the glacier, whereas Acidobacteria were abundant further away from the glacier. Diversity indices indicated that the bacterial community changed from homogeneous to heterogeneous structure along the glacier chronosequence/distance from the glacier. Although the bacterial community structure differed on basis of the presence or absence of plants, the soil properties varied depending on soil age. These findings suggest that bacterial succession occurs over time in glacier forelands but on a timescale that is different from that of soil development.

• Animal Bioscience
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• 제35권8호
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• pp.1162-1173
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• 2022

Objective: This study aimed to investigate the fermentation profiles, bacterial community and predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) during ensiling. Methods: First-cutting Sudangrass was harvested at the vegetative stage and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30, and 60 days of ensiling, respectively. The bacterial communities on day 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional profiles were analyzed according to the Kyoto encyclopedia of genes and genomes using Tax4Fun. Results: The Sudangrass silages showed good fermentation quality, indicated by higher lactic acid contents, and lower pH, butyric acid and ammonia nitrogen contents. The dominant genus Lactococcus on day 3 was replaced by Lactobacillus on day 60. The metabolism of amino acid, energy, cofactors and vitamins was restricted, and metabolism of nucleotide and carbohydrate was promoted after ensiling. The 1-phosphofructokinase and pyruvate kinase of bacterial community seemed to play important roles in stimulating the lactic acid fermentation, and the promotion of arginine deiminase could help lactic acid bacteria to tolerate the acidic environment. Conclusion: High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of Sudangrass ensiling not only for distinct bacterial community but also for specific functional metabolites. The results could provide a comprehensive insight into bacterial community and metabolic characteristics to further improve the silage quality.

• 한국해양생명과학회지
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• 제6권1호
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• pp.9-22
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• 2021

We determined the composition of water and sediment bacterial assemblages from the East Sea using 16S rRNA gene sequencing. Total bacterial reads were greater in surface waters (<100 m) than in deep seawaters (>500 m) and sediments. However, total OTUs, bacterial diversity, and evenness were greater in deep seawaters than in surface waters with those in the sediment comparable to the deep sea waters. Proteobacteria was the most dominant bacterial phylum comprising 67.3% of the total sequence reads followed by Bacteriodetes (15.8%). Planctomycetes, Verrucomicrobia, and Actinobacteria followed all together consisting of only 8.1% of the total sequence. Candidatus Pelagibacter ubique considered oligotrophic bacteria, and Planctomycetes copiotrophic bacteria showed an opposite distribution in the surface waters, suggesting a potentially direct competition for available resources by these bacteria with different traits. The bacterial community in the warm surface waters were well separated from the other deep cold seawater and sediment samples. The bacteria exclusively associated with deep sea waters was Actinobacteriacea, known to be prevalent in the deep photic zone. The bacterial group Chromatiales and Lutibacter were those exclusively associated with the sediment samples. The overall bacterial community showed similarities in the horizontal rather than vertical direction in the East Sea.

• Journal of Microbiology
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• 제37권1호
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• pp.10-13
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• 1999

The bacterial abundance, proportion of respiring bacteria, and bacterial community of southern Lake Baikal were analyzed at 1 m and 400m depths during winter. The total bacterial numbers were 5.1${\times}$105 cells ml-1 at 1 m and 2.5${\times}$105 cells ml-1 at 400 m depth, which are about half and quarter of the numbers of other lakes. The proportion of respiring bacteria was as low as 2.5% at 1 m and 1.4% at 400 m depth. Considering the amount of organic carbon which need to be degraded and low proportion of respiring bacteria, the bacteria could be assumed to have high activities. The EUB/DAPI ratios were 77 and 89% at 1 m and 400 m depths, respectively. Of the bacterial community, the other group was dominant at both depths, and gamma group of protebacteria followed next. But the beta group of proteobacteria and Cytophaga-Flavobacterium groups occupied very small proportions.

• Membrane and Water Treatment
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• 제10권6호
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• pp.395-404
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• 2019

The influence of chlorine on marine bacterial communities was examined in this study. A non-chlorine-adapted marine bacterial community (NCAM) and a chlorine-adapted bacterial community (CAM, bacterial community treated with $0.2mg-Cl_2/L$ chlorine) were cultivated for 1 month. A distinct difference was observed between the NCAM and CAM, which shared only eight operational taxonomic units (OTUs), corresponding to 13.1% of the total number of identified OTUs. This result suggested that chlorine was responsible for the changes in the marine bacterial communities. Kordiimonas aquimaris was found to be a chlorine-resistant marine bacterium. The effect of intermittent chlorination on the two marine biofilm communities formed on the reverse osmosis (RO) membrane surface was investigated using various chlorine concentrations (0, 0.2, 0.4, 0.6 and 0.8 mg $Cl_2/L$). Although the average number of adherent marine bacteria on the RO membrane over a period of 7 weeks decreased with increasing chlorine concentration, disinfection efficiencies showed substantial fluctuations throughout the experiment. This is due to chlorine depletion that occurs during intermittent chlorination. These results suggest that intermittent chlorination is not an effective disinfection strategy to control biofilm formation.

• The Plant Pathology Journal
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• 제38권3호
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• pp.203-211
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• 2022

Bacterial wilt, which is a major soil-borne disease with widespread occurrence, poses a severe danger in the field of tobacco production. However, there is very limited knowledge on bacterial wilt-induced microecological changes in the tobacco root system and on the interaction between Ralstonia solanacearum and fungal communities in the rhizosphere soil. Thus, in this study, changes in fungal communities in the rhizosphere soil of tobaccos with bacterial wilt were studied by 18S rRNA gene sequencing. The community composition of fungi in bacterial wilt-infected soil and healthy soil in two tobacco areas (Gengma and Boshang, Lincang City, Yunnan Province, China) was studied through the paired comparison method in July 2019. The results showed that there were significant differences in fungal community composition between the rhizosphere soil of diseased plants and healthy plants. The changes in the composition and diversity of fungal communities in the rhizosphere soil of tobaccos are vital characteristics of tobaccos with bacterial wilt, and the imbalance in the rhizosphere microecosystem of tobacco plants may further aggravate the disease.

• Journal of Microbiology and Biotechnology
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• 제29권1호
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• pp.91-104
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• 2019

The taxonomic and functional characteristics of bacterial communities in the pre-chlorinated rapid filters and ozonated biological activated carbon (BAC) filters were compared using Illumina MiSeq sequencing of the 16S rRNA gene and community-level physiological profiling (CLPP) based on sole-carbon-source utilization patterns. Both the rapid filters and BAC filters were dominated by Rhizobiales within ${\alpha}-proteobacteria$, but other abundant orders and genera were significantly different in both types of filter. Firmicutes were abundant only in the intermediate chlorinated rapid filter, while Acidobacteria were abundant only in the BAC filters. Bacterial communities in the rapid filter showed high utilization of carbohydrates, while those in the BAC filters showed high utilization of polymers and carboxylic acids. These different characteristics of the bacterial communities could be related to the different substrates in the influents, filling materials, and residual disinfectants. Chlorination and ozonation inactivated the existing bacteria in the influent and formed different bacterial communities, which could be resistant to the oxidants and effectively utilize different substrates produced by the oxidant, including Phreatobacter in the rapid filters and Hyphomicrobium in the BAC filters. Bradyrhizobium and Leptothrix, which could utilize compounds adsorbed on the GAC, were abundant in the BAC filters. Ozonation increased taxonomic diversity but decreased functional diversity of the bacterial communities in the BAC filters. This study provides some new insights into the effects of oxidation processes and filling materials on the bacterial community structure in the biological filters of drinking water treatment plants.

• 한국환경농학회지
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• 제40권3호
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• pp.194-202
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• 2021

BACKGROUND: Towards achievement of sustainable agriculture, using microbial inoculants may present promising alternatives without adverse environmental effects; however, there are challenging issues that should be addressed in terms of effectiveness and ecology. Viability and stability of the bacterial inoculants would be one of the major issues in effectiveness of microbial pesticide uses, and the changes within the indigenous microbial communities by the inoculants would be an important factor influencing soil ecology. Here we investigated the stability of the introduced bacterial strains in the soils planted with barley and its effect on the diversity shifts of the rhizosphere soil bacteria. METHODS AND RESULTS: Two different types of bacterial strains of Bacillus thuringiensis and Shewanella oneidensis MR-1 were inoculated to the soils planted with barley. To monitor the stability of the inoculated bacterial strains, genes specific to the strains (XRE and mtrA) were quantified by qPCR. In addition, bacterial community analyses were performed using v3-v4 regions of 16S rRNA gene sequences from the barley rhizosphere soils, which were analyzed using Illumina MiSeq system and Mothur. Alpha- and beta-diversity analyses indicated that the inoculated rhizosphere soils were grouped apart from the uninoculated soil, and plant growth also may have affected the soil bacterial diversity. CONCLUSION: Regardless of the survival of the introduced non-native microbes, non-indigenous bacteria may influence the soil microbial community and diversity.

• Fisheries and Aquatic Sciences
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• 제24권9호
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• pp.297-310
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• 2021

The rockworm gut flora was identified at each growth stage to elucidate the composition of the bacterial community. The source material was Marphysa sanguinea fed regular feed and fed biofloc at the adult stage in parallel. The systematic bacterial community composition was determined based on the next-generation sequencing method, and alpha diversity and beta diversity were conducted to access the species diversity within and between the bacterial communities, respectively. The composition of the gut flora changed considerably as the rockworms developed. The shift in the gut flora was confirmed at the phylum, family, and genera level of the bacterial communities. The Vibrio species associated with high rockworm mortality occupied 7.7% of the gut flora at the larval stage; however, they disappeared in the healthy adult gut. Moreover, different gut flora was observed between adults fed regular feed and those fed biofloc. Specifically in the biofloc-fed adult gut, several immune relevant and water-purifying bacteria were detected. The biofloc-fed adult gut flora could decompose and mineralize organic sediment, and thus be effectively utilized for integrated multitrophic aquaculture. The Venn diagram revealed that only two bacterial species were shared throughout all growth stages, and the biofloc-fed adults exhibited the highest diversity within the bacterial community.