• Ocean and Polar Research
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• 제39권4호
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• pp.245-255
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• 2017

There are a number of pieces of evidences that suggest a link between marine diatoms and microorganisms, but knowledge about related microbial communities is greatly lacking. The present study investigated the microbial community structures related to the growth of the marine diatom Cyclotella meneghiniana. We collected free-living bacteria (FLB) and particle-associated bacteria (PAB) at each growth stage (e.g., lag, exponential, stationary and death) of the diatom, and analyzed their bacterial 16S rDNA using pyrosequencing. Metagenomics analysis showed that community structures of FLB and PAB differed considerably with the progress of growth stages. FLB showed higher diversity than PAB, but variation in the different growth stages of C. meneghiniana was more evident in PAB. The proportion of the genus Hoeflea, belonging to the order Rhizobiales, was dominant in both FLB and PAB, and it gradually increased with the growth of C. meneghiniana. However, Enhydrobacter clade tended to considerably decrease in PAB. In addition, Marinobacter decreased steadily in FLB, but first increased and then decreased in PAB. These results suggest that Hoeflea, Enhydrobacter, and Marinobacter may be closely related to the growth of diatom C. meneghiniana.

• The Plant Pathology Journal
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• 제37권4호
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• pp.396-403
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• 2021

Fire blight disease, caused by Erwinia amylovora, could damage rosaceous plants such as apples, pears, and raspberries. In this study, we designed to understand how E. amylovora affected other bacterial communities on apple rhizosphere; twig and fruit endosphere; and leaf, and fruit episphere. Limited studies on the understanding of the microbial community of apples and changes the community structure by occurrence of the fire blight disease were conducted. As result of these experiments, the infected trees had low species richness and operational taxonomic unit diversity when compared to healthy trees. Rhizospheric bacterial communities were stable regardless of infection. But the communities in endosphere and episphere were significanlty affected by E. amylovora infection. We also found that several metabolic pathways differ significantly between infected and healthy trees. In particular, we observed differences in sugar metabolites. The finding provides that sucrose metabolites are important for colonization of E. amylovora in host tissue. Our results provide fundamental information on the microbial community structures between E. amylovora infected and uninfected trees, which will contribute to developing novel control strategies for the fire blight disease.

• Journal of Microbiology and Biotechnology
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• 제17권1호
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• pp.67-73
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• 2007

The present study compared the microbial diversity and activity during the application of various bioremediation processes to crude oil-contaminated soil. Five different treatments, including natural attenuation (NA), biostimulation (BS), biosurfactant addition (BE), bioaugmentation (BA), and a combined treatment (CT) of biostimulation, biosurfactant addition, and bioaugmentation, were used to analyze the degradation rate and microbial communities. After 120 days, the level of remaining hydrocarbons after all the treatments was similar, however, the highest rate (k) of total petroleum hydrocarbon (TPH) degradation was observed with the CT treatment (P<0.05). The total bacterial counts increased during the first 2 weeks with all the treatments, and then remained stable. The bacterial communities and alkane monooxygenase gene fragment, alkB, were compared by denaturing gradient gel electrophoresis (DGGE). The DGGE analyses of the BA and CT treatments, which included Nocardia sp. H17-1, revealed a simple dominant population structure, compared with the other treatments. The Shannon-Weaver diversity index (H') and Simpson dominance index (D), calculated from the DGGE profiles using 16S rDNA, showed considerable qualitative differences in the community structure before and after the bioremediation treatment as well as between treatment conditions.

• Animal Bioscience
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• 제37권4호
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• pp.655-667
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• 2024

Objective: This study aimed to assess the impact of a hydroethanolic extract of walnut green husks (WGH) on rumen fermentation and the diversity of bacteria, methanogenic archaea, and fungi in sheep fed a high-concentrate diet. Methods: Five healthy small-tailed Han ewes with permanent rumen fistula were selected and housed in individual pens. This study adopted a self-controlled and crossover design with a control period and an experimental period. During the control period, the animals were fed a basal diet (with a ratio of concentrate to roughage of 65:35), while during the treatment period, the animals were fed the basal diet supplemented with 0.5% hydroethanolic extract of WGH. Fermentation parameters, digestive enzyme activities, and microbial diversity in rumen fluid were analyzed. Results: Supplementation of hydroethanolic extract of WGH had no significant effect on feed intake, concentrations of total volatile fatty acids, isovalerate, ammonia nitrogen, and microbial protein (p>0.05). However, the ruminal pH, concentrations of acetate, butyrate and isobutyrate, the ratio of acetate to propionate, protozoa count, and the activities of filter paper cellulase and cellobiase were significantly increased (p<0.05), while concentrations of propionate and valerate were significantly decreased (p<0.05). Moreover, 16S rRNA gene sequencing revealed that the relative abundance of rumen bacteria Christensenellaceae R7 group, Saccharofermentans, and Ruminococcaceae NK4A214 group were significantly increased, while Ruminococcus gauvreauii group, Prevotella 7 were significantly decreased (p<0.05). The relative abundance of the fungus Pseudomonas significantly increased, while Basidiomycota, Fusarium, and Alternaria significantly decreased (p<0.05). However, there was no significant change in the community structure of methanogenic archaea. Conclusion: Supplementation of hydroethanolic extract of WGH to a high-concentrate diet improved the ruminal fermentation, altered the structure of ruminal bacterial and fungal communities, and exhibited beneficial effects in alleviating subacute rumen acidosis of sheep.

• The Plant Pathology Journal
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• 제37권6호
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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.

• Journal of Korean Society of Environmental Engineers
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• 제32권2호
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• pp.113-120
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• 2010

Air-cathode microbial fuel cell consisted of 4 unit cells were operated under batch condition and electricity generation and microbial community structure variation were investigated, depending on separator types and cathode characteristics: A) PEM(Proton Exchange Membrane)-30% Wet proofing Carbon Cloth(WC), B) AEM(Anion Exchange Membrane-WC, C) CEM(Cation Exchange Membrane)-WC, D) PEM-No Wet proofing Carbon Cloth(NC). Maximum power densities of PEM-WC, AEM-WC and CEM-WC were 510.9, 522.1 and 504.8 $mW/m^2$, respectively. But PEM-NC showed relatively lower maximum power density of 218.3 $mW/m^2$. And PEM-WC, AEM-WC and CEM-WC showed similar internal resistances(20.0-28.2 ${\Omega}$). PCRDGGE, PCA and diversity indices showed that uncultured bacteria which reported in previous MFC studies were detected in suspended growth bacteria and attached growth bacteria would be affected not by separator type but by cathode characteristic. Thus, cathode characteristic can be one of the critical factors for power generation in air-cathode MFC using PEM, AEM, and CEM as separator.

• Proceedings of the Korean Sanitation Conference
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• 대한위생학회 2004년도 심포지움
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• pp.45-53
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• 2004

• Korean Journal of Soil Science and Fertilizer
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• 제49권2호
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Journal of Veterinary Science
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• 제22권3호
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• pp.37.1-37.14
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• 2021

Background: Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs. Objectives: To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China. Methods: A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied. Results: After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs. Conclusions: The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.

• Journal of Microbiology and Biotechnology
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• 제34권7호
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• pp.1464-1474
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• 2024

Soil extracellular enzyme plays a vital role in changing soil nitrogen (N) mineralization of rice field. However, the effects of soil extracellular enzyme activities (EEA) and microbial community composition response to N mineralization of rice field under short-term tillage treatment needed to be further explored. In this study, we investigated the impact of short-term (8-year) tillage practices on rhizosphere soil N transformation rate, soil enzyme activities, soil microbial community structure, and the N mineralization function gene abundances in double-cropping rice field in southern China. The experiment consisted of four tillage treatments: rotary tillage with crop straw input (RT), conventional tillage with crop straw input (CT), no-tillage with crop straw retention (NT), and rotary tillage with all crop straw removed as a control (RTO). The results indicated that the rhizosphere soil N transformation rate in paddy field under the NT and RTO treatments was significantly decreased compared to RT and CT treatments. In comparison to the NT and RTO treatments, soil protease, urease, β-glucosaminidase, and arginase activities were significantly improved by the CT treatment, as were abundances of soil sub, npr, and chiA with CT and RT treatments. Moreover, the overall diversity of soil bacterial communities in NT and RTO treatments was significantly lower than that in RT and CT treatments. Soil chitinolytic and bacterial ureolytic communities were also obviously changed under a combination of tillage and crop straw input practices.