Similarity of Bacterial Community Structure between Asian Dust and Its Sources Determined by rRNA Gene-Targeted Approaches

Nishimura, Yasumasa; Kenzaka, Takehiko; Sueyoshi, Akio; Li, Pinfang; Fujiyama, Hideyasu; Baba, Takashi; Yamaguchi, Naohito; Nasu, Masao

doi:10.1264/jsme2.me09166

Cited by 21 publications

(24 citation statements)

References 32 publications

(29 reference statements)

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“…Realtime PCR was performed with universal primer sets EUB f933 (5′-GCA CAA GCG GTG GAG CAT GTG G-3′) and EUB r1387 (5′-GCC CGG GAA CGT ATT CAC CG-3′) 27) according to the procedure reported by Nishimura et al 28) To determine the recovery rate of DNA during extraction, known amounts of DNA fragment of the luciferase gene (luc) were inoculated into the samples before DNA extraction as an internal standard and quantified after DNA extraction.…”

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confidence: 99%

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Yamaguchi

Baba

Ichijo

et al. 2016

Biological & Pharmaceutical Bulletin

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Approximately 180 t/km2 of Asian dust particles are estimated to fall annually on Beijing, China, and there is significant concern about the influence of microbes transported by Asian dust events on human health and downwind ecosystems. In this study, we collected Asian dust particles in Beijing, and analyzed the bacterial communities on these particles by culture-independent methods. Bacterial cells on Asian dust particles were visualized first by laser scanning microscopy, which demonstrated that Asian dust particles carry bacterial cells to Beijing. Bacterial abundance, as determined by quantitative polymerase chain reaction (PCR), was 10 8 to 10 9 cells/g, a value about 10 times higher than that in Asian dust source soils. Interseasonal variability of bacterial community structures among Asian dust samples, as compared by terminal restriction fragment length polymorphism (T-RFLP), was low during the Asian dust season. Several viable bacteria, including intestinal bacteria, were found in Asian dust samples by denaturing gradient gel electrophoresis (DGGE). Clone library analysis targeting 16S ribosomal RNA (rRNA) gene sequences demonstrated that bacterial phylogenetic diversity was high in the dust samples, and most of these were environmental bacteria distributed in soil and air. The dominant species in the clone library was Segetibacter aerophilus (Bacteroidetes), which was first isolated from an Asian dust sample collected in Korea. Our results also indicate the possibility of a change in the bacterial community structure during transportation and increases in desiccation-tolerant bacteria such as Firmicutes.

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confidence: 99%

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Yamaguchi

Baba

Ichijo

et al. 2016

Biological & Pharmaceutical Bulletin

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“…The transport of microbes by Asian dust has been reported Lee et al, 2009), and the presence of pathogens and allergens, with the potential to affect the health of downwind populations and ecosystems, was also revealed (Kellogg and Griffin, 2006). More than 2 × 10 13 to 4 × 10 16 bacterial cells km − 2 per month were estimated to be transported to Beijing by Asian dust (Nishimura et al, 2010). To identify bacteria in Asian dust, classical cultivation methods have been used to compare the differences in atmospheric colony-forming units (CFU) between normal and Asian dust days (Choi et al, 1997;Iwasaka et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…As a minority of environmental bacteria can be cultured under standard laboratory conditions (Amann et al, 1995), the observed CFU counts likely represent a fraction of the actual bacterial diversity. Cultureindependent methods, such as denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism, are being increasingly used in these studies (Lee et al, 2009;Jeon et al, 2010;Nishimura et al, 2010). Using terminal restriction fragment length polymorphism analysis, Nishimura et al (2010) showed that the bacterial community structures in Asian dust samples differed greatly according to the scale of the dust event.…”

Section: Introductionmentioning

confidence: 99%

Modification of atmospheric sand-associated bacterial communities during Asian sandstorms in China and South Korea

Sin

DuBow

2014

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The transport of desert soil into the atmosphere during desert sandstorms can affect the Earth's climate and environmental health. Asian desert sandstorms occur almost every year during the Spring, as the atmosphere in the Northern hemisphere warms. It is conceivable that these Asian desert sandstorms may transport microbes from deserts, such as the Gobi and Taklamaken deserts, over long distances in China, east Asia and the Pacific. In this study, we examined local atmospheric sand particle-associated bacterial populations collected in the absence (sterile sand exposed for 24 h to the air in the absence of a sandstorm) and presence of sandstorms in five Asian cities. We used pyrosequencing of PCR-amplified 16S rDNA genes from sand-extracted total DNA to overcome cultivation limitations of bacterial enumeration. We found that 490% of the control and sandstorm sequences could be classified as representing bacteria belonging to four phyla: Proteobacteria, Bacteriodetes, Actinobacteria and Firmicutes. The sand-associated bacterial populations in sandstorm samples were distinct from sandassociated bacteria in the absence of a sandstorm. Members of the phylum Proteobacteria were found to significantly increase in sandstorm samples (P = 0.01). Principal component analyses showed that the sand-associated bacterial populations were best clustered by sampling year, rather than location. DNA sequences representing bacteria belonging to several genera (including putative human pathogens) were observed to increase in sand-associated samples from sandstorms, whereas others were found to decrease, when comparing sand-associated bacterial populations versus those in control samples, suggesting human/ environmental implications of sandstorm events.

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“…In particular, denaturing gradient gel electrophoresis (DGGE) 9) has been used to determine the genetic diversity of natural microbial communities and to identify the phylogenetic affiliation of community members. [10][11][12] Polymerase chain reaction (PCR)-amplified DNA fragments of the eubacterial 16S ribosomal RNA (rRNA) gene that have the same length but different sequences can be separated by DGGE. However, PCR-DGGE analysis is often difficult to implement with freshwater samples from eutrophic environments that contain PCR-inhibitors, such as humic acid.…”

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16S Ribosomal RNA Gene-Based Phylogenetic Analysis of Abundant Bacteria in River, Canal and Potable Water in Bangkok, Thailand

Yamaguchi

Nishiguchi

Utrarachkij

et al. 2013

Biological & Pharmaceutical Bulletin

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In Southeast Asian countries, industrialization and urbanization is occurring rapidly, and water pollution in rivers and canals poses serious problems in some areas, especially in cities. Excess inflow of domestic, agricultural, and industrial wastewater to freshwater environments disturbs the aquatic microbial ecosystem, which can further pollute water by inhibiting biodegradation of pollutants. Therefore, monitoring of microbes in freshwater environment is important to identify changes in indigenous microbial populations and to estimate the influence of wastewater inflows on them. Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis is suitable for monitoring changes in microbial communities caused by human activities, but this method can be difficult in eutrophic freshwater samples that contain PCR inhibitors. In this study, we optimized DNA extraction procedures and PCR conditions for DGGE analysis of bacterial populations in freshwater samples (canal, river, and tap water) collected in Bangkok, Thailand. A simple freeze-thaw procedure was effective for extracting DNA from bacterial cells in the samples, and LA Taq with added bovine serum albumin provided the best PCR amplification. The PCR-DGGE approach revealed that the most common bacteria in freshwater samples belonged to Gammaproteobacteria, while a Gram-positive bacterium was present at Bangkok Noi Canal. Temporally and spatially continuous analyses of bacterial populations in Bangkok canals and rivers by PCR-DGGE approach should be useful to recognize disturbances of microbial ecosystems caused by excess inflows of wastewater.

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Similarity of Bacterial Community Structure between Asian Dust and Its Sources Determined by rRNA Gene-Targeted Approaches

Cited by 21 publications

References 32 publications

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Modification of atmospheric sand-associated bacterial communities during Asian sandstorms in China and South Korea

16S Ribosomal RNA Gene-Based Phylogenetic Analysis of Abundant Bacteria in River, Canal and Potable Water in Bangkok, Thailand

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