Ehime University Institutional Repository

Ehime University (愛媛大学)博士(学術)thesi

Md., Rokunuzzaman

（第３号様式）(Form No. 3) 
学  位  論  文  要  旨  
Dissertation Abstract 
 
 
氏名：  
Name 
Md. Rokunuzzaman 
 
学位論文題目：  
Title of Dissertation 
Study on soil bacterial communities in response to different 
agricultural activities 
(農業活動による土壌細菌叢の変動に関する研究) 
 
学位論文要旨：  
Dissertation Abstract 
 
Soils are considered to be complex and dynamic living substances with diverse 
microbial habitats in Earth. Soil bacterial communities are very important especially for 
agriculture owing to play an essential role to maintain soil ecosystem functions and 
biogeochemical cycle by decomposing organic matters, nutrient recycling and 
mineralization processes. In this study, I studied soil bacterial communities in response 
to three different aspects of agricultural management. I used PCR-DGGE and amplicon 
pyrosequencing using 16S rRNA gene partial sequences for analyzing bacterial 
communities.  
Little is known about the effect of soil disinfection on bacterial communities. I 
used four chemical and biological materials against natural farm soil. Soil was treated 
with wheat bran and ethanol for soil reduction, chloropicrin for chemical fumigation, 
and mustard greens (Brassica juncea) for soil reduction plus biofumigation. Tomato 
seedlings were planted after disinfection treatment. Total organic carbon, which reflects 
microbial biomass, was significantly low in chloropicrin-applied soils. The overall 
bacterial community structures were similar based on DGGE analyses among soils 
except chloropicrin treatment. Several chloropicrin-treated specific bands were observed. 
Bacterial species richness in chloropicrin-applied soils was about one-half of those in 
other soils and recovered to some extent after planting tomato. The two most abundant 
phyla were Acidobacteria and Proteobacteria in farm soil. Soil reduction with ethanol, 
wheat bran, and mustard greens did not change phylum structure very much. However, 
chemical fumigation with chloropicrin made the phylum Firmicutes dominant by 
occupying more than 80%. After planting tomato, the proportion of Firmicutes was 
reduced to basal level and the phyla Bacteroidetes and Proteobacteria became dominant. 
A taxonomic classification on OTU level supported this observation. Beta diversity 
analyzed by Principal Coordinate Analysis (PCoA) showed bacterial communities in 
soils except chloropicrin treatment formed a cluster. A community of 
chloropicrin-applied soil was quite different from those of other soils and also distinct 
after planting tomato, assuming that bacterial community structure was dramatically 
altered by chemical chloropicrin fumigation and shifted over time, while it did not go 
（第３号様式）(Form No. 3) 
back to original state.  
Most of the terraced rice-fields were abandoned or have been changed to citron 
fields and planted forests in the hilly and mountainous area at Otoyo, Kochi, Japan. 
DGGE band patterns of each soil were quite similar, although the several paddy-field 
specific DNA bands were observed. Based on pyrosequencing data, bacterial species 
richness and diversity was slightly higher in paddy fields than in other soils. While 
overall bacterial community structures of soils at different land uses were similar, 
beta-diversity analysis clearly indicated soils were divided into three clusters. Detail 
bacterial community structure of paddy fields was different from those of non-paddy 
field lands. Interestingly, community structures of crop fields, which had not been used 
as paddy field, were different from those of at least one-time paddy fields. This might 
reflect the history of land use.  
Aseptically grown seedlings of tobacco and eggplant were planted in pots filled 
with soil prepared from normal experimental greenhouse of Kochi University and grown 
under 16h light and 8h dark at 25 C. Although no plants were planted on the same soil 
as a control, weeds happened to grow on several pots. This might be because of 
preexisting seeds in greenhouse soil. I used these pots as another control. As expected, 
overall bacterial community structures of five soils, original dried soil, water-fed soil 
without plants, soil with tobacco, eggplant, and weed, did not show much differences. 
Several species of cyanobacteria belonging to genus Bacillariophyta became dominant 
only in wet soil. Fed fertilizer might cause the emergence of these bacteria under light. 
Pyrosequencing analysis indicated that the original dried soil was mainly dominated by 
bacterial species belonging to phyla Firmicutes, Actinobacteria and Proteobacteria, 
which are quite normal bacterial communities. In other four wet soils, cyanobacteria 
OTU1280 belonging to genus Bacillariophyta was dominant. DGGE and pyrosequencing 
analyzed the different hypervariable regions of 16S rRNA gene. Although it is difficult 
to identify the two dominant cyanobacteria found in both DGGE and pyrosequencing, it 
seemed to be the same clone. OTU2821 belonging to genus Sediminibacter was found 
only in eggplant rhizosphere. The closest clone to OTU2821 is identified in tomato soil, 
indicating that this clone is indeed specific in eggplant rhizosphere. OTU3300 
belonging to Gammaproteobacteria was dominant only in tobacco rhizosphere. OTU263 
belonging to order Rhodospirillales was not detected in control, indicating that this 
clone could be a common bacterium residing in rhizosphere. Interestingly dominant 
clones only in weed rhizosphere were not observed. This might indicate that weed grows 
routinely in greenhouse soil and adapts to the environment. As a result, weed-root 
associated bacteria are already fixed in the soil. 
 


English

Study on soil bacterial communities in response to different agricultural activities

愛媛大学Ehime University博士(理学)thesi

IDHAM, ANDRI KURNIAWAN

（第３号様式）(Form No. 3) 
学 位 論 文 要  約 
Dissertation Abstract
氏   名 (Name)  Idham Andri Kurniawan 
論 文 名：  
(Dissertation Title) Petrological Studies of the AD 2011-2013 Volcanic Ash from Sakurajima Volcano, Southern Kyushu, 
Japan. 
 
 
 
 
 
 
 
 
 
 
 
 
 
Previous petrological studies of explosive eruption sequences have included a variety of 
techniques, but still have enigmatic to provide the useful information for mitigation of 
volcanic disaster. The studies have focused on properties of magma without integration to the 
geophysical observation. The petrological studies have used to interrogate recent volcanic 
eruptions and compare those to the geophysical observation. The integration of petrological 
and geophysical studies over the time is very important to provide the useful information for 
mitigation of volcanic disaster. 
On basis of the above background, the aims of present study are to reconstruct the 
evolution of magma system, conduit and magma chamber, over the time based on the 
petrological studies of volcanic ash, and to integrate these studies into the geophysical 
observation in active volcano. Sakurajima in southern Kyushu, Japan, is one of the most 
active volcanoes in the world. Types of eruption and crater have changed until present time. 
This study analyzed 53 samples of volcanic ash during the eruptions of January 2011 to 
October 2013.  
These studies use several steps of methods. First, this study presents the interstitial glass 
and microlite composition and calculates the melt composition of groundmass in each recent 
eruption for knowing variation composition in magma system. Second, the magma condition 
as well as temperature, water content and pressure is estimated by using pyroxene and 
plagioclase microcrystal. Third, this study shows the result of quantitative microlite textural 
analysis for understanding process of magma ascent such as decompression and ascent rate in 
magma conduit at temporal time. Fourth, the zoning pattern of phenocryst is observed for 
identifying process deeper part into reservoir magma chamber. Finally, integrate these studies 
into the geophysical observation and propose a simple model that explains the magmatic 
system in Sakurajima during 2011 until 2013. The analyses of volcanic ash were made using 
a JEOL JSM-6510LV Scanning Electron Microscope (SEM) and X-max 50 mm
2
 Oxford 
electron microprobe at Ehime University, Matsuyama, Japan.  
The petrological studies of volcanic ash show the volcanic ash consist of black vesicular 
volcanic rock (BVVR), black non vesicular volcanic rock (BNVVR), light brown volcanic 
rock (LBVR), white volcanic rock (WVR), isolated phenocrysts (IP), silicified rock (SR), 
oxidized rock (OR), and altered volcanic rock (AVR). Juvenile materials are made up of 
BVVR, BNVVR, LBVR, WVVR, and IP, whereas the accidental materials consist of SR, OR, 
and AVR. 
Microcrystal crystallization process has occurred while magma ascended in the magma 
conduit. The degree of microcrystal crystallization process starts from BVVR, and followed 
by BNVVR, LBVR and WVR. Based on the ratio of microlite size and number density of 
plagioclase, the microcrystal crystallization process is nucleation-dominated crystallization, 
indicating crystallization by the addition of crystals. The groundmass of juvenile materials is 
composed of plagioclase; orthopyroxene, clinopyroxene, Fe-Ti minerals and matrix glass. 
SiO2 content of interstitial glass of the BVVR is lower than that of the BNVVR, LBVR 
and WVR interstitial glass and over the time, the SiO2 has vibration data in each type. The An 
mol.% of microlite plagioclase exhibits that the BVVR has higher than the other rock type, 
and is followed by BNVVR, LBVR and WVR. The microlite pyroxene of BVVR has highest 
range of Mg content compared to with other types and the lowest range of Mg content is 
WVR. Also on the Fe-Ti minerals, magnetite, MgO wt.% content of BVVR has larger than 
other type and WVR is the lowest. Among of both types are BNVVR and LBVR.  
Based on the plot of the major oxide of the estimation melt composition to SiO2 content 
exhibits all of the estimation melt compositions have wide range composition. The major 
oxide of TiO2, Al2O3, FeO, MgO, and CaO have negative correlation to SiO2 content, but for 
Na2O and K2O have positive correlation with SiO2 content. 
The phenocryts zoning pattern of both plagioclase and pyroxene consist of normal, reverse 
and complex zoning. This study is focus on the change of zoning pattern of microphenocryst 
with euhedral crystal in the outer mantle zoning pattern and in the same scale time between 
both plagioclase and pyroxene. This study suggests that the time of the change of zoning 
pattern from normal to reverse zoning over the time is correlated to the supply magma on the 
magma system.  
This study observes the geophysical data which consists of the number of eruption per 
months, the ground deformation, the hypocenter and epicenter location, and total amount of 
SO2 gas data. Based on the integration of the geochemical feature and the geophysical data, 
the phases of magma condition could be distinguished into 3 main phases, as follows:  
Phase 1 from January – December 2011. This phase is characterized by multiple of small 
supply magma. The multiple of small supply magma is represented by the fluctuation of the 
SiO2 content of interstitial glass, the wide of SiO2 melt composition, the appearance of 
reverse zoning on phenocryst, and the number of eruptions. This fluctuation happens almost 
3-4 months during this phase. The range of estimation temperature, water content and 
pressure are 1023 – 1322 ºC, 1.73 – 7.34 wt.% and 2.60 – 23.8 kbar, respectively. The 
position of shallow reservoir is 0-6 km depth beneath of Minamidake and Showa crater. 
Phase 2 from December 2011 – December 2012. This phase is very different with the 
previous phases. The large amount of magma is supplied beneath shallow reservoir magma. 
The source of magma is still same because the estimation of melt composition has same 
range composition, but relatively hotter than before. This feature is supported by the low SiO2 
content of interstitial glass at beginning and the high estimation temperature of magma. Also 
the evidence come from the mineral composition, with have high An mol.% (0.60 – 0.80) of 
plagioclase and high Al content (0.40 - 0.80) on clinopyroxene. The range of estimation 
temperature, water content and pressure are 1030 – 1468 ºC, 0.56 – 6.86 wt.% and 3.99 – 
24.1 kbar, respectively. On this phase, the time gap between petrological and geophysical 
data is observed. The different petrological changing occurs on the January 2012, but the 
geophysical data has change earlier than petrological data at December 2011. 
The location of shallow reservoir magma is 0-4 km depth beneath of Minamidake and 
Showa crater. Due to of the shallow reservoir magma, it makes the other geophysical data is 
increasing from before. The change of ground deformation is high and also the SO2 gas 
volume is increasing. This study suggests that the conduit magma of Showa crater becomes 
more open than before.  
Phase 3 from January – October 2013. The position of shallow reservoir of magma 
reverses changing into deeper location than before. The location of shallow reservoir magma 
is 2-6 km depth beneath of Showa crater. The source of magma is still same, but the 
estimation melt composition has little changing, more acid than before. This feature could be 
explained by the fractionation microcrystal and the change of the location of reservoir magma. 
The range of estimation temperature, water content and pressure are 1026 – 1443 ºC, 0.06 – 
6.60 wt.% and 3.26 – 26.5 kbar, respectively. The fluctuation of the number SiO2 content of 
interstitial glass, number eruption and phenocryst zoning pattern in this phase could be 
clarified by the multiple of supply magma beneath Showa crater. 
The decompression and magma ascent rate between phases also have the differences. 
Phase 1 has the range value of decompression and magma ascent rate are 3.62 – 23.5 kPa/s 
and 0.15 – 0.94 m/s, respectively. Phase 2 is relatively similar with phase 1, with 3.64 – 21.5 
kPa/s for decompression rate and 0.15 – 0.88 m/s for magma ascent rate. Different with the 
phase 1 and 2, phase 3 has relatively low average of decompression and magma ascent rate, 
with 2.08 – 11.6 kPa/s and 0.09 – 0.47 m/s. 
Over all between phases 1 to 3, in the magma reservoir, the magma mixing process 
happens between andesitic and dacitic magma with different volume. The andesitic magma 
has SiO2 melt composition of 57.9 – 62.2 wt.% and characterized by high An content (0.60 - 
0.80) and high Al content of clinopyroxene. The estimation of temperature of this magma is 
around 1100 – 1468 ºC. Furthermore, for the dacitic magma characterized by 64.0 - 67.2 
wt.% of SiO2 content of melt composition, low An content (0.20 - 0.60), low of Al content of 
clinopyroxene and estimation temperature 1023 – 1308 ºC. Other mineral like orthopyroxene 
and magnetite occurs on both of the magma. 
The integration of this data could be useful information for monitoring of an active 
volcano. In order to reevaluate the geophysical data and to revise the model of the magma 
plumbing system of the volcano, additional petrological and geochemical investigations for 
the rocks from recent eruptive activity must be carried out.  
 
 
 


Petrological Studies of the AD 2011-2013 Volcanic Ash from Sakurajima Volcano, Southern Kyushu, Japan

愛媛大学Ehime University博士(理学)doctoral thesi

藤井, 卓

FUJII, Taku

Japanese

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