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1.
Tai-Ying Chiou Wataru Suda Kenshiro Oshima Masahira Hattori Tomoya Takahashi 《Bioscience, biotechnology, and biochemistry》2017,81(2):403-410
Kôso is a Japanese fermented beverage made with over 20 kinds of vegetables, mushrooms, and sugars. The changes in the bacterial population of kôso during fermentation at 25 °C over a period of 10 days were studied using 454 pyrosequencing of the 16S rRNA gene. The analysis detected 224 operational taxonomic units (OTUs) clustered from 8 DNA samples collected on days 0, 3, 7, and 10 from two fermentation batches. Proteobacteria were the dominant phylum in the starting community, but were replaced by Firmicutes within three days. Seventy-eight genera were identified from the 224 OTUs, in which Bifidobacterium, Leuconostoc, Lactococcus, and Lactobacillus dominated, accounting for over 96% of the total bacterial population after three days’ fermentation. UniFrac–Principal Coordinate Analysis of longitudinal fermented samples revealed dramatic changes in the bacterial community in kôso, resulting in significantly low diversity at the end of fermentation as compared with the complex starting community. 相似文献
2.
Kaluzhnaya Oksana V. Itskovich Valeria B. McCormack Grace P. 《World journal of microbiology & biotechnology》2011,27(8):1955-1959
In this study, for the first time the diversity of bacteria associated with the endemic freshwater sponge Lubomirskia baicalensis collected from the Sousern Basin of Lake Baikal was investigated employing cultivation-independent approaches. In total,
102 bacterial 16S rRNA clones were screened using restriction fragment length polymorphism (RFLP) and 30 were selected for
sequencing. BLASTN and phylogenetic analysis based on near full length 16S rDNA sequences showed that 22 operational taxonomic
units (OTUs) were clustered in six known phyla: Actinobacteria (8 OTUs), alpha-Proteobacteria (4 OTUs), beta-Proteobacteria
(4 OTUs), Verrucomicrobia (4 OTUs), Nitrospiracea (1 OTU) and Bacteroidetes (1 OTU). Remarkably all phylotypes were affiliated
to uncultured microorganisms, however, all alpha-Proteobacteria sequences were closely related to bacteria derived from the
freshwater sponge Spongilla lacustris. Our results reveal a high diversity in the L. baicalensis bacterial community and provide an insight into microbial ecology and diversity within freshwater sponges inhabiting the
ancient Lake Baikal ecosystem. 相似文献
3.
Analysis and comparison of the bacterial community in fermented grains during the fermentation for two different styles of Chinese liquor 总被引:2,自引:0,他引:2
Wang HY Zhang XJ Zhao LP Xu Y 《Journal of industrial microbiology & biotechnology》2008,35(6):603-609
Bacterial populations in fermented grains during fermentation may play important roles in Chinese liquor flavor. PCR-based denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene library analysis were performed to analyze the bacterial community structure of two styles of liquor. The results of DGGE profiles showed that bacterial diversity decreased with the fermentation process and Lactobacillus acetotolerans became the predominant species at the end of the fermentation. But the obvious differences of bacterial community appeared in the middle stage of two styles of liquor fermentation, in which the different upstream production techniques were used. Moreover, 16S rRNA gene libraries of two styles were constructed. A total of 125 and 107 clones, chosen from two libraries, were grouped into 46 and 49 operational taxonomic units (OTUs) by amplified ribosomal DNA restriction analysis. According to sequencing results of clones, the predominant bacteria in strong aroma style fermented grains were those from the class Bacilli, Bacteroidetes, and Clostridia, whereas the predominant bacteria in fermented grains of roasted sesame aroma style belonged to Bacilli, Flavobacteria, and Gammaproteobacteria. Molecular analysis of the bacterial diversity of the liquor fermentation will benefit the analysis of important microorganisms playing key roles in the formation of liquor flavor components. 相似文献
4.
Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria.
Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse
with representatives of the high G + C Gram-positive bacteria, cyanobacteria, low G + C Gram-positive bacteria, and proteobacteria
(α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall,
300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates
by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes. Approximately 1,000
16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for
RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs
(19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (≤97%)
with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of
a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed
that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition
to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the
results may have ecological implications. This study expands our knowledge of the diversity of sponge-associated bacteria
and contributes to the growing database of the bacterial communities within sponges. 相似文献
5.
Chris Lasher Glen Dyszynski Karin Everett Jennifer Edmonds Wenying Ye Wade Sheldon Shiyao Wang Samantha B. Joye Mary Ann Moran William B. Whitman 《Microbial ecology》2009,58(2):244-261
The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were
examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed
817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence
similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database.
While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order.
Similarly, nearly 25% of the clones were only distantly related (<90% sequence similarity) to other environmental clones,
illustrating the unique composition of this community. One quarter of the clones were related to one or more undescribed orders
within the γ-Proteobacteria. Other abundant groups included the δ-Proteobacteria, Bacteroidetes, and Cyanobacteria. While these phyla were abundant in other estuarine sediments, the specific members at Sapelo Island appeared to be different
from those previously described in other locations, suggesting that great diversity exists between as well as within estuarine
intertidal sediments. In spite of the large differences in pore water chemistry with season and depth, differences in the
bacterial community were modest over the temporal and spatial scales examined and generally restricted to only certain taxa.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
6.
Change in Bacterial Community Structure in Response to Disturbance of Natural Hardwood and Secondary Coniferous Forest Soils in Central Taiwan 总被引:1,自引:0,他引:1
Forest management often results in changes in the soil and its microbial communities. In the present study, differences in
the soil bacterial community caused by forest management practices were characterized using small subunit (SSU) ribosomal
RNA (rRNA) gene clone libraries. The communities were from a native hardwood forest (HWD) and two adjacent conifer plantations
in a low-elevation montane, subtropical experimental forest at the Lienhuachi Experimental Forest (LHCEF) in central Taiwan.
At this locality, the elevation ranges from 600 to 950 m, the mean annual precipitation is 2,200 mm, the mean annual temperature
is 20.8°C, and the soil pH is 4. The conifer forests included a Cunninghamia konishii Hay (CNH) plantation of 40 years and an old growth Calocedrus formosana (Florin) Florin (CLC) forest of 80 years. A total of 476 clones were sequenced and assigned into 12 phylogenetic groups.
Proteobacteria-affiliated clones (53%) predominated in the library from HWD soils. In contrast, Acidobacteria was the most abundant phylum and comprised 39% and 57% in the CLC and CNH libraries, respectively. Similarly, the most abundant
OTUs in HWD soils were greatly reduced or absent in the CLC and CNH soils. Based on several diversity indices, the numbers
of abundant OTUs and singletons, and rarefaction curves, the diversity of the HWD community (0.95 in evenness and Shannon
diversity indices) was somewhat less than that in the CNH soils (0.97 in evenness and Shannon diversity indices). The diversity
of the community in CLC soils was intermediate. The differences in diversity among the three communities may also reflect
changes in abundances of a few OTUs. The CNH forest soil community may be still in a successional phase that is only partially
stabilized after 40 years. Analysis of molecular variance also revealed that the bacterial community composition of HWD soils
was significantly different from CLC and CNH soils (p = 0.001). These results suggest that the disturbance of forest conversion and tree species composition are important factors
influencing the soil bacterial community among three forest ecosystems in the same climate. 相似文献
7.
Ming Zhao Wei Xiao Yan Ma Tingting Sun Wenxia Yuan Na Tang Donglian Zhang Yongxia Wang Yali Li Hongjie Zhou Xiaolong Cui 《World journal of microbiology & biotechnology》2013,29(10):1877-1884
Microbes are thought to have key roles in the development of the special properties of post-fermented pu-erh tea (pu-erh shucha), a well-known traditional Chinese tea; however, little is known about the bacteria during the fermentation. In this work, the structure and dynamics of the bacterial community involved in the production of pu-erh shucha were investigated using 16S rRNA gene clone libraries constructed from samples collected on days zero (LD-0), 5 (LD-5), 10 (LD-10), 15 (LD-15) and 20 (LD-20) of the fermentation. A total of 747 sequences with individual clone library containing 115–174 sequences and 4–20 unique operational taxonomic units (OTUs) were obtained. These OTUs were grouped into four phyla (Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria) and further identified as members of 10 families, such as Alcaligenaceae, Bacillaceae, Enterobacteriaceae, etc. The dominant bacteria were Enterobacteriaceae in the raw material (LD-0) and in the initial stages of fermentation (LD-5 and LD-10), which changed to Bacillaceae at the last stages of fermentation (LD-15 and LD-20) at a temperature of 40–60 °C. It is interesting that the dominant OTUs in libraries LD-15 and LD-20 were very closely related to Bacillus coagulans, which is a safe thermoduric probiotic. Together the bacterial diversity and dynamics during a fermentation of pu-erh shucha were demonstrated, and a worthy clue for artificial inoculation of B. coagulans to improve the health benefits of pu-erh shucha or produce probiotic pu-erh tea were provided. 相似文献
8.
Minako Nishiyama Shuichi Yamamoto Norio Kurosawa 《Journal of microbiology (Seoul, Korea)》2013,51(4):413-422
Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota. 相似文献
9.
Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce (Picea mariana) Seedlings Grown in a Nursery 总被引:2,自引:0,他引:2
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Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries. 相似文献
10.
Baati H Guermazi S Amdouni R Gharsallah N Sghir A Ammar E 《Extremophiles : life under extreme conditions》2008,12(4):505-518
16S rRNA gene clone libraries were separately constructed from three ponds with different salt concentrations, M2 (15%), TS38
(25%) and S5 (32%), located within a multipond solar saltern of Sfax. The 16S rRNA genes from 216 bacterial clones and 156
archaeal clones were sequenced and phylogenetically analyzed. 44 operational taxonomic units (OTUs) were generated for Bacteria and 67 for Archaea. Phylogenetic groups within the bacterial domain were restricted to Bacteroidetes and Proteobacteria, with the exception that one cyanobacterial OTU was found in the TS38 pond. 85.7, 26.6 and 25.0% of the bacterial OTUs from
M2, TS38 and S5 ponds, respectively, are novel. All archaeal 16S rRNA gene sequences were exclusively affiliated with Euryarchaeota. 75.0, 60.0 and 66.7% of the OTUs from, respectively, M2, TS38 and S5 ponds are novel. The result showed that the Tunisian
multipond solar saltern harbored novel prokaryotic diversity that has never been reported before for solar salterns. In addition,
diversity measurement indicated a decrease of bacterial diversity and an increase of archaeal diversity with rising salinity
gradient, which was in agreement with the previous observation for thalassohaline systems. Comparative analysis showed that
prokaryotic diversity of Tunisian saltern was higher than that of other salterns previously studied.
A. Sghir and E. Ammar have equally contributed to this work. 相似文献
11.
Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis 总被引:2,自引:0,他引:2
The endophytic bacterial diversity in the roots of rice (Oryza sativa L.) growing in the agricultural experimental station in Hebei Province, China was analyzed by 16S rDNA cloning, amplified
ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast
DNA and mitochondrial DNA of rice, a pair of bacterial PCR primers (799f–1492r) was selected to specifically amplify bacterial
16S rDNA sequences directly from rice root tissues. Among 192 positive clones in the 16S rDNA library of endophytes, 52 OTUs
(Operational Taxonomic Units) were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed
diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of
the Proteobacteria, Cytophaga/Flexibacter/Bacteroides (CFB) phylum, low G+C gram-positive bacteria, Deinococcus-Thermus, Acidobacteria, and archaea. The dominant group was Betaproteobacteria (27.08% of the total clones), and the most dominant
genus was Stenotrophomonas. More than 14.58% of the total clones showed high similarity to uncultured bacteria, suggesting that nonculturable bacteria
were detected in rice endophytic bacterial community. To our knowledge, this is the first report that archaea has been identified
as endophytes associated with rice by the culture-independent approach. The results suggest that the diversity of endophytic
bacteria is abundant in rice roots. 相似文献
12.
Comparison of bacterioplankton communities in three mariculture ponds farming different commercial animals in subtropical Chinese coast 总被引:1,自引:0,他引:1
In order to explore the responses of the bacterioplankton community to different types of aquaculture environments, three
mariculture ponds comprised of groupers (Epinephelus diacanthus, ED), prawns (Penaeus vannamei, PV), and abalone (Haliotis
diversicolor supertexta, HDS) in southeast, coastal China were investigated. The free-living bacterial diversity was analyzed through
the construction of 16S rDNA clone library. A total of 203 16S rDNA sequences from three clone libraries were classified into
118 operational taxonomic units (OTUs), of which 51, 31, and 42 OTUs were distributed in the ED, PV, and HDS pond, respectively,
with Bacteroidetes (30.6%), Actinobacteria (55.2%), and Cyanobacteria (32.8%) as the dominant division in the respective ponds. Meanwhile, each pond occupied some unique OTUs that were affiliated
with uncommon (sub-)phyla, such as candidate OP11 division, Acidobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia. Bacterial diversity in the ED pond was the richest, followed by the HDS and the PV pond. OTUs of 61.9% and 94.9% have less
than 90% and 97% similarity to their nearest neighbors in public databases, respectively. All OTUs were grouped into 67 clusters,
covering 11 (sub-)phyla. The OTUs only from single pond distributed in 53 clusters (79.1%), the OTUs shared by two ponds were
affiliated with 14 clusters (20.9%), and none of clusters was formed by the OTUs which commonly originated from the three
pond libraries, suggesting that the composition of bacterial populations in these ponds were significantly different. These
results indicate that the aquatic environment created by different mariculture animals may foster very special and complex
bacterial communities.
Handling editor: David Philip Hamilton 相似文献
13.
Mariana P. Reis Francisco A. R. Barbosa Edmar Chartone-Souza Andréa M. A. Nascimento 《Extremophiles : life under extreme conditions》2013,17(2):301-309
Mining negatively affects the environment by producing large quantities of metallic tailings, such as those contaminated with arsenic, with harmful consequences for human and aquatic life. A culture-independent molecular analysis was performed to assess the prokaryotic diversity and community structural changes of the tropical historically metal-contaminated Mina stream (MS) and the relatively pristine Mutuca stream (MTS) sediments. A total of 234 bacterial operational taxonomic units (OTUs) were affiliated with 14 (MS) and 17 (MTS) phyla and 53 OTUs were associated with two archaeal phyla. Although the bacterial community compositions of these sediments were markedly distinct, no significant difference in the diversity indices between the bacterial communities was observed. Additionally, the rarefaction and diversity indices indicated a higher bacterial diversity than archaeal diversity. Most of the OTUs were affiliated with the Proteobacteria and Bacteroidetes phyla. Alphaproteobacteria, Gemmatimonadetes and Actinobacteria were only found in the MS clone library. Crenarchaeal 16S rDNA sequences constituted 75 % of the MS archaeal clones, whereas Euryarchaeota were dominant in the MTS clones. Despite the markedly different characteristics of these streams, their bacterial communities harbor high diversity, suggesting that historically mining-impacted sediments promote diversity. The findings also provide basis for further investigation of members of Alphaproteobacteria as potential biological indicators of arsenic-rich sediments. 相似文献
14.
Jizhong Zhou Beicheng Xia Heshu Huang Anthony V. Palumbo James M. Tiedje 《Applied microbiology》2004,70(3):1723-1734
Microbial community diversity and heterogeneity in saturated and unsaturated subsurface soils from Abbott's Pit in Virginia (1.57, 3.25, and 4.05 m below surface) and Dover Air Force Base in Delaware (6.00 and 7.50 m below surface) were analyzed using a culture-independent small-subunit (SSU) rRNA gene (rDNA)-based cloning approach. Four to six dominant operational taxonomic units (OTUs) were identified in 33 to 100 unique SSU rDNA clones (constituting about 40 to 50% of the total number of SSU rDNA clones in the clone library) from the saturated subsurface samples, whereas no dominant OTUs were observed in the unsaturated subsurface sample. Less than 10% of the clones among samples from different depths at the same location were identical, and the proportion of overlapping OTUs was lower for the samples that were vertically far apart than for adjacent samples. In addition, no OTUs were shared between the Abbott's Pit and Dover samples. The majority of the clones (80%) had sequences that were less than 5% different from those in the current databases. Phylogenetic analysis indicated that most of the bacterial clones were affiliated with members of the Proteobacteria family (90%), gram-positive bacteria (3%), and members of the Acidobacteria family (3%). Principal component analysis revealed that samples from different geographic locations were well separated and that samples from the same location were closely grouped together. In addition, the nonsaturated subsurface samples from Abbott's Pit clustered together and were well separated from the saturated subsurface soil sample. Finally, the overall diversity of the subsurface samples was much lower than that of the corresponding surface soil samples. 相似文献
15.
Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia 总被引:2,自引:0,他引:2
Kimura H Sugihara M Yamamoto H Patel BK Kato K Hanada S 《Extremophiles : life under extreme conditions》2005,9(5):407-414
To investigate the biomass and phylogenetic diversity of the microbial community inhabiting the deep aquifer of the Great Artesian Basin (GAB), geothermal groundwater gushing out from the aquifer was sampled and analyzed. Microbial cells in the groundwater were stained with acridine orange and directly counted by epifluorescence microscopy. Microbial cells were present at a density of 108–109 cells per liter of groundwater. Archaeal and bacterial small-subunit rRNA genes (rDNAs) were amplified by PCR with Archaea- and Bacteria-specific primer sets, and clone libraries were constructed separately. A total of 59 clones were analyzed in archaeal and bacterial 16S rDNA libraries, respectively. The archaeal 16S rDNA clones were divided into nine operated taxonomic units (OTUs) by restriction fragment length polymorphism. These OTUs were closely related to the methanogenic genera Methanospirillum and Methanosaeta, the heterotrophic genus Thermoplasma, or miscellaneous crenarchaeota group. More than one-half of the archaeal clones (59% of total 59 clones) were placed beside phylogenetic clusters of methanogens. The majority of the methanogen-related clones (83%) was closely related to a group of hydrogenotrophic methanogens (genus Methanospirillum). The bacterial OTUs branched into seven phylogenetic clusters related to hydrogen-oxidizing thermophiles in the genera Hydrogenobacter and Hydrogenophilus, a sulfate-reducing thermophile in the genus Thermodesulfovibrio, chemoheterotropic bacteria in the genera Thermus and Aquaspirillum, or the candidate division OP10. Clones closely related to the thermophilic hydrogen-oxidizers in the genera Hydrogenobacter and Hydrogenophilus were dominant in the bacterial clone library (37% of a total of 59 clones). The dominancy of hydrogen-users strongly suggested that H2 plays an important role as a primary substrate in the microbial ecosystem of this deep geothermal aquifer. 相似文献
16.
Bacterial diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis 总被引:1,自引:0,他引:1
P. R. Pandya K. M. Singh S. Parnerkar A. K. Tripathi H. H. Mehta D. N. Rank R. K. Kothari C. G. Joshi 《Journal of applied genetics》2010,51(3):395-402
Bacterial communities in buffalo rumen were characterized using a culture-independent approach for a pooled sample of rumen
fluid from 3 adult Surti buffaloes. Buffalo rumen is likely to include species of various bacterial phyla, so 16S rDNA sequences
were amplified and cloned from the sample. A total of 191 clones were sequenced and similarities to known 16S rDNA sequences
were examined. About 62.82% sequences (120 clones) had >90% similarity to the 16S rDNA database sequences. Furthermore, about
34.03% of the sequences (65 clones) were 85–89% similar to 16S rDNA database sequences. For the remaining 3.14%, the similarity
was lower than 85%. Phylogenetic analyses were also used to infer the makeup of bacterial communities in the rumen of Surti
buffalo. As a result, we distinguished 42 operational taxonomic units (OTUs) based on unique 16S r DNA sequences: 19 OTUs
affiliated to an unidentified group (45.23% of total OTUs), 11 OTUs of the phylum Firmicutes, also known as the low G+C group
(26.19%), 7 OTUs of theCytophaga-Flexibacter-Bacteroides phylum (16.66%), 4 OTUs of Spirochaetes (9.52%), and 1 OTU of Actinobacteria (2.38%). These include 10 single-clone OTUs,
so Good’s coverage (94.76%) of 16S rRNA libraries indicated that sequences identified in the libraries represent the majority
of bacterial diversity present in rumen. 相似文献
17.
Xuexia Yang Zhangjun Cao Jihong Lao Yunxia Deng Hui Chen 《Engineering in Life Science》2009,9(4):331-335
The presence of oil is the major limitation to the regeneration of spun silk from waste silk. A pure culture fermentation process was developed to remove oil from waste silk. Fourteen strains were isolated from natural fermentation liquor of waste silk. The strain D3 showed highest lipase activity and oil‐removing ability. This strain was identified as Rhodococcus sp. on the basis of morphological and biochemical characteristics and 16S rRNA sequence analysis. The strain D3 was used to remove oil from waste silk by pure culture fermentation. The effects of various parameters on oil removal were investigated. A pH of 7.0, a temperature of 35–40°C, an incubation time of three days and an inoculum of 10% were optimum conditions for removing oil from waste silk by stain D3. This study shows that pure culture fermentation is a promising process to improve the oil removal of waste silk. 相似文献
18.
三江源地区不同植被土壤固氮微生物的群落结构研究 总被引:15,自引:0,他引:15
利用PCR_RFLP和测序分析法对位于青藏高原腹地三江源自然保护区的高寒草甸、高寒草原和高山森林等不同植被类型的土壤固氮微生物的群落组成进行了探讨。经过PCR_RFLP分析固氮基因nifH ,在3个样品中共得到2 33个克隆和99个可操作分类单元(OTUs) ,NQ_1样地具有最多的克隆数和OTUs,多样性为4 9 74 % ,在所有样品中分别具有1~2个明显的优势种群(占总克隆数>15 % ) ,并且具有4个共同的OTUs。选取了2 6个克隆进行基因测序分析,通过DNAMAN比较表明,这些序列间具有6 6 %~98%的相似性,并且在GenBank数据库中没有发现完全匹配的序列,因此这些序列可能代表着新的固氮生物株系。最后利用ClustalW与Mega软件构建了系统发育树,结果发现,这些序列被分为4个不同的簇,部分序列与属于蛋白细菌(Proteobacteria)的已知细菌具有近的亲缘关系,但是更多的序列与已知细菌具有较远的亲缘关系,而且nifH基因序列的分布在样地间没有明显的聚类 相似文献
19.
LeLeng To Isaacs Jinjun Kan Linh Nguyen Patrick Videau Matthew A. Anderson Toby L. Wright Russell T. Hill 《Marine biotechnology (New York, N.Y.)》2009,11(6):758-770
The red-beard sponge Clathria prolifera, which is widely distributed in the USA, has been widely used as a model system in cell biology and has been proposed as
a suitable teaching tool on biology and environmental sciences. We undertook the first detailed microbiological study of this
sponge on samples collected from the Chesapeake Bay. A combination of culture-based studies, denaturing gradient gel electrophoresis,
and bacterial community characterization based on 16S rRNA gene sequencing revealed that C. prolifera contains a diverse assemblage of bacteria that is different from that in the surrounding water. C. prolifera individuals were successfully maintained in a flow-through or recirculation aquaculture system for over 6 months and shifts
in the bacterial assemblages of sponges in aquaculture compared with wild sponges were examined. The proteobacteria, bacteroidetes,
actinobacteria, and cyanobacteria represented over 90% of the species diversity present in the total bacterial community of
the wild C. prolifera. Actinobacteria, cyanobacteria, and spirochetes were not represented in clones obtained from C. prolifera maintained in the aquaculture system although these three groups comprised ca. 20% of the clones from wild C. prolifera, showing a significant effect of aquaculture on the bacterial community composition. This is the first systematic characterization
of the bacterial community from a sponge found in the Chesapeake Bay. Changes in sponge bacterial composition were observed
in sponges maintained in aquaculture and demonstrate the importance of monitoring microbial communities when cultivating sponges
in aquaculture systems. 相似文献
20.
Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern
Baati H Jarboui R Gharsallah N Sghir A Ammar E 《Canadian journal of microbiology》2011,57(12):975-981
The microbial community of a magnesium-rich bittern brine saturated with NaCl (380-400 g/L) from a Tunisian solar saltern was investigated using a molecular approach based on 16S rRNA gene analysis and viability tests. The results revealed the existence of microbial flora. Viability test assessment showed that 46.4% of this flora was viable but not detectable by culturability tests. 16S rRNA genes from 49 bacterial clones and 38 archaeal clones were sequenced and phylogenetically analyzed. Eleven operational taxonomic units (OTUs) determined by the DOTUR program with 97% sequence similarity were generated for Bacteria. These OTUs were affiliated with Bacteroidetes and Gammaproteobacteria. The archaeal community composition exhibited more diversity with 38 clones, resulting in 13 OTUs affiliated with the Euryarchaeota phylum. Diversity measurement showed a more diverse archaeal than bacterial community at the saturated pond. 相似文献