Amplified Ribosomal DNA Restriction Analysis Patterns Research Articles

Antimicrobial Activity of Extremely Halophilic Archaea Isolated from Southern Thai Salt-Fermented Products and Solar Saltern of Pattani, Thailand

This research aimed to study the diversity and antimicrobial activity of culturable haloarchaea in soil samples of solar saltern in Pattani Province, Thailand and Southern Thai salt-fermented food. Seventy-seven extremely haloarchaea were isolated on Halophilic medium agar containing 25% NaCl at 37°C for 7-21 days. They were grouped by Amplified Ribosomal DNA Restriction Analysis (ARDRA) with two restriction enzymes, RsaI and HindIII. The ARDRA patterns illustrated 6 different Operation Taxonomic Units (OTUs). Partial 16S rRNA gene sequences (938 bp) of the representative of each OTUs were aligned with the GenBank database. The results showed that the representatives of OTU1, OTU2, OTU3, OTU4, OTU5, and OTU6 had 99-100% similarity to Halobacterium salinarum, 99-100% similarity to Halostagnicola larsenii, 99% similarity to Natronococcus sp., 99-100% similarity to Haloferax alexandrinus, 99-100% similarity to Natrialba sp. and 97% similarity to Halococcus sp., respectively. The antimicrobial activity testing of the 17 isolated haloarchaeal strains from solar saltern was performed against 5 tested strains of Hbt. salinarum and 1 strain of Natrialba sp. were isolated from fermented food. Seven (41.2%) were candidate halocin-producing strains. In addition, no phage activity was observed. The 14-day fermentation broth of Natronococcus sp. SS13 showed the highest antimicrobial activity against Hbt. salinarum PK08, BD07 and BD09 (>5,120 AU/ml).

Characterisations of Probiotic <i>Lactobacillus</i> Strains by Amplified Ribosomal DNA Restriction Analysis (ARDRA)

Twelve probiotic Lactobacillus strains for poultry were characterised by amplified ribosomal DNA restriction analysis (ARDRA) using Sau3AI, TaqI, HaeIII and AluI restriction endonucleases. Species-specific and strain-specific restriction patterns were observed from the bacterial strains. Numerical analysis of composite analysis of ARDRA exhibited D value of 0.8456. Whereas, the caculated D values of ARDRA patterns generated by Sau3AI, TaqI, HaeIII and AluI were 0.8309, 0.8382,0.8088 and 0.8088, repectively. Composite analysis of ARDRA was the most discriminative method when compared to the individual analysis. ARDRA could distinguished L. reuteri C 10 and L. panis C 17 into single strains. The 16S rRNA gene restriction patterns were also able to group L. gallinarum I 16 and I 26 into single strains. Lactobacillus brevis I 12, I 23, I 25, I 211 and I 218 seem to be multiple clones of the same bacterial strain as are L. reuteri C 1 and C 16. ARDRA is a valuable fingerprinting method to discriminate probiotic Lactobacillus strains.

Gardnerella vaginalis Subgroups Defined by cpn60 Sequencing and Sialidase Activity in Isolates from Canada, Belgium and Kenya.

Increased abundance of Gardnerella vaginalis and sialidase activity in vaginal fluid is associated with bacterial vaginosis (BV), a common but poorly understood clinical entity associated with poor reproductive health outcomes. Since most women are colonized with G. vaginalis, its status as a normal member of the vaginal microbiota or pathogen causing BV remains controversial, and numerous classification schemes have been described. Since 2005, sequencing of the chaperonin-60 universal target (cpn60 UT) has distinguished four subgroups in isolate collections, clone libraries and deep sequencing datasets. To clarify potential clinical and diagnostic significance of cpn60 subgroups, we undertook phenotypic and molecular characterization of 112 G. vaginalis isolates from three continents. A total of 36 subgroup A, 33 B, 35 C and 8 D isolates were identified through phylogenetic analysis of cpn60 sequences as corresponding to four “clades” identified in a recently published study, based on sequencing 473 genes across 17 isolates. cpn60 subgroups were compared with other previously described molecular methods for classification of Gardnerella subgroups, including amplified ribosomal DNA restriction analysis (ARDRA) and real-time PCR assays designed to quantify subgroups in vaginal samples. Although two ARDRA patterns were observed in isolates, each was observed in three cpn60 subgroups (A/B/D and B/C/D). Real-time PCR assays corroborated cpn60 subgroups overall, but 13 isolates from subgroups A, B and D were negative in all assays. A putative sialidase gene was detected in all subgroup B, C and D isolates, but only in a single subgroup A isolate. In contrast, sialidase activity was observed in all subgroup B isolates, 3 (9%) subgroup C isolates and no subgroup A or D isolates. These observations suggest distinct roles for G. vaginalis subgroups in BV pathogenesis. We conclude that cpn60 UT sequencing is a robust approach for defining G. vaginalis subgroups within the vaginal microbiome.

药用植物凤丹(Paeonia suffruticosa)根际土壤细菌群落16S rRNA基因的ARDRA分析

PDF HTML阅读 XML下载 导出引用 引用提醒 药用植物凤丹(Paeonia suffruticosa)根际土壤细菌群落16S rRNA基因的ARDRA分析 DOI: 10.5846/stxb201503030405 作者: 作者单位: 安徽师范大学,安徽师范大学,安徽师范大学,安徽师范大学,安徽师范大学,安徽师范大学 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金（81173491）；安徽省自然科学基金资助项目（1308085MC42） Bacterial diversity in rhizosphere soil of the medicinal tree peony (Paeonia suffruticosa) revealed by amplified ribosomal DNA restriction analysis Author: Affiliation: Anhui normal university,Anhui normal university,Anhui normal university,,Anhui normal university,Anhui normal university Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:凤丹（Paeonia suffruticosa Andr.）为芍药科多年生植物，是一种重要的传统中药资源。在其生长发育的周期中与土壤微生物尤其是根际土壤微生物有密切的关系。通过构建16S rRNA基因克隆文库及文库的限制性片段长度多态性分析（ARDRA），对中国药用植物凤丹5大主要分布区域的根际土壤细菌群落多样性进行了研究。采用限制性内切酶HinfI和Csp6I对克隆文库中随机挑选的1000个白色克隆子进行了酶切分型，根据酶切图谱的不同，将其分为324个OTUs，并对38个优势OTUs进行了测序和系统发育分析。16S rRNA基因序列分析结果表明，凤丹根际土壤细菌种群主要包括：变形菌门（包括alpha、beta、gamma、detla亚门）、酸杆菌门、放线菌门、拟杆菌门及厚壁菌门等11类细菌，此外还包含了3个未归类的细菌。变形菌门和酸杆菌门为文库中的主要菌群，分别占克隆总数的47.34%和14.36%，其中Pseudomonas sp.、Burkholderia sp.和Arthrobacter sp.为优势菌属。研究结果表明，我国药用植物凤丹5大主要分布区域的根际土壤细菌种群不仅具有丰富的多样性，还存在丰富的潜在新菌种。 Abstract:The medicinal tree peony (Paeonia suffruticosa) is an important resource in traditional Chinese medicine. Soil bacteria, especially rhizosphere bacteria, have strong effects on plant health and growth. In this study, the bacterial community structure and diversity in P. suffruticosa rhizosphere soil in five major distribution areas in China were investigated by amplified ribosomal DNA restriction analysis (ARDRA). The ARDRA patterns of the amplified 16S rRNA gene produced an average of 2-6 bands that ranged in size from 100 to 1302 bp, which indicated that the fragments of the 16S rRNA gene were efficiently double-digested with the restriction endonucleases HinfI and Csp6I. ARDRA-based cluster analysis showed that 702 positive clones were clustered into 74, 69, 76, 73, and 72 operational taxonomic units (OTUs) in the FH, YS, BZ, HZ, and LY libraries, respectively. Most of the OTUs contained 1-3 clones, which implied high diversity in the peony rhizosphere soil; twenty-six OTUs contained 4-6 clones; and five OTUs contained 7-12 clones. Rarefaction analysis showed that the positive clones in each library covered the diversity of bacterial taxa, which was further confirmed by clone library coverage (range:71.32%-81.40%). Diversity analysis indicated high bacterial diversity in the soils (Shannon diversity index 3.949-4.184; Chao1 index range 89.52-107.25). Sequence analysis revealed diverse bacterial phyla in the 16S rRNA gene library, consisting of α, β, γ, and δ subclasses of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, TM7, Gemmatimonadetes, and three unclassified bacteria. The dominant phyla were Proteobacteria and Acidobacteria (47.34% and 14.36% of the total clones, respectively), and the dominant genera in the clone libraries were Pseudomonas, Burkholderia, and Arthrobacter. In addition, a portion of the clones was only distantly related to sequences in the GenBank database, suggesting that bacteria in rhizosphere soil of the medicinal tree peony were unique and diverse. Furthermore, the relative abundance of Firmicutes (mainly Bacillus spp.) was positively correlated with soil Cu content. The rhizosphere bacteria belonged the same dominant phyla (Proteobacteria, Acidobacteria, and Actinobacteria) and showed high diversity between geo-authentic and non-authentic areas, implying that P. suffruticosa tended to form a similar microenvironment and select similar bacterial communities in the rhizosphere soil. 参考文献 相似文献 引证文献

Culture dependent diversity and phylogeny of thermophilic bacilli from a natural hot spring reservoir in the Gir Forest, Gujarat (India)

The thermophilic bacteria, isolated from a natural hot spring reservoir, Tulsi Shyam (Gir Forest, Gujarat, India) were characterized and diversified using the conventional approaches; Gram reaction, cell morphology, growth patterns, biochemical properties and antibiotic sensitivity. The bacteria were Gram positive, rod shaped and catalase positive. Majority of them produced amylase, indicating their ecological and biotechnological significance. The bacteria were further categorized on the basis of the amplified ribosomal DNA restriction analysis (ARDRA) patterns, generated by a tetracutter RE, HaeIII. As a polyphasic taxonomy approach, the isolates were clustered into 9 different groups, based on the conventional approaches and the ARDRA patterns. The further analysis was based on the 16S rRNA gene sequencing. The trend suggested that the phenotypic and phylogenetic diversity data considerably coincided. Overall, the part of Tulsi Shyam hot spring bacterial community represented by cultivated aerobic organotrophs can be clustered into 3 Genera, Anoxybacillus, Geobacillus/Aeribacillus and Bacillus. They can further be grouped into sub-clusters at the species level to establish phylogenetic and phenotypic relationship. Further, the diversity indices; Simpson’s index, Dominance index and Shannon index indicated the species diversity, species richness and distribution evenness, respectively. A lower Simpson’s index (0.1905) and higher Dominance index (0.8095) revealed significant bacterial diversity. While a higher Shannon index (2.987) suggested evenness in the bacterial distribution in different soil and water samples. The lower values of Berger-Parker Dominance index and Ginni coefficient supported the trends of the Shannon index. As the studied habitat was not earlier explored for the bacterial diversity, the findings would significantly add to the knowledge of the cultivation based microbial diversity.

Study of Lactic Acid Bacteria Community From Raw Milk of Iranian One Humped Camel and Evaluation of Their Probiotic Properties.

Background:Camel milk is amongst valuable food sources in Iran. On the other hand, due to the presence of probiotic bacteria and bacteriocin producers in camel milk, probiotic bacteria can be isolated and identified from this food product.Objectives:The objectives of the present research were the isolation and molecular identification of lactic acid bacteria from camel milk and evaluation of their probiotic properties.Materials and Methods:A total of ten samples of camel milk were collected from the Golestan province of Iran under aseptic conditions. Bacteria were isolated by culturing the samples on selective medium. Isolates were identified by amplification of the 16S rDNA and Internal Transcribed Spacer (ITS) region between the 16S and 23S rRNA genes by Polymerase Chain Reaction (PCR) and were then screened and grouped by the Amplified Ribosomal DNA Restriction Analysis (ARDRA) method. To evaluate probiotic properties, representative isolates of different ARDRA profiles were analyzed. The antimicrobial activity of Lactic Acid Bacteria (LAB) against Pediococcus pentosaceus, Escherichia coli and Bacillus cereus was examined by the agar diffusion assay. Acid and bile tolerance of isolates were evaluated.Results:A total of 64 isolates were analyzed based on biochemical tests and morphological characteristics. The most frequently isolated LAB was Enterococci. Weissella, Leuconostoc, Lactobacilli and Pediococci were less frequently found. Based on restriction analysis of the ITS, the isolates were grouped into nine different ARDRA patterns that were identified by ribosomal DNA sequencing as P. pentosaceus, Enterococcus faecium strain Y-2, E. faecium strain JZ1-1, E. faecium strain E6, E. durans, E. lactis, Leuconostoc mesenteroides, Lactobacillus casei and Weissella cibaria. The results showed that antimicrobial activity of the tested isolates was remarkable and P. pentosaceus showed the most antibacterial activity. In addition, E. durans, E. lactis, L. casei and P. pentosaceus were selected as probiotic bacteria.Conclusions:This study revealed the presence of bacteriocin-producing bacteria and probiotic bacteria in camel milk from the Golestan province of Iran.

A survey on cultivable heterotrophic bacteria inhabiting a thermally unstratified water column in an Atlantic Rainforest lake.

Due to the importance of heterotrophic bacteria in biogeochemical cycles and their influence on water quality, many studies have assessed the composition of the bacterial community. Most of these were made in temperate freshwaters. Eighteen heterotrophic bacteria communities distributed over time and space in the water column of Carioca Lake, not exposed to anthropogenic activities, were analyzed to characterize their composition. A polyphasic approach was used, including 16S rDNA restriction analysis, 16S rRNA gene sequence analysis, BIOLOG Ecoplates and statistical methods. The physiological profiles among the 18 microbial communities were diverse. Clustering analysis and the metabolic fingerprint of the Biolog EcoplateTM system data separated the communities based on temporal scale. A set of 673 isolates were recovered on high nutrient medium. The 673 isolates obtained yielded 360 Amplified Ribosomal DNA Restriction Analysis (ARDRA) Operational Taxonomic Units (OTUs). Most (313) of the ARDRA patterns, OTUs, were from isolates obtained in a single sampling point, in temporal and spatial scales, indicating changes in the bacterial community. A subset of representative isolates for each ARDRA OTU was identified by 16S rRNA gene fragment sequencing and categorized into five phyla, Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Deinococcus-Thermus, represented by 38 genera. The results of this work contribute to a better understanding about the phylogeny of tropical freshwater heterotrophic bacteria.

Analisis Keragaman Genetik Isolat Bakteri Xanthomonas oryzae pv. oryzae dari Jawa Barat dan Jawa Tengah Berdasarkan Analisis ARDRA Gen 16SrRNA

Fifteen Xanthomonas oryzae pv. oryzae isolates from several regions in West Java and Central Java have been studied for their genetic diversity using amplified ribosomal DNA restriction analysis (ARDRA) 16SrRNA gene.Total of 13 ARDRA patterns from digestion of DNA with RsaI restriction enzyme was obtained, indicated higher genetic diversity of X. oryzae pv. oryzae. Phylogenetic analysis revealed a close genetic relationships among isolates. Isolates X. oryzae pv. oryzae 1/96pml and 61pml are closely related with isolates 29d, 59pml, and 60pml although they are isolated from different locations. The other closely related isolates were between X. oryzae pv. oryzae 5mgl with 23d, 38d, 10sbg, 8myd; while 6klt was close to 3ind and 2kr. The result of X. oryzae pv. oryzae genetic diversity can be used as a reference for strain or/isolates selection for development ofbacterial leaf blight resistance in Indonesia.

Bacterial Diversity Analysis of Coal Mine Drainage Enriched by Different Energy Sources

Coal mine drainage (CMD) collected from Meitanba mine (Hunan province, China) was studied. Coal, sulfur, ferrous sulfate, and a mixture of sulfur and ferrous sulfate were employed as selective energy substrates to culture CMD cells, and the bacterial biodiversities of each group were investigated. Four groups, C group [coal (15%, m/v) + CMD], S group [sulfur (10%, m/v) + CMD], SF group [sulfur (5%, m/v) + ferrous sulfate (22.35%, m/v) + CMD], and F group [ferrous sulfate (44.7%, m/v) + CMD] were set up. A total of 211 clones were recovered and evaluated by amplified ribosomal DNA restriction analysis (ARDRA). A total of 26 different ARDRA patterns were obtained and studied as operational taxonomic units (OTUs). The results showed that the F group could not be studied because of its extremely low cell concentration. The S, SF, and C groups all obtain their OTUs of 7, 8, and 11, respectively. Although they had the same original CMD, obvious differences were detected among these three groups. Additionally, A...

Amplified Ribosomal DNA Restriction Analysis를 이용한 광양만 해수의 세균 군집의 계절적 변화

To determine the seasonal variation of bacterial community in the seawater of Gwangyang Bay, three hundred thirty six bacterial strains were isolated on February, May, July and October 2011. Amplified Ribosomal DNA Restriction Analysis (ARDRA) was used to construct the phylotyes of the isolates using the restriction endonuclease, Hae III. Diversity indices of ARDRA patterns were calculated. One hundred and one phylotypes including 40 unique pylotypes were found at the 80% similarity level. Partial 16S rRNA genes of one hundred thirty nine strains representing each phylotypes were sequenced and compared. Bacterial community composed of 4 different phyla which include Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. Proteobacteria was the prevailing phylum in all seasons, followed by Bacteroidetes in winter, spring and autumn while Actinobacteria in summer. At the family level, Flavobacteriaceae dominated in winter and spring and Pseudoalteromonadaceae did in summer and autumn. Genera Altererythrobacter, Loktanella, Pseudoalteromonas and Vibrio were encountered in all seasons. The most diverse bacterial community was found in autumn followed by the order of spring, winter and summer.

Development of genus‐specific primers for better understanding the diversity and population structure of Sphingomonas in soils

Genus Sphingomonas has received increasing attentions due to its somewhat unique metabolic versatilities in the contaminated environment. However, due to the lack of genus-specific primers, the ecological significance of Sphingomonas in polluted soils has been rarely documented by 16S rDNA finger-printing methods. In this study, three genus-specific primer sets targeted at the 16S rRNA gene of Sphingomonas were developed and their specificities were tested with four contaminated soils from Shenfu petroleum-wastewater irrigation zone by constructing clone libraries, amplified ribosomal DNA restriction analysis (ARDRA) and sequencing the represented ARDRA patterns. Meanwhile, the newly designed primer sets and a previously reported primer set were compared, and the results showed that the newly developed primer set SA/429f-933r could detect a larger spectrum (90%) of Sphingomonas strains with higher specificity. Despite the superiority of primer set SA/429f-933r in specifically detecting Sphingomonas from contaminated soils, we cannot blink the fact that different primer sets preferentially amplified different dominant species. Therefore, two or more primer sets are recommended for evaluating the diversity and population structure of genus Sphingomonas. Additionally, a proportion (9.7%) of the cloned sequences discovered in this study were different from known Sphingomonas sequences, suggesting that new Sphingomonas sequences might present in soils from Shenfu irrigation zone.

Effects of methamidophos on the community structure, antagonism towards Rhizoctonia solani, and phlD diversity of soil Pseudomonas

A microcosm incubation study using an aquic brown soil from northeast China (a Cambisol in the UN Food and Agriculture Organization FAO Soil Taxonomy) was conducted to examine the effects of different concentrations (0, 50, 150, and 250 mg kg−1) of methamidophos (O,S-dimethyl phosphoramidothioato) on Pseudomonas, one of the most important gram-negative bacteria in soil. Amplified ribosomal DNA restriction analysis (ARDRA) was performed to study the Pseudomonas community structure, an in vitro assay was made to test the antagonistic activity of isolated Pseudomonas strains against soil-borne Rhizoctonia solani, a major member of the pathogens highly related to soil-borne plant diseases, and special primer amplification and sequencing were performed to investigate the diversity of phlD, an essential gene in the biosynthesis of 2, 4-diacetylphloroglucinol (2, 4-DAPG), which has biocontrol activity in phlD +isolates. With exposure to increasing methamidophos concentrations, the total number of soil Pseudomonas ARDRA patterns decreased significantly, but with less change in the same treatments over 1, 3, and 5 weeks of incubation. The number of isolated Pseudomonas strains with antagonistic activity against R. solani as well as the diversity and appearance frequency of the strains' phlD gene also decreased with increasing concentrations of methamidophos, especially at high methamidophos concentrations. Applying methamidophos could increase the risk of soil-borne plant diseases by decreasing the diversity of the soil Pseudomonas community and the amount of R. solani antagonists, particularly those with the phlD gene.

Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere.

The genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal DNA restriction analysis (ARDRA), 16S rRNA sequence homology and phylogenetics analysis methods. Studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. A total of 28 ARDRA patterns were identified among the 299 siderophore-producing bacterial isolates. The 28 ARDRA patterns represented bacteria of 14 different genera belonging to six bacterial divisions, namely β-, γ-, α-Proteobacteria, Sphingobacteria, Bacilli, and Actinobacteria. Especially, γ-Proteobacteria consisting of Pseudomonas, Enterobacter, Serratia, Pantoea, Erwinia and Stenotrophomonas genus encountered 18 different ARDRA groups. Results also showed a greater siderophore-producing bacterial diversity than previous researches. For example, Sphingobacterium (isolates G-2-21-1 and G-2-27-2), Pseudomonas poae (isolate G-2-1-1), Enterobacter endosymbiont (isolates G-2-10-2 and N-5-10), Delftia acidovorans (isolate G-1-15), and Achromobacter xylosoxidans (isolates N-46-11HH and N-5-20) were reported to be able to produce siderophores under low-iron conditions for the first time. Gram-negative isolates were more frequently encountered, with more than 95% total frequency. For Gram-positive bacteria, the Bacillus and Rhodococcus were the only two genera, with 1.7% total frequency. Furthermore, the Pseudomonas and Enterobacter were dominant in this environment, with 44.5% and 24.7% total frequency, respectively. It was also found that 75 percent of the isolates that had the high percentages of siderophore units (% between 40 and 60) belonged to Pseudomonas. Pseudomonas sp. G-229-21 screened out in this study may have potential to apply to low-iron soil to prevent plant soil-borne fungal pathogen diseases.

Archaeal diversity in acid mine drainage from Dabaoshan Mine, China

Three acid mine drainage (AMD) samples collected from Dabaoshan Mine (Guangdong Province, China) were studied. In addition to physicochemical analyses, the diversity and community structures of the archaeal communities in these samples were described at the genetic level by amplified ribosomal DNA restriction analysis (ARDRA). Nine different ARDRA patterns were obtained from 146 clones and were studied as operational taxonomic units (OTUs), which were re-amplified and sequenced. Sequence data and phylogenetic analysis showed that most of the clones belonged to the Thermoplasmatales, and that archaea belonging to the Sulfolobales were absent. Only 1 OTU attributed to Ferroplasma was found and was observed to be abundant in all 3 samples. Eight OTUs were related to 2 new undefined groups in the Thermoplasmatales. Of the 8 OTUs, the clones in 2 similar units were isolated from samples collected from an abandoned sulfide mine (Huelva, Spain) and those in 5 similar units were isolated from samples collected from a closed copper mine (Tonglushan, China). These diversities were characterized by the reciprocal of Simpson's index (1/D) and correlated with the concentrations of ferrous ions and toxic ions in the AMD samples. The high temperature of the sampling sites was one of the factors that could explain why archaea belonging to the Thermoplasmatales were abundant in the analyzed AMD samples while those belonging to the Sulfolobales were absent.

Microbial Response to Na2SO4 Additions in a Volcanic Soil

We studied the effects of increased electrical conductivity (EC) of a soil on the activity and structure of its microbial community. Dry soil samples were added with 0, 11, 22, and 45 g kg−1 of Na2SO4 and left to incubate for 40 d before microbial respiration, microbial biomass C (MBC), microbial biomass N (MBN), K2SO4-extractable C (Ext-C), K2SO4-extractable N (Ext-N), and potentially mineralizable N (PMN) were determined. Amplified ribosomal DNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis (DGGE) were applied on α-, β-proteobacterial, and actinomycete 16S rDNA fragments amplified by PCR from total DNA in order to better understand the effect of osmotic stress on the soil microbial communities. The increase in EC significantly reduced respiratory activity of the microbial biomass and lowered microbial C; moreover, it increased the soluble fraction of both C and N. Greater N mineralization was found in soils to which 11 and 22 g kg−1 of Na2SO4 had been added as compared with both the untreated soil, and that receiving 45 g kg−1 of Na2SO4. The two former soils were also richer in aerobic bacteria (107 CFU g−1 soil) than the other two soils (106 CFU g−1 soil), and the ARDRA and DGGE analyses showed an activation of the α-proteobacteria. No significant differences were found in the ARDRA and DGGE patterns of the β-proteobacteria and actinomyces groups, suggesting a no-detectable response of these microorganisms to the Na2SO4 addition within the concentration range in this study.

Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 47:141-151 (2007) - doi:10.3354/ame047141 Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China Yu Yang1,2, Min-xi Wan1, Wu-yang Shi1, Hong Peng1, Guan-zhou Qiu1,2, Ji-zhong Zhou3, Xue-duan Liu1,2,* 1School of Minerals Processing and Bioengineering, Central South University, 25 South Lushan Road, Changsha, Hunan 410083, China 2Key Laboratory of Biometallurgy, Ministry of Education, 25 South Lushan Road, Changsha, Hunan 410083, China 3Department of Botany and Microbiology, 770 Van Vleet Oval, University of Oklahoma, Norman, Oklahoma 73019-4110, USA *Email: xueduanliu@yahoo.com ABSTRACT: Three samples of acid mine drainage (AMD) collected from Dabaoshan Mine (Guangdong Province, China) were studied. In addition to physico-chemical analyses, bacterial diversities and community structures of these samples were described at genetic level by amplified ribosomal DNA restriction analysis (ARDRA). A total of 60 different ARDRA patterns were obtained from 377 clones and were studied as operational taxonomic units (OTUs), which were re-amplified and sequenced. The sequence data and phylogenetic analysis showed that Acidithiobacillus ferrooxidans represented 88.0% of the bacterial population in Sample LC. However, Samples JX and FS contained more diverse colonies of bacteria, such as Leptospirillum ferrooxidans (JX: 16.9%, FS: 39.1%), Acidiphilum sp. (JX: 38.7%, FS: 25.8%) and A. ferrooxidans (JX: 12.1%, FS: 10.2%). These diversities were characterized by the reciprocal of Simpson’s index (1/D) and correlated with the concentrations of ferrous iron and toxic ions in AMD. KEY WORDS: Bacterial diversity · Microbial community · Acid mine drainage · Amplified ribosomal DNA restriction analysis Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 47, No. 2. Online publication date: May 16, 2007 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2007 Inter-Research.

Seasonal Dynamics of the Bacterial Community of a Mudflat at the Mouth of a Major Kentucky Lake Reservoir Tributary

ABSTRACT Sediment samples were taken from the mudflat of Ledbetter embayment at the mouth of the stream, at summer pool when it was submerged and at winter pool when it was exposed. DNA was extracted and molecular techniques were applied to avoid problems associated with bacterial culture. Amplified Ribosomal DNA Restriction Analysis (ARDRA) found 96 different fingerprints in 350 clones containing amplified sediment 16S rDNA. There were 54 different patterns in the 180 clones examined from summer samples and 55 in the 170 clones examined from winter samples. Only 13 ARDRA patterns were found in both winter and summer. These were among the most abundant organisms found and were found frequently in both summer and winter. Sequence analysis of clones with different ARDRA patterns showed that the α and β Proteobacteria were the most abundant bacteria in these samples and were abundant in both winter and summer. The α Proteobacteria, however, were the most abundant group in winter and the β Proteobacteria were...

New species of rumen treponemes

Three strains of rumen treponemes were isolated and partially characterized. The strains differed significantly one from another in morphology, fermentation characteristics and plasmid profiles. Their genetic variability was assayed using DNA-based molecular approaches. Easily differentiated ARDRA (amplified ribosomal DNA restriction analysis) patterns indicated that the strains represent different bacterial species.

Rapid identification of marine bioluminescent bacteria by amplified 16S ribosomal RNA gene restriction analysis

To rapidly identify natural isolates of marine bioluminescent bacteria, we developed amplified ribosomal DNA restriction analysis (ARDRA) methods. ARDRA, which is based on the restriction patterns of 16S rRNA gene digested with five enzymes (EcoRI, DdeI, HhaI, HinfI, RsaI), clearly distinguished the 14 species of marine bioluminescent bacteria currently known, which belong to the genera Vibrio, Photobacterium, and Shewanella. When we applied ARDRA to 129 natural isolates from two cruises in Sagami Bay, Japan, 127 were grouped into six ARDRA types with distinctive restriction patterns; these isolates represented the bioluminescent species, P. angustum, P. leiognathi, P. phosphoreum, S. woodyi, V. fischeri, and V. harveyi. The other two isolates showing unexpected ARDRA patterns turned out to have 16S rRNA gene sequences similar to P. leiognathi and P. phosphoreum. Nevertheless, ARDRA provides a simple and fairly robust means for rapid identification of the natural isolates of marine bioluminescent bacteria, and is therefore useful in studying their diversity.

Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis

Amplified ribosomal DNA restriction analysis (ARDRA) was used for assessing the effect of copper contamination on the microbial community in soil. ARDRA is a DNA fingerprinting technique based on PCR amplification of 16S ribosomal DNA using primers for conserved regions, followed by restriction enzyme digestions and agarose gel electrophoresis. This results in distinguishable fingerprints for different bacterial species. Microbial community structure in soil was investigated by studying ARDRA patterns of the whole community, and by comparing ARDRA patterns of cloned 16S RNA gene sequences from soil and isolates obtained from soil by cultivation. Distinct differences in microbial community structure and a lower diversity were found in a soil contaminated with copper compared with non-contaminated soil. Diversity of ARDRA patterns from the clones was higher than that from isolates, supporting the general idea that the culturable population represents only a part of the total (amplifiable) population in soil. To compare microbial communities from various soils a method is described for the construction of a dendrogram representing the relatedness of the populations. ARDRA appears to be suitable for analysing microbial communities in soil and gives interesting information with respect to microbial ecology.