scholarly journals Influence of Biostimulation Treatment Using Composted Plant Biomass on Bacterial Diversity of an Aged Petroleum Contaminated Soil as Determined by Culture-dependent and 16S rRNA Gene PCR-DGGE Based Identification Methods

2018 ◽  
pp. 1-16 ◽  
Author(s):  
Leera Solomon ◽  
Chimezie Jason Ogugbue ◽  
Gideon Chijioke Okpokwasili
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Contaminated Soil ◽  
Plant Biomass ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Identification Methods ◽  
Culture Dependent

Influence of biostimulation treatment using composted plant biomass on bacterial diversity of an aged crude oil contaminated soil (ACOCS) was determined using culture-dependent and 16S rRNA gene PCR-DGGE based identification methods. Seven treatment plots were designed and included treatments A (TPA) through G (TPG). Samples were collected bi-weekly from 7 treatment plots designed in situ during a 70-day study period that spanned 10 weeks. Composted (2,500 g each) Water hyacinth (EC), Mexican sunflower (TD) and Bermuda grass (CD) were used as nutrient supplements in 4,000 g of ACOCS in situ. TPA was un-amended while TPB, TPC, and TPD had EC, TD and CD added singly. TPE had EC and TD while TPF contained EC and CD in combination. TPG consisted of EC, TD and CD combined. Bacterial isolates were obtained on mineral salts medium and identified based on their morphological and biochemical characteristics. DGGE fingerprints of PCR-amplified 16S rRNA bacterial gene fragments were also determined using the universal primer set: 7F: 5’-GAGTTTGATCCTGGCTCAG-3’ and 1492R:5’-GGTTACCTTGTTACGACT-3’that corresponded to positions 968 and 1401 of Escherichia coli 16S rRNA gene sequence. DGGE bands fell into corresponding operational taxonomic units based on a threshold of 91-100% sequence similarity. Dendrogram showed dominant DGGE bands in TPB though TPG over time with TPA having no band. The isolates are known crude oil utilizers and are closely related to Gordonia sp. BS261404 with 98% sequence similarity, Aquitalea magnusonii KG26145 (96%), Sphingobacterium sp. K1261411 (97%) and Achromobacter sp. HQ261417 (100%). Data indicated that pseudomonads are the dominant bacteria involved in hydrocarbon biodegradation after biostimulation with the composted plant materials. Cultural and molecular methods of cultivation of microorganisms are neither contradictory nor excluding and should be considered as complementary to interrogate the bacterial diversity in the natural soil environment.

scholarly journals Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil

2011 ◽  
Vol 61 (3) ◽  
pp. 674-679 ◽  
Author(s):  
Guang-Li Wang ◽  
Li Wang ◽  
Hong-Hong Chen ◽  
Bin Shen ◽  
Shun-Peng Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium

An aerobic, Gram-negative bacterial strain, designated CTN-1T, capable of degrading chlorothalonil was isolated from a long-term chlorothalonil-contaminated soil in China, and was subjected to a polyphasic taxonomic investigation. Strain CTN-1T grew at 15–37 °C (optimum 28–30 °C) and at pH 6.0–9.0 (optimum pH 7.0–7.5). The G+C content of the total DNA was 67.1 mol%. Based on 16S rRNA gene sequence analysis, strain CTN-1T was related most closely to Lysobacter daejeonensis DSM 17634T (97.1 % similarity), L. soli DCY21T (95.7 %), L. concretionis Ko07T (95.5 %), L. gummosus LMG 8763T (95.3 %) and L. niastensis DSM 18481T (95.2 %). The novel strain showed less than 95.0 % 16S rRNA gene sequence similarity to the type strains of other Lysobacter species. The major cellular fatty acids of strain CNT-1T were iso-C16 : 0 (23.0 %), iso-C15 : 0 (21.4 %) and iso-C17 : 1 ω9c (15.3 %). The major isoprenoid quinone was Q-8 (99 %), and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. These chemotaxonomic data supported the affiliation of strain CTN-1T to the genus Lysobacter. Levels of DNA–DNA relatedness between strain CTN-1T and L. daejeonensis DSM 17634T were 34.6–36.1 %. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain CTN-1T from recognized species of the genus Lysobacter. Strain CTN-1T is therefore considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter ruishenii sp. nov. is proposed. The type strain is CTN-1T (=DSM 22393T =CGMCC 1.10136T).

scholarly journals Microbacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2634-2638 ◽  
Author(s):  
Devi Lal ◽  
Sanjay Kumar Gupta ◽  
Peter Schumann ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Sequence Similarity ◽  
North India ◽  
Molar Ratio ◽  
Rrna Gene ◽  
The Family ◽  
Cross Linkage ◽  
Diamino Acid

A Gram-stain-positive, aerobic, rod-shaped, yellow actinobacterium, designated MNA2T, was isolated from a hexachlorocyclohexane-contaminated soil in North India. Strain MNA2T showed 95 % 16S rRNA gene sequence similarity with Microbacterium halotolerans YIM 70130T. Phylogenetic analysis of 16S rRNA gene sequences showed that strain MNA2T belonged to a clade represented by the genus Microbacterium of the family Microbacteriaceae. Strain MNA2T contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the predominant fatty acids and diphosphatidylglycerol, phosphatidylglycerol and two unknown polar lipids. The menaquinones were MK-12, MK-11, MK-13 and MK-10, in an approximate molar ratio of 45 : 40 : 13 : 3, respectively. The DNA G+C content was 65.3 mol%. The peptidoglycan was of the B type of cross-linkage with ornithine as the diagnostic diamino acid. The results of the phylogenetic, phenotypic and chemotaxonomic analysis indicate that strain MNA2T belongs to a previously unrecognized species of the genus Microbacterium, for which the name Microbacterium lindanitolerans sp. nov. is proposed. The type strain is MNA2T (=DSM 22422T =CCM 7585T).

scholarly journals Cultivable Microbial Diversity in Speleothems Using MALDI-TOF Spectrometry and DNA Sequencing from Krem Soitan, Krem Lawbah, Krem Mawpun, Khasi Hills, Meghalaya, India

2021 ◽  
Author(s):  
Mudgil Devender ◽  
Dhiraj Paul ◽  
Sushmitha Baskar ◽  
Ramanathan Baskar ◽  
Yogesh S Shouche
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Maldi Tof ◽  
Rrna Gene Sequencing ◽  
Culture Dependent

Abstract This study reports on the culturable microbial communities in caves from the Indian sub-continent. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. This approach helped to detect a number bacterial strains from the Indian caves. The microbial diversity in the Indian caves is inadequately characterized. The study aims to expand the current understanding of bacterial diversity in the speleothems from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. 91% of the total bacterial diversity was dominated by Proteobacteria and Actinobacteria. The other important phyla detected include the Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%). At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. A culture-dependent approach was employed for elucidating the community structure colonizing the speleothems and wall deposits in the caves using MALDI-TOF and 16S rRNA gene sequencing. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.

scholarly journals Bacterial diversity from the source to the tap: a comparative study based on 16S rRNA gene-DGGE and culture-dependent methods

2012 ◽  
Vol 83 (2) ◽  
pp. 361-374 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Conceição Egas ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Comparative Study ◽  
Bacterial Diversity ◽  
Rrna Gene ◽  
Culture Dependent

scholarly journals Successional Development of Sulfate-Reducing Bacterial Populations and Their Activities in a Wastewater Biofilm Growing under Microaerophilic Conditions

2002 ◽  
Vol 68 (3) ◽  
pp. 1392-1402 ◽  
Author(s):  
Tsukasa Ito ◽  
Satoshi Okabe ◽  
Hisashi Satoh ◽  
Yoshimasa Watanabe
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Cloning ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Sulfide Production ◽  
Microaerophilic Conditions ◽  
Successional Development

ABSTRACT A combination of fluorescence in situ hybridization, microprofiles, denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA fragments, and 16S rRNA gene cloning analysis was applied to investigate successional development of sulfate-reducing bacteria (SRB) community structure and in situ sulfide production activity within a biofilm growing under microaerophilic conditions (dissolved oxygen concentration in the bulk liquid was in the range of 0 to 100 μM) and in the presence of nitrate. Microelectrode measurements showed that oxygen penetrated 200 μm from the surface during all stages of biofilm development. The first sulfide production of 0.32 μmol of H2S m−2 s−1 was detected below ca. 500 μm in the 3rd week and then gradually increased to 0.70 μmol H2S m−2 s−1 in the 8th week. The most active sulfide production zone moved upward to the oxic-anoxic interface and intensified with time. This result coincided with an increase in SRB populations in the surface layer of the biofilm. The numbers of the probe SRB385- and 660-hybridized SRB populations significantly increased to 7.9 × 109 cells cm−3 and 3.6 × 109 cells cm−3, respectively, in the surface 400 μm during an 8-week cultivation, while those populations were relatively unchanged in the deeper part of the biofilm, probably due to substrate transport limitation. Based on 16S rRNA gene cloning analysis data, clone sequences that related to Desulfomicrobium hypogeium (99% sequence similarity) and Desulfobulbus elongatus (95% sequence similarity) were most frequently found. Different molecular analyses confirmed that Desulfobulbus, Desulfovibrio, and Desulfomicrobium were found to be the numerically important members of SRB in this wastewater biofilm.

scholarly journals Filamentous “Epsilonproteobacteria” Dominate Microbial Mats from Sulfidic Cave Springs

2003 ◽  
Vol 69 (9) ◽  
pp. 5503-5511 ◽  
Author(s):  
Annette Summers Engel ◽  
Natuschka Lee ◽  
Megan L. Porter ◽  
Libby A. Stern ◽  
Philip C. Bennett ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Mats ◽  
Class Group ◽  
Sequence Similarity ◽  
Extreme Environments ◽  
Rrna Gene ◽  
Group I ◽  
Group Ii

ABSTRACT Hydrogen sulfide-rich groundwater discharges from springs into Lower Kane Cave, Wyoming, where microbial mats dominated by filamentous morphotypes are found. The full-cycle rRNA approach, including 16S rRNA gene retrieval and fluorescence in situ hybridization (FISH), was used to identify these filaments. The majority of the obtained 16S rRNA gene clones from the mats were affiliated with the “Epsilonproteobacteria” and formed two distinct clusters, designated LKC group I and LKC group II, within this class. Group I was closely related to uncultured environmental clones from petroleum-contaminated groundwater, sulfidic springs, and sulfidic caves (97 to 99% sequence similarity), while group II formed a novel clade moderately related to deep-sea hydrothermal vent symbionts (90 to 94% sequence similarity). FISH with newly designed probes for both groups specifically stained filamentous bacteria within the mats. FISH-based quantification of the two filament groups in six different microbial mat samples from Lower Kane Cave showed that LKC group II dominated five of the six mat communities. This study further expands our perceptions of the diversity and geographic distribution of “Epsilonproteobacteria” in extreme environments and demonstrates their biogeochemical importance in subterranean ecosystems.

scholarly journals Pedobacter nanyangensis sp. nov., isolated from herbicide-contaminated soil

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3517-3521 ◽  
Author(s):  
Hao Zhang ◽  
Jing Zhang ◽  
Man Song ◽  
Ming-gen Cheng ◽  
Ya-dong Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Physiological And Biochemical Characteristics ◽  
Ph Range

A Gram-stain-negative, strictly aerobic, non-spore-forming, motile, rod-shaped bacterium, designated Q-4T, was isolated from a herbicide-contaminated soil sample in Nanyang, Henan province, China. Strain Q-4T grew optimally in the LB medium without NaCl supplement at a pH range of 6.0–7.0 and a temperature of 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Q-4T was most closely related to ‘Pedobacter zeaxanthinifaciens’ TDMA-5 (97.4 % 16S rRNA gene sequence similarity), followed by Pedobacter xixiisoli S27T (95.8 %). The genomic DNA G+C content of strain Q-4T was 41.8 mol%. MK-7 was the major respiratory quinone. Phosphatidylethanolamine and phosphoaminolipid were the major polar lipids. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3) and C16 : 1ω7c/C16 : 1ω6c (summed feature 3). Strain Q-4T showed low DNA–DNA relatedness with ‘P. zeaxanthinifaciens’ TDMA-5 (21.4 ± 0.6 %). Physiological and biochemical characteristics are able to distinguish strain Q-4T from the most closely related species of the genus Pedobacter. On the basis of genotypic and phenotypic data, strain Q-4T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter nanyangensis sp. nov. is proposed. The type strain is Q-4T ( = KCTC 42442T = ACCC 19798T).

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach

2021 ◽  
Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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