Quantifying bacterial population dynamics in compost using 16S rRNA gene probes

2004 ◽  
Vol 66 (4) ◽  
pp. 457-463 ◽  
Author(s):  
Patrick D. Schloss ◽  
Anthony G. Hay ◽  
David B. Wilson ◽  
James M. Gossett ◽  
Larry P. Walker
Keyword(s):  
Population Dynamics ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Population ◽  
Rrna Gene ◽  
Gene Probes

scholarly journals Rumen Microbial Population Dynamics during Adaptation to a High-Grain Diet

2010 ◽  
Vol 76 (22) ◽  
pp. 7482-7490 ◽  
Author(s):  
S. C. Fernando ◽  
H. T. Purvis ◽  
F. Z. Najar ◽  
L. O. Sukharnikov ◽  
C. R. Krehbiel ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Population Structure ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Population ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Libraries ◽  
The 16S Rrna Gene ◽  
Number Of Bacteria

ABSTRACT High-grain adaptation programs are widely used with feedlot cattle to balance enhanced growth performance against the risk of acidosis. This adaptation to a high-grain diet from a high-forage diet is known to change the rumen microbial population structure and help establish a stable microbial population within the rumen. Therefore, to evaluate bacterial population dynamics during adaptation to a high-grain diet, 4 ruminally cannulated beef steers were adapted to a high-grain diet using a step-up diet regimen containing grain and hay at ratios of 20:80, 40:60, 60:40, and 80:20. The rumen bacterial populations were evaluated at each stage of the step-up diet after 1 week of adaptation, before the steers were transitioned to the next stage of the diet, using terminal restriction fragment length polymorphism (T-RFLP) analysis, 16S rRNA gene libraries, and quantitative real-time PCR. The T-RFLP analysis displayed a shift in the rumen microbial population structure during the final two stages of the step-up diet. The 16S rRNA gene libraries demonstrated two distinct rumen microbial populations in hay-fed and high-grain-fed animals and detected only 24 common operational taxonomic units out of 398 and 315, respectively. The 16S rRNA gene libraries of hay-fed animals contained a significantly higher number of bacteria belonging to the phylum Fibrobacteres, whereas the 16S rRNA gene libraries of grain-fed animals contained a significantly higher number of bacteria belonging to the phylum Bacteroidetes. Real-time PCR analysis detected significant fold increases in the Megasphaera elsdenii, Streptococcus bovis, Selenomonas ruminantium, and Prevotella bryantii populations during adaptation to the high-concentrate (high-grain) diet, whereas the Butyrivibrio fibrisolvens and Fibrobacter succinogenes populations gradually decreased as the animals were adapted to the high-concentrate diet. This study evaluates the rumen microbial population using several molecular approaches and presents a broader picture of the rumen microbial population structure during adaptation to a high-grain diet from a forage diet.

scholarly journals 16S rRNA Gene Amplicon Data Set-Based Bacterial Diversity in a Water-Soil Sample from Pangong Tso Lake, a High-Altitude Grassland Lake of the Northwest Himalayas

2018 ◽  
Vol 7 (17) ◽  
Author(s):  
Garima Bisht ◽  
Anuradha Sourirajan ◽  
David J. Baumler ◽  
Kamal Dev
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Altitude ◽  
Bacterial Diversity ◽  
Bacterial Population ◽  
Species Level ◽  
Rrna Gene ◽  
Data Set ◽  
High Altitude Grassland ◽  
Northwest Himalayas

We report here 16S rRNA-based bacterial diversity existing during freezing conditions in a high-altitude Himalayan lake through sequencing a 16S rRNA gene amplicon data set. A total of 121,857 high-quality reads were obtained; 40.78% of the bacterial population was classified to the genus level, while 1.26% was classified to the species level.

scholarly journals Defluorination of Sodium Fluoroacetate by Bacteria from Soil and Plants in Brazil

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Expedito K. A. Camboim ◽  
Michelle Z. Tadra-Sfeir ◽  
Emanuel M. de Souza ◽  
Fabio de O. Pedrosa ◽  
Paulo P. Andrade ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Population ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Mineral Medium ◽  
Fluoride Ion ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
First Time

The aim of this work was to isolate and identify bacteria able to degrade sodium fluoroacetate from soil and plant samples collected in areas where the fluoroacetate-containing plantsMascagnia rigidaandPalicourea aenofuscaare found. The samples were cultivated in mineral medium added with 20 mmol L−1sodium fluoroacetate. Seven isolates were identified by 16S rRNA gene sequencing asPaenibacillussp. (ECPB01),Burkholderiasp. (ECPB02),Cupriavidussp. (ECPB03),Staphylococcussp. (ECPB04),Ancylobactersp. (ECPB05),Ralstoniasp. (ECPB06), andStenotrophomonassp. (ECPB07). All seven isolates degraded sodium-fluoroacetate-containing in the medium, reaching defluorination rate of fluoride ion of 20 mmol L−1. Six of them are reported for the first time as able to degrade sodium fluoroacetate (SF). In the future, some of these microorganisms can be used to establish in the rumen an engineered bacterial population able to degrade sodium fluoroacetate and protect ruminants from the poisoning by this compound.

scholarly journals Bacterial Community in the Crop of the Hoatzin, a Neotropical Folivorous Flying Bird

2008 ◽  
Vol 74 (19) ◽  
pp. 5905-5912 ◽  
Author(s):  
Filipa Godoy-Vitorino ◽  
Ruth E. Ley ◽  
Zhan Gao ◽  
Zhiheng Pei ◽  
Humberto Ortiz-Zuazaga ◽  
...  
Keyword(s):  
Species Richness ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Population ◽  
Species Level ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Digestive Efficiency ◽  
Operational Taxonomic Units

ABSTRACT The hoatzin is unique among known avian species because of the fermentative function of its enlarged crop. A small-bodied flying foregut fermenter is a paradox, and this bird provides an interesting model to examine how diet selection and the gut microbiota contribute to maximizing digestive efficiency. Therefore, we characterized the bacterial population in the crop of six adult hoatzins captured from the wild. A total of 1,235 16S rRNA gene sequences were grouped into 580 phylotypes (67% of the pooled species richness sampled, based on Good's coverage estimator, with CACE and Chao1 estimates of 1,709 and 1,795 species-level [99% identity] operational taxonomic units, respectively). Members of 9 of the ∼75 known phyla in Bacteria were identified in this gut habitat; the Firmicutes were dominant (67% of sequences, belonging to the classes Clostridia, Mollicutes, and Bacilli), followed by the Bacteroidetes (30%, mostly in the order Bacteroidales), Proteobacteria (1.8%), and Lentisphaerae, Verrucomicrobia, TM7, Spirochaetes, Actinobacteria, and Aminanaerobia (all <0.1%). The novelty in this ecosystem is great; 94% of the phylotypes were unclassified at the “species” level and thus likely include novel cellulolytic lineages.

16S rRNA Gene Probes for Deinococcus species

1996 ◽  
Vol 19 (3) ◽  
pp. 365-369 ◽  
Author(s):  
Mark G. Wise ◽  
J Vaun Mcarthur ◽  
Lawrence J. Shimkets
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Probes

scholarly journals Bacterial Population Changes in a Membrane Bioreactor for Graywater Treatment Monitored by Denaturing Gradient Gel Electrophoretic Analysis of 16S rRNA Gene Fragments

2003 ◽  
Vol 69 (2) ◽  
pp. 852-860 ◽  
Author(s):  
David M. Stamper ◽  
Marianne Walch ◽  
Rachel N. Jacobs
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Membrane Bioreactor ◽  
Bacterial Population ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Treatment System ◽  
Rrna Gene ◽  
Nitrogen And Phosphorus ◽  
Dgge Analysis

ABSTRACT The bacterial population of a graywater treatment system was monitored over the course of 100 days, along with several wastewater biochemical parameters. The graywater treatment system employed an 1,800-liter membrane bioreactor (MBR) to process the waste, with essentially 100% recycling of the biomass. Graywater feed consisting of 10% galley water and 90% laundry water, selected to approximate the graywater composition on board U.S. Navy ships, was collected offsite. Five-day biological oxygen demand (BOD5), oils and greases (O/G), nitrogen, and phosphorus were monitored in the feed and were found to vary greatly day to day. Changes in the bacterial population were monitored by PCR amplification of region 332 to 518 (Escherichia coli numbering) of the 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE) analysis of the resultant PCR products. DGGE analysis indicated a diverse and unstable bacterial population throughout the 100-day period, with spikes in feed strength causing significant changes in community structure. Long-term similarity between the communities was 0 to 25%, depending on the method of analysis. In spite of the unstable bacterial population, the MBR system was able to meet effluent quality parameters approximately 90% of the time.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

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