scholarly journals Comparison of bacterial community structures in digestive tract between healthy and disease whiteleg shrimp (Litopenaeus vannamei) in Soc Trang, Vietnam

2018 ◽  
Vol 16 (3) ◽  
pp. 543-551
Author(s):  
Tran Trung Thanh ◽  
Nathan Bott ◽  
Le Hoang Duc ◽  
Dang Thi Hoang Oanh ◽  
Nguyen Trung Nam ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Litopenaeus Vannamei ◽  
Penaeus Monodon ◽  
Gut Bacteria ◽  
Shrimp Pond ◽  
Sequencing Method ◽  
Gradient Gel Electrophoresis ◽  
The Stability ◽  
Generation Sequencing

Gut bacteria comprise a complex bacterial community related to many functions in a host. The stability of gut bacteria plays important models in the health and immunology of a host. Many studies on intestine bacteria constructed via cultivation and Denaturation Gradient Gel Electrophoresis (DDGE) methods have proved a limited efficiency. In order to tackle these drawbacks, the next generation sequencing method was developed on 16S-rRNA-based sequences (Metabarcoding). The composition of bacterial communities was revealed based on the analysis of 16S rRNA sequences of intestine bacteria in Litopenaeus vannamei ponds in comparison with microbial communities in a Penaeus monodon pond and a muscle of shrimp. These results showed that the dominant phyla of intestine bacteria in Litopenaeus vannamei were Proteobacteria (49.3–57.4%), Firmicutes (15.6–34.4%) and Bacteroidetes (0.1–16.9%). Rhizobium(0.4%-26.1%), Vibrio(0–23.9%) and Spongiimonas(0–16,7%) were dominant genera in Litopenaeus vannamei gut. A higher proportion of Fusobacterium (10%), a shrimp pathogen group, was found in a disease shrimp pond (ST4) in comparison with a low growth shrimp pond (ST3) (0%) and a healthy shrimp pond (ST1) (0.6%). Vibrio was marked as shrimp pathogen genus accounted for 22.3% of total genera in ST4 in comparison with 2.4% in ST3 and 3.5% in ST1. Interestingly, a higher percentage of Vibrio rotiferianus (7.98%) was found in ST4 compared to ST3 (1%) and ST1 (0%). Fusobacterium and Vibrio will be the objects for the next experiments to discover shrimp pathogens specifically.

scholarly journals Bacterial abundance and community composition in green, brown and red water from intensive catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia

2021 ◽  
Vol 22 (9) ◽  
Author(s):  
Karunia Adetera Nungki Wijayanti ◽  
Indah Istiqomah ◽  
Murwantoko Murwantoko
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Water Samples ◽  
Bacterial Abundance ◽  
Rrna Gene ◽  
Next Generation ◽  
Aquaculture System ◽  
Generation Sequencing

Abstract. Wijayanti KAN, Istiqomah I, Murwantoko. 2021. Bacterial abundance and community composition in green, brown and red water from intensive Catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia. Biodiversitas 22: 3677-3684. Catfish (Clarias sp.) is an important aquaculture commodity in Indonesia and cultured in an intensive system. Microorganisms play an important role in maintaining water quality of aquaculture system. The objective of this study was to determine the bacterial abundance and community composition of green, brown and red water collected from intensive catfish culture ponds in Yogyakarta using next-generation sequencing method. The water samples were collected from intensive catfish culture ponds with different colors, namely green, brown and red ponds located in Yogyakarta. The DNA from water samples was extracted using DNA extraction kit and used as template for 16S rRNA amplification. The V3-V4 hypervariable regions of the 16S rRNA gene were amplified apply for next-generation sequencing technology. This study could explore effectively the bacterial community in water samples. The bacterial communities in this catfish culture water showed higher bacterial richness compared to the other aquaculture system. The diversity of the green, brown and red catfish culture water ponds was similar with the number OTUs of the green, brown and red water samples, which were 1269; 1387 and 1323 OTUs respectively. The 694 OTUs (34.42%) were common core microbiomes in all catfish culture ponds, the 212 OTUs (10.51%) are present on green and brown water ponds, the 182 OTUs (9.02%) were on green and red water ponds, and the 183 OTUs (9.07%) were present on green and brown water ponds. However, the composition of the bacterial community was different. The most dominant phylum in green and brown water ponds was Proteobacteria with relative abundance in green water and brown water 71.6% and 47.0% respectively, whereas, the most dominant phylum in red water was Firmicutes (29.5%). The dominance of Firmicutes phylum in red water ponds may be caused by application of probiotic bacteria, the high organic content, and low oxygen concentration.

scholarly journals Elucidating the Key Member of a Linuron-Mineralizing Bacterial Community by PCR and Reverse Transcription-PCR Denaturing Gradient Gel Electrophoresis 16S rRNA Gene Fingerprinting and Cultivation

2005 ◽  
Vol 71 (7) ◽  
pp. 4144-4148 ◽  
Author(s):  
Sebastian R. Sørensen ◽  
Jim Rasmussen ◽  
Carsten S. Jacobsen ◽  
Ole S. Jacobsen ◽  
René K. Juhler ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gel Electrophoresis ◽  
Agricultural Soil ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Carbon And Nitrogen ◽  
Reverse Transcription Pcr ◽  
Gradient Gel Electrophoresis

ABSTRACT A bacterial community from Danish agricultural soil was enriched with linuron [N-(3,4-dichlorophenyl)-N′-methoxy-N′-methylurea] as the sole carbon and nitrogen source. The community mineralized [ring-U-14C]linuron completely to 14CO2 and 14C-biomass. Denaturing gradient gel electrophoresis analysis and cultivation revealed that a Variovorax sp. was responsible for the mineralization activity.

scholarly journals Response of a Soil Bacterial Community to Grassland Succession as Monitored by 16S rRNA Levels of the Predominant Ribotypes

2000 ◽  
Vol 66 (9) ◽  
pp. 3998-4003 ◽  
Author(s):  
Andreas Felske ◽  
Arthur Wolterink ◽  
Robert Van Lis ◽  
Willem M. De Vos ◽  
Antoon D. L. Akkermans
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Agricultural Production ◽  
Total Activity ◽  
Rt Pcr ◽  
Dot Blot ◽  
Bacterial Ribosome ◽  
Pcr Products ◽  
Mineralization Of Organic Matter ◽  
Gradient Gel Electrophoresis

ABSTRACT The composition of predominant soil bacteria during grassland succession was investigated in the Dutch Drentse A area. Five meadows, taken out of agricultural production at different time points, and one currently fertilized plot represented different stages of grassland succession. Since fertilization and agricultural production were stopped, the six plots showed a constant decline in the levels of nutrients and vegetation changes. The activity of the predominant bacteria was monitored by direct ribosome isolation from soil and temperature gradient gel electrophoresis of reverse transcription (RT)-PCR products generated from bacterial 16S rRNA. The amounts of 16S rRNA of 20 predominant ribosome types per gram of soil were monitored via multiple competitive RT-PCR in six plots at different succession stages. These ribosome types mainly represented Bacillusand members of the Acidobacterium cluster and the α subclass of the class Proteobacteria. The 20 16S rRNA molecules monitored represented approximately half of all bacterial soil rRNA which was estimated by dot blot hybridizations of soil rRNA with the Bacteria probe EUB338. The grasslands showed highly reproducible and specific shifts of bacterial ribosome type composition. The total bacterial ribosome level increased during the first years after agricultural production and fertilization stopped. This correlated with the collapse of the dominant Lolium perenne population and an increased rate of mineralization of organic matter. The results indicate that there is a true correlation between the total activity of the bacterial community in soil and the amount of bacterial ribosomes.

Sign in / Sign up

Export Citation Format

Share Document