scholarly journals Bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae at a low salinity

2022 ◽  
Author(s):  
Hai-Hong Huang ◽  
Chao-Yun Li ◽  
Yan-Ju Lei ◽  
Wei-Qi Kuang ◽  
Wan-Sheng Zou ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Litopenaeus Vannamei ◽  
High Throughput Sequencing ◽  
Inorganic Nitrogen ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Low Salinity ◽  
Low Concentrations ◽  
Salinity Condition ◽  
Microbial Dna

This study aimed to investigate the bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae (PL) at a low salinity condition. PL (~ stage 15) were stocked in four parallel tanks filled in water with a salinity of 5.0‰ at a density of 4000 individuals per m3 for a 28-days culture experiment, during which glucose was added as carbon source with a C:N of 20:1. At the end of experiment, water was sampled from each tank and pooled to extract microbial DNA for high-throughput sequencing of V3-V4 region of 16S rRNA gene. Results showed that the bacterial community at 28 d was dominated by phyla of Proteobacteria (45.8%), Bacteroidetes (21.1%), Planctomycetes (13.5%), Chlamydiae (10.3%) and Firmicutes (6.8%). A proportion of 81% inferring KEGG functions of this bacterial community associated with metabolism. Among functions relating to nitrogen metabolism, 48.5% were involved in the conversion of ammonia to glutamate, but the proportion of those involved in transformation among ammonia, nitrite and nitrate was 18.0% in total, inferring higher protein-synthesis but lower inorganic nitrogen-transformation capacities of the bacterial community. At the same time (28 d), high levels of total nitrogen (231.3±6.0 mg L-1) and biofloc (127.0±63.0 mL L-1), but low concentrations of ammonia (0.04±0.01 mg L-1), nitrite (0.2±0.1 mg L-1) and nitrate (12.9±2.5 mg L-1) were observed. The results supply a novel insight for understanding the function of bacterial community in the biofloc system nursing L. vannamei PL at a low salinity.

scholarly journals Investigation of the Potential Effects of Host Genetics and Probiotic Treatment on the Gut Bacterial Community Composition of Aquaculture-raised Pacific Whiteleg Shrimp, Litopenaeus vannamei

2019 ◽  
Vol 7 (8) ◽  
pp. 217 ◽  
Author(s):  
Angela Landsman ◽  
Benoit St-Pierre ◽  
Misael Rosales-Leija ◽  
Michael Brown ◽  
William Gibbons
Keyword(s):  
Litopenaeus Vannamei ◽  
Genetic Background ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
Genetic Line ◽  
Bacterial Composition ◽  
Probiotic Treatment ◽  
Whiteleg Shrimp

This study presents the potential effects of the genetic background and use of probiotics on the gut bacterial composition of Pacific whiteleg shrimp (Litopenaeus vannamei) grown in an indoor aquaculture facility. The strains investigated were Shrimp Improvement Systems (SIS, Islamorada, FL, USA), a strain genetically selected for disease resistance, and an Oceanic Institute (OI, Oahu, HI, USA) strain, selected for growth performance. BioWish 3P (BioWish Technologies, Cincinnati, OH, USA) was the selected probiotic. The study consisted of two separate trials, where all shrimp were raised under standard industry conditions and fed the same diet. Shrimp were stocked in 2920 L production tanks at a density of 200/m3 and acclimated for 14 days. After the acclimation period, triplicate tanks were supplemented daily for a duration of 28 days with probiotics, while three other tanks did not receive any treatment (controls). During the 28-day trial period, there was no statistically supported difference (p > 0.05) in either performance or health status as a result of genetic background or probiotic treatment. However, differences in gut bacterial composition, as assessed by high throughput sequencing of amplicons generated from the V1-V3 region of the bacterial 16S rRNA gene, were observed. The relative abundance of five major operational taxonomic units (OTUs) were found to vary significantly across experimental groups (p < 0.05). Notably, operational taxonomic unit (OTU) SD_Shr-00006 was at its highest abundance in d43 SIS samples, with levels greater than d71 samples of the same genetic line or any of the OI shrimp samples. OTUs for SD_Shr-00098 displayed a similar type of profile, but with highest abundance in the OI genetic line and lowest in the SIS shrimp. SD_Shr-00004 showed an opposite profile, with highest abundance in the SIS d71 samples and lowest in the SIS d43 samples. Together, these results suggest that host genetic background can be an important determinant of gut bacterial composition in aquaculture-raised whiteleg shrimp and indicate that development of strategies to manipulate the microbiome of this important seafood will likely need to be customized depending on the genetic line.

scholarly journals Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Matteo Daghio ◽  
Francesca Ciucci ◽  
Arianna Buccioni ◽  
Alice Cappucci ◽  
Laura Casarosa ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Lipid Composition ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Daily Weight Gain ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

Molecular characterization and structure of intestinal micro flora for postmortem interval estimation in SD rats

2019 ◽  
Author(s):  
Huan Li ◽  
Lu Yuan ◽  
Ruina Liu ◽  
Siruo Zhang ◽  
E Yang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Interval Estimation ◽  
Pcr Amplification ◽  
Postmortem Interval ◽  
The Body ◽  
Rrna Gene ◽  
Variable Regions ◽  
Time Points ◽  
Almost All

Abstract Background The human rectum flora consists of a huge variety of bacteria and the association between individuals and their rectum bacterial community begins presently after birth and continues the whole lifetime. Once the body dies, the inherent microbes begin to break down from the inside and play a key role thereafter. Results The aim of this study was to investigate the probable shift of the rectum flora at different time intervals up to 15 days after death and to characterize the contribution for of this shift to estimate the time of death. The rectum of rats was wiped with a sterile cotton swab and the samples were proceeded for DNA extraction, PCR amplification of the 16S rRNA gene with the V3+V4 variable regions, and high throughput sequencing carried out on IonS5TMXL platform. The results were analyzed for intra-group and inter-group diversity, similarity and difference at different time points. At phylum level, Proteobacteria and Firmicutes showed major shifts, checked at 11 different intervals and emerged in the most of postmortem intervals. At the genus level, Enterococcus appeared in all groups except alive samples, Lactobacillus and Proteus appeared in most time points, and the latter showed an increasing trend after 3 days postmortem samples. At the species level, Enterococcus_faecalis and Proteus_mirabilis existed in most postmortem intervals, and the former had a downward trend after day 5 postmortem, while the latter had an upward trend. Corynebacterium_amycolatum , Entero_isolate_group_2 , Bacteroides_uniformis , Enterococcus_faecalis , Streptococcus_gallolyticus_subsp_macedonics , Clostridium_sporogenes were more abundant in 0-hour, day 1, 3, 5, 7, 13 postmortem intervals, respectively, while Proteus_mirabilis and Vagococcus_lutrae were abundant in day 15 postmortem. In addition, functional capacity analysis of Membrane_Transport, Amino_Acid_Metabolism, Nucleotide_Metabolism and Energy_Metabolism showed significant differences between alive and almost all other time points after death ( P <0.05). Conclusions All in all, bacteria at different levels (phylum, genera, species) showed different characteristic during the process of decomposition and possessed entirely different relative abundance and the structure of bacterial community in each time point shifted obviously, which suggested that the specific bacteria might imply the specific postmortem interval during decomposition.

scholarly journals Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Tengxiang Lian ◽  
Yingyong Huang ◽  
Xianan Xie ◽  
Xing Huo ◽  
Muhammad Qasim Shahid ◽  
...  
Keyword(s):  
Salt Stress ◽  
Bacterial Community ◽  
Management Practices ◽  
High Throughput Sequencing ◽  
Crop Productivity ◽  
Soil Salinization ◽  
Rrna Gene ◽  
Content Type ◽  
Rice Mutant ◽  
Rhizosphere Bacterial Community

ABSTRACT Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

scholarly journals PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 358
Author(s):  
Pamela Aravena ◽  
Rodrigo Pulgar ◽  
Javiera Ortiz-Severín ◽  
Felipe Maza ◽  
Alexis Gaete ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
In Silico Analysis ◽  
Cost Effective ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Bacterial Dna ◽  
Phenotypic Differences ◽  
Field Samples ◽  
Pcr Rflp ◽  
Digestion Pattern

Piscirickettsia salmons, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the P. salmonis genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the P. salmonis genogroups. Using an in silico analysis of the P. salmonis 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 P. salmonis strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the P. salmonis genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation.

scholarly journals Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

2015 ◽  
Vol 81 (20) ◽  
pp. 7067-7077 ◽  
Author(s):  
W. Ahmed ◽  
C. Staley ◽  
M. J. Sadowsky ◽  
P. Gyawali ◽  
J. P. S. Sidhu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Fecal Pollution ◽  
Rrna Gene ◽  
Potential Sources

ABSTRACTIn this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways.

scholarly journals Probiotic modulation of the gut bacterial community of juvenile Litopenaeus vannamei challenged with Vibrio parahaemolyticus CAIM 170

2017 ◽  
Vol 43 (4) ◽  
pp. 766-775
Author(s):  
Irasema E. Luis-Villaseñor ◽  
Domenico Voltolina ◽  
Bruno Gomez-Gil ◽  
Felipe Ascencio ◽  
Ángel I. Campa-Córdova ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Litopenaeus Vannamei ◽  
Vibrio Parahaemolyticus ◽  
Single Strand Conformation Polymorphism ◽  
Positive Control ◽  
Negative Control ◽  
Rrna Gene ◽  
Protective Effects ◽  
Probiotic Treatment ◽  
Significant Difference

The protective effects of two probiotic mixtures was studied using the fingerprints of the bacterial community of Litopenaeus vannamei juveniles exposed to probiotics and challenged with Vibrio parahaemolyticus CAIM 170. Fingerprints were constructed using 16S rRNA gene and the PCR-SSCP (Single strand conformation polymorphism) technique, and the probiotics used were an experimental Bacillus mixture (Bacillus tequilensis YC5-2 + B. endophyticus C2-2 and YC3-B) and the commercial probiotic Alibio. The DNA for PCR-SSCP analyses was extracted directly from the guts of shrimps treated for 20 days with the probiotics and injected with 2.5×105 CFU g-1 of V. parahaemolyticus one week after suspension of the probiotic treatment. Untreated shrimps served as positive (injected with V. parahaemolyticus) and negative (not injected) controls Analysis of the bacterial community carried out after inoculation and 12 and 48 h later confirmed that V. parahaemolyticus was present in shrimps of the positive control , but not in the negative control or treated with the probiotic mixtures. A significant difference in the diversity of the bacterial community was observed between times after infection. The band patterns in 0-12 h were clustered into a different group from that determined after 48 h, and suggested that during bacterial infection the guts of whiteleg shrimp were dominated by gamma proteobacteria represented by Vibrio sp. and Photobacterium sp. Our results indicate that the experimental and the commercial mixtures are suitable to modulate the bacterial community of L. vannamei and could be used as a probiotic to control vibriosis in juvenile shrimp.

scholarly journals Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

2016 ◽  
Vol 82 (12) ◽  
pp. 3525-3536 ◽  
Author(s):  
Nikea Ulrich ◽  
Abigail Rosenberger ◽  
Colin Brislawn ◽  
Justin Wright ◽  
Collin Kessler ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Storm Event ◽  
Rrna Gene ◽  
Content Type

ABSTRACTBacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in whichBetaproteobacteriaandGammaproteobacteriadecreased in 16S rRNA gene relative abundance, while the relative abundance of members of theFirmicutesincreased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains ofLegionella,Campylobacter,Arcobacter, andHelicobacter, as well as bacteria of fecal origin (e.g.,Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.IMPORTANCEIn order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.

Sign in / Sign up

Export Citation Format

Share Document