scholarly journals Bacterial Community Dynamics During Nursery Rearing of Pacific White Shrimp (Litopenaeus vannamei) Revealed via High-Throughput Sequencing

2020 ◽  
Vol 60 (2) ◽  
pp. 214-221 ◽  
Author(s):  
Maocang Yan ◽  
Xiang Zhang ◽  
Lihua Hu ◽  
Xianke Huang ◽  
Qianjin Zhou ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Litopenaeus Vannamei ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Bacterial Community Dynamics

scholarly journals Different Soil Salinity Imparts Clear Alteration In Rhizospheric Bacterial Community Dynamics In Rice And Peanut.

2021 ◽  
Author(s):  
Md Majharul Islam ◽  
Rajarshi Bhattacharya ◽  
Biraj Sarkar ◽  
Pulak Kumar Maiti ◽  
Shouvik Mahanty ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Host Plant ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Alpha Diversity ◽  
Rhizospheric Soil ◽  
Bacterial Community Dynamics

Abstract The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in overall health of the host-plant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community-dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence-analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community-structure is related to both the adjoining soil characters and the type of the hosts.

Bacterial community dynamics across developmental stages of fungal fruiting bodies

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Daniyal Gohar ◽  
Mari Pent ◽  
Kadri Põldmaa ◽  
Mohammad Bahram
Keyword(s):  
Bacterial Community ◽  
Fruiting Body ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Developmental Stages ◽  
Body Parts ◽  
Fruiting Bodies ◽  
Bacterial Community Dynamics ◽  
Host Development

ABSTRACT Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.

scholarly journals Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Chunfang Zhang ◽  
Shuo Jiao ◽  
Duntao Shu ◽  
Gehong Wei
Keyword(s):  
Bacterial Community ◽  
Nitrogen Fertilization ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Temporal Variations ◽  
Interspecies Interactions ◽  
Bacterial Community Dynamics ◽  
Nitrogen Inputs ◽  
Negative Interactions

AbstractUnderstanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

scholarly journals Different Soil Salinity Imparts Clear Alteration in Rhizospheric Bacterial Community Dynamics in Rice and Peanut.

2021 ◽  
Author(s):  
Md Majharul Islam ◽  
Rajarshi Bhattacharya ◽  
Biraj Sarkar ◽  
Pulak Kumar Maiti ◽  
Shouvik Mahanty ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Host Plant ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Alpha Diversity ◽  
Rhizospheric Soil ◽  
Bacterial Community Dynamics

Abstract The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in overall health of the host-plant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community-dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence-analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community-structure is related to both the adjoining soil characters and the type of the hosts.

scholarly journals Transcriptome Analysis of juvenile Pacific White Shrimp (Litopenaeus vannamei) with symptom of stunted growth

2019 ◽  
Author(s):  
Huaiyi Fang ◽  
Jingjing Song ◽  
Bin Gong ◽  
Tingcai Pang ◽  
Chunyan Peng
Keyword(s):  
Transcriptome Analysis ◽  
Litopenaeus Vannamei ◽  
Antigen Processing ◽  
High Throughput Sequencing ◽  
Average Length ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Cdna Libraries ◽  
Virus Family ◽  
Stunted Growth

AbstractIn search for viruses associated with Litopenaeus vannamei with symptom of stunted growth, we have undertaken a comparative transcriptome analysis of total RNA sequences using Illumina based high-throughput sequencing (HTS). We obtain 89000242 and 95126160 high-quality clean reads from cDNA libraries of L.vannamei with stunted growth symptom (sick group) and health shrimp (health group control), respectively. Totally, 108221 unigenes with an average length of 716 bp were obtained from RNA-seq data. The unigenes were annotated against NR, NT, KO, KOG, SwissProt, PFAM and GO databases. 3975 (3.67%) showed significant matches in all the above databases and 39812 (36.78%) unigenes were annotated in at least one database. Comparative transcriptomic analysis revealed that 807 significantly differentially expressed unigenes were identified, including 282 down-regulated genes and 525 up-regulated genes. Thirteen up-regulated virus-related genes were only discovered in the sick shrimp groups, but not in health ones. Five of them were closely related to virus family Picornaviridae. From phylogenetic tree, we could find five viral genes were closely related to genus Ampvirus, Falcovirus, Aquamavirus (Seal picornavirus). Some up-regulated genes in the Sick groups mainly included genes involved in virus infecting processes concerning antigen processing and presenting, apoptosis, lysosome, phagosome and inflammation. While, many down-regulated genes in the Sick groups mainly involved in the process of starch and sucrose metabolism, and protein digestion and absorption. Our research provided some useful information about pathogenic factor and mechanism on the stunted growth symptom of L.vannamei, and was significant for the control and prevention of this disease.

A SNP Genetic Map for Pacific White Shrimp (Litopenaeus vannamei)

2010 ◽  
Author(s):  
Zhi-Qiang Du ◽  
Suneel K. Onteru ◽  
Danielle Gorbach ◽  
Max F. Rothschild
Keyword(s):  
Genetic Map ◽  
Litopenaeus Vannamei ◽  
Pacific White Shrimp ◽  
White Shrimp
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