scholarly journals Bacterial community diversity associated with blood cockle (Anadara granosa) in Penang, Malaysia

2018 ◽  
Vol 16 (2) ◽  
Author(s):  
Kamarul Zaman Zarkasi ◽  
Koh Fu Sheng ◽  
Teh Faridah Nazari ◽  
Nurfitri Amir Muhammad ◽  
Amirul Al-Ashraf Abdullah
Keyword(s):  
Bacterial Communities ◽  
Community Diversity ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Sampling Locations ◽  
Wet Market ◽  
Blood Cockle ◽  
And Storage ◽  
Anadara Granosa ◽  
Sampling Times

Bacterial communities of blood cockles (Anadara granosa) collected from wet market across Penang, Malaysia, were examined using a cultivation method. This study aimed to describe the major abundance of blood cockle bacteria and its relationship with different sampling locations. 16S rRNA gene analysis and culturable bacterial numbers were found to be slightly different between samples in two different locations potentially due to management, handling, transport and storage practices by the farmers, distributors and retailers. Results from this study indicated that most of bacteria found were typically present in blood cockles. The results revealed that there were slight similarities between sampling times; and slight differences on bacterial numbers between two different sampling locations. Based on the results, the blood cockle microbial communities comprised of members of the genera Klebsiella and Bacillus, which are greatly predominant, with highly dynamic of bacterial communities. Other bacterial genera found were E.coli, Vibrio, Pseudomonas, Staphylococcus and Micrococcus. The overall data demonstrated dynamic bacterial communities in blood cockles (Anadara granosa) and its diversity.

Composition of Acridid gut bacterial communities as revealed by 16S rRNA gene analysis

2008 ◽  
Vol 97 (3) ◽  
pp. 265-272 ◽  
Author(s):  
R.J. Dillon ◽  
G. Webster ◽  
A.J. Weightman ◽  
V.M. Dillon ◽  
S. Blanford ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis

scholarly journals Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows1

2019 ◽  
Vol 97 (10) ◽  
pp. 4298-4304 ◽  
Author(s):  
Taylor B Ault ◽  
Brooke A Clemmons ◽  
Sydney T Reese ◽  
Felipe G Dantas ◽  
Gessica A Franco ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Artificial Insemination ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Beef Cows ◽  
Community Diversity ◽  
Rrna Gene ◽  
Bacterial Community Diversity ◽  
Hypervariable Regions ◽  
Time Of Breeding

Abstract The present study evaluated the bovine vaginal and uterine bacterial community diversity and its relationship to fertility. Postpartum beef cows (n = 68) were synchronized beginning on day −21 and ending with timed artificial insemination (TAI) on day 0. Pregnancy was diagnosed 30 d after TAI. Uterine and vaginal flushes were collected on day −21, −9, and −2 for bacterial DNA extraction to sequence the V1 to V3 hypervariable regions of the 16S rRNA gene. Results indicated a decrease in the number of bacterial species over time in the uterus of resulting pregnant and nonpregnant beef cows (P < 0.0001). Principal coordinate analyses (PCoA) depicted clustering of samples, indicating closely related bacterial communities, by day in the uterus and vagina (P < 0.0001). At day −2, uterine samples from nonpregnant and pregnant animals clustered separately (P < 0.0001), with nonpregnant animal samples clustering tightly together. Overall, the current study suggests the shift in the reproductive bacterial communities’ diversity and phylogenetic relationship leading up to the time of breeding may contribute to successful pregnancy establishment.

scholarly journals Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

2020 ◽  
Vol 8 (11) ◽  
pp. 1708
Author(s):  
Savvas Genitsaris ◽  
Natassa Stefanidou ◽  
Kleopatra Leontidou ◽  
Theodora Matsi ◽  
Katerina Karamanoli ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Properties ◽  
Bacterial Communities ◽  
Mediterranean Ecosystems ◽  
Community Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Sodic Soils ◽  
Drought Tolerant ◽  
Tolerant Plants

The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant’s compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.

scholarly journals Bacterial community structure upstream and downstream of cascade dams along the Lancang River in southwestern China

2020 ◽  
Vol 27 (34) ◽  
pp. 42933-42947
Author(s):  
Xia Luo ◽  
Xinyi Xiang ◽  
Guoyi Huang ◽  
Xiaorui Song ◽  
Peijia Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Spatial Distance ◽  
Rrna Gene ◽  
Lancang River ◽  
Hydroelectric Dam ◽  
Cascade Dams

Abstract Extensive construction of dams by humans has caused alterations in flow regimes and concomitant alterations in river ecosystems. Even so, bacterioplankton diversity in large rivers influenced by cascade dams has been largely ignored. In this study, bacterial community diversity and profiles of seven cascade dams along the720 km of the Lancang River were studied using Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Spatiotemporal variations of bacterial communities in sediment and water of the Gongguoqiao hydroelectric dam and factors affecting these variations were also examined. Microbial diversity and richness in surface water increased slightly from upstream toward downstream along the river. A significant positive correlation between spatial distance and dissimilarities in bacterial community structure was confirmed (Mantel test, r = 0.4826, p = 0.001). At the Gongguoqiao hydroelectric dam, temporal differences in water overwhelmed spatial variability in bacterial communities. Temperature, precipitation, and nutrient levels were major drivers of seasonal microbial changes. Most functional groups associated with carbon cycling in sediment samples decreased from winter to summer. Our findings improve our understanding of associations, compositions, and predicted functional profiles of microbial communities in a large riverine ecosystem influenced by multiple cascade dams.

scholarly journals Bacterial Communities of Ixodes scapularis from Central Pennsylvania, USA

Insects ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 718
Author(s):  
Joyce Megumi Sakamoto ◽  
Gabriel Enrique Silva Diaz ◽  
Elizabeth Anne Wagner
Keyword(s):  
Bacterial Communities ◽  
Ixodes Scapularis ◽  
Life Stage ◽  
Geographic Location ◽  
Community Diversity ◽  
Rrna Gene ◽  
Infection Frequency ◽  
16S Sequencing ◽  
Specific Pcr ◽  
Central Pennsylvania

Native microbiota represent a potential resource for biocontrol of arthropod vectors. Ixodes scapularis is mostly inhabited by the endosymbiotic Rickettsia buchneri, but the composition of bacterial communities varies with life stage, fed status, and/or geographic location. We compared bacterial community diversity among I. scapularis populations sampled within a small geographic range in Central Pennsylvania. We collected and extracted DNA from ticks and sequenced amplicons of the eubacterial 16S rRNA gene from individuals and pooled samples. We then used taxon-specific PCR and/or qPCR to confirm the abundance or infection frequency of select pathogenic and symbiotic bacteria. Bacterial communities were more diverse in pools of males than females and the most abundant taxon was Rickettsia buchneri followed by Coxiellaceae (confirmed by sequencing as an unknown Rickettsiella species). High Rickettsiella titers in pools were likely due to a few heavily infected males. We determined that the infection frequency of Borrelia burgdorferi ranged from 20 to 75%. Titers of Anaplasma phagocytophilum were significantly different between sexes. Amplicon-based bacterial 16S sequencing is a powerful tool for establishing the baseline community diversity and focusing hypotheses for targeted experiments, but care should be taken not to overinterpret data based on too few individuals. We identified intracellular bacterial candidates that may be useful as targets for manipulation.

scholarly journals Study of duodenal bacterial communities by 16S rRNA gene analysis in adults with active celiac disease vs non-celiac disease controls

2016 ◽  
Vol 120 (6) ◽  
pp. 1691-1700 ◽  
Author(s):  
E. Nistal ◽  
A. Caminero ◽  
A.R. Herrán ◽  
J. Pérez-Andres ◽  
S. Vivas ◽  
...  
Keyword(s):  
Celiac Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis

scholarly journals Associated bacteria of Botryococcus braunii (Chlorophyta)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6610 ◽  
Author(s):  
Joao D. Gouveia ◽  
Jie Lian ◽  
Georg Steinert ◽  
Hauke Smidt ◽  
Detmer Sipkema ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Biomass Productivity ◽  
Botryococcus Braunii ◽  
Community Diversity ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Culture Collections ◽  
Green Microalga ◽  
Different Strains ◽  
Species Specific

Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.

scholarly journals Investigation of Oscillatoria spongeliae-Dominated Bacterial Communities in Four Dictyoceratid Sponges

2005 ◽  
Vol 71 (11) ◽  
pp. 7366-7375 ◽  
Author(s):  
Christian P. Ridley ◽  
D. John Faulkner ◽  
Margo G. Haygood
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Marine Invertebrates ◽  
Marine Sponges ◽  
Sponge Species ◽  
Epithelial Tissue ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Oscillatoria Spongeliae

ABSTRACT Certain species of marine sponges in the order Dictyoceratida harbor large populations of the cyanobacterial symbiont Oscillatoria spongeliae in the mesohyl (interior) of the sponge. We show that in four of these sponge species (Lamellodysidea herbacea, Lamellodysidea chlorea, Lendenfeldia chondrodes, and Phyllospongia papyracea) from Palau there is a consistent community of α-proteobacteria in addition to O. spongeliae that fall within the Rhodobacter group based on 16S rRNA gene analysis. Some of the α-proteobacteria in Lendenfeldia chondrodes and P. papyracea but not in the Lamellodysidea spp. contained site-specific insertions in the 16S rRNA gene. Reverse transcription-PCR experiments demonstrated that the largest insertion found in this study (63 bp) is present in the mature rRNA. Lendenfeldia chondrodes was the only sponge found to have another cyanobacterium in the tissue, a Synechocystis sp. We found that the Synechocystis sp. was present in both the pinacoderm (surface epithelial tissue) and mesohyl, in contrast to O. spongeliae, which was only found in the mesohyl through the use of specific fluorescence in situ hybridization experiments. Of the four sponge species, only P. papyracea was found to contain a significant number of γ-proteobacteria. These results demonstrate that O. spongeliae-dominated bacterial communities in different sponge species can vary considerably and increase our understanding of the bacterial communities found in marine invertebrates.

scholarly journals Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259515
Author(s):  
Fating Yin ◽  
Fenghua Zhang ◽  
Haoran Wang
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Acid Metabolism ◽  
Rhizosphere Soil ◽  
Soil Bacterial Community ◽  
Rhizosphere Bacteria ◽  
Community Diversity ◽  
Rrna Gene ◽  
Soil Bacterial ◽  
Suaeda Glauca

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.

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