Dynamic Subspecies Population Structure of Vibrio Cholerae in Dhaka, Bangladesh

2021 ◽  
Author(s):  
Mohammad Islam ◽  
Tania Nasreen ◽  
Kevin Y. H. Liang ◽  
Fatema-Tuz Johura ◽  
Paul C. Kirchberger ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Temporal Dynamics ◽  
Sampling Period ◽  
Amplicon Sequencing ◽  
Rapid Expansion ◽  
Capital City ◽  
Dhaka City ◽  
Physiochemical Parameters ◽  
Subspecies Level ◽  
Abundance And Distribution

Abstract Cholera has been endemic to the Ganges delta for centuries. Although the causative agent, Vibrio cholerae, is autochthonous to coastal and brackish water, cholera occurs continually in Dhaka, the inland capital city of Bangladesh which is surrounded by fresh water. Despite the persistence of this problem, little is known about the environmental abundance and distribution of lineages of V. cholerae, the most important being the pandemic generating lineage (PG) consisting mostly of serogroup O1 strains. To understand spatial and temporal dynamics of PG and other lineages belonging to the V. cholerae species in surface water in and around Dhaka city, we used qPCR and high throughput amplicon sequencing. Seven different freshwater sites across Dhaka were investigated for six consecutive months and physiochemical parameters were measured in situ. Total abundance of V. cholerae was found to be relatively stable throughout the six months sampling period, with 2×105 to 4×105 genome copies/L at six sites and around 5 ×105 genome copies/L at the site located in the most densely populated part of Dhaka city. PG O1 V. cholerae was present in high abundance during the entire sampling period and composed between 24-92% of the total V. cholerae population, only showing occasional but sudden reductions in abundance. In instances where PG O1 lost its dominance, other lineages underwent a rapid expansion while the size of the total V. cholerae population remained almost unchanged. Intraspecies richness of V. cholerae was positively correlated to salinity, conductivity and total dissolved solids (TDS), while it was negatively correlated to dissolved oxygen (DO) concentration in water. Interestingly, negative correlation was observed specifically between PG O1 and salinity, even though the changes in this variable were minor (0-0.8 ppt). Observations in this study suggest that at the subspecies level, population composition of naturally occurring V. cholerae can be influenced by fluctuations in environmental factors, which can lead to altered competition dynamics among the lineages.

scholarly journals Relationships between Environmental Factors and Pathogenic Vibrios in the Northern Gulf of Mexico

2010 ◽  
Vol 76 (21) ◽  
pp. 7076-7084 ◽  
Author(s):  
C. N. Johnson ◽  
A. R. Flowers ◽  
N. F. Noriea ◽  
A. M. Zimmerman ◽  
J. C. Bowers ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Water Column ◽  
Vibrio Vulnificus ◽  
Environmental Parameters ◽  
Sampling Period ◽  
Pathogenicity Factor ◽  
Hemolysin Gene ◽  
Thermostable Direct Hemolysin ◽  
Pathogenic Vibrios ◽  
Abundance And Distribution

ABSTRACT Although autochthonous vibrio densities are known to be influenced by water temperature and salinity, little is understood about other environmental factors associated with their abundance and distribution. Densities of culturable Vibrio vulnificus containing vvh (V. vulnificus hemolysin gene) and V. parahaemolyticus containing tlh (thermolabile hemolysin gene, ubiquitous in V. parahaemolyticus), tdh (thermostable direct hemolysin gene, V. parahaemolyticus pathogenicity factor), and trh (tdh-related hemolysin gene, V. parahaemolyticus pathogenicity factor) were measured in coastal waters of Mississippi and Alabama. Over a 19-month sampling period, vibrio densities in water, oysters, and sediment varied significantly with sea surface temperature (SST). On average, tdh-to-tlh ratios were significantly higher than trh-to-tlh ratios in water and oysters but not in sediment. Although tlh densities were lower than vvh densities in water and in oysters, the opposite was true in sediment. Regression analysis indicated that SST had a significant association with vvh and tlh densities in water and oysters, while salinity was significantly related to vibrio densities in the water column. Chlorophyll a levels in the water were correlated significantly with vvh in sediment and oysters and with pathogenic V. parahaemolyticus (tdh and trh) in the water column. Furthermore, turbidity was a significant predictor of V. parahaemolyticus density in all sample types (water, oyster, and sediment), and its role in predicting the risk of V. parahaemolyticus illness may be more important than previously realized. This study identified (i) culturable vibrios in winter sediment samples, (ii) niche-based differences in the abundance of vibrios, and (iii) predictive signatures resulting from correlations between environmental parameters and vibrio densities.

scholarly journals Predictions for ‘Purbachal’: Learning from ‘Dhanmondi’

2017 ◽  
Vol 16 (1) ◽  
pp. 11-18
Author(s):  
M. Arefeeen Ibrahim ◽  
Ajmeri Nusrat Shoma ◽  
Saiful Hasan Tariq
Keyword(s):  
Road Network ◽  
Residential Area ◽  
Capital City ◽  
Master Plan ◽  
Traffic Situation ◽  
Dhaka City ◽  
Government Organization ◽  
New Town ◽  
Capital Development ◽  
A Current

Township planning was introduced from early ‘50s in Dhaka, the capital city of Bangladesh having a current population of 14 million approximately. To meet the demand of growing number of population, Dhaka has witnessed different new township projects from the ‘60s to ‘90s. Example of some of these similar developments by government, includes Dhanmondi, Banani, Gulshan, Uttara, Baridhara etc. Hence, old Dhaka city is expanding its civic facilities by urbanizing in the vicinity of city. Under this scenario, a new township project, Purbachal New Town, was planned by concerned government organization namely “Rajdhani Unnayaan Kortipokkha” (RAJUK) which was previously called “Dhaka Improvement Trust” (DIT). This new township is much larger than any other previously planned ones in Dhaka city. This paper aims to compare Purbachal New Town with a previous Development, Dhanmondi Residential Area, which was designed by the same Capital Development Auhtority (RAJUK/DIT) in early ‘50s. The comparison takes place in terms of road network and land-use. Future possible impact of traffic situation on newly designed master plan in Purbachal is also sought for. Findings from the study show some similarities in master plan of Purbachal with existing Dhanmondi, which may create similar situation of current Dhanmondi in proposed Purbachal New Town too.

scholarly journals Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Kevin P. Dillon ◽  
Florence Correa ◽  
Celine Judon ◽  
Martine Sancelme ◽  
Donna E. Fennell ◽  
...  
Keyword(s):  
Human Health ◽  
Green Algae ◽  
Sampling Period ◽  
Amplicon Sequencing ◽  
Cloud Water ◽  
Atmospheric Processes ◽  
Culture Independent ◽  
Cyanobacteria And Algae ◽  
Dispersal Vector ◽  
Photoautotrophic Microbes

ABSTRACT The atmosphere contains diverse living microbes, of which the heterotrophic community has been the best studied. Microbes with other trophic modes, such as photoautotrophy, have received much less attention. In this study, culture-independent and dependent methods were used to examine the presence and diversity of oxygenic photoautotrophic microbes in clouds and rain collected at or around puy de Dôme Mountain, central France. Cloud water was collected from the summit of puy de Dôme (1,465 m above sea level [a.s.l.]) for cultivation and metagenomic analysis. Cyanobacteria, diatoms, green algae, and other oxygenic photoautotrophs were found to be recurrent members of clouds, while green algae affiliated with the Chlorellaceae were successfully cultured from three different clouds. Additionally, rain samples were collected below the mountain from Opme meteorological station (680 m a.s.l.). The abundance of chlorophyll a-containing cells and the diversity of cyanobacteria and green algae in rain were assessed by flow cytometry and amplicon sequencing. The corresponding downward flux of chlorophyll a-containing organisms to the ground, entering surface ecosystems with rain, varied with time and was estimated to be between ∼1 and >300 cells cm−2 day−1 during the sampling period. Besides abundant pollen from Pinales and Rosales, cyanobacteria of the Chroococcidiopsidales and green algae of the Trebouxiales were dominant in rain samples. Certain members of these taxa are known to be ubiquitous and stress tolerant and could use the atmosphere for dispersal. Overall, our results indicate that the atmosphere carries diverse, viable oxygenic photoautotrophic microbes and acts as a dispersal vector for this microbial guild. IMPORTANCE Information regarding the diversity and abundance of oxygenic photoautotrophs in the atmosphere is limited. More information from diverse locations is needed. These airborne organisms could have important impacts upon atmospheric processes and on the ecosystems they enter after deposition. Oxygenic photoautotrophic microbes are integral to ecosystem functioning, and some have the potential to affect human health. A better understanding of the diversity and the movements of these aeolian dispersed organisms is needed to understand their ecology, as well as how they could affect ecosystems and human health.

scholarly journals A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera

2020 ◽  
Vol 202 (24) ◽  
Author(s):  
Kevin Y. H. Liang ◽  
Fabini D. Orata ◽  
Mohammad Tarequl Islam ◽  
Tania Nasreen ◽  
Munirul Alam ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Geographic Origin ◽  
Data Set ◽  
Epidemiological Research ◽  
Content Type ◽  
Typing Scheme ◽  
Subspecies Level ◽  
Allelic Differences

ABSTRACT Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/). IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae. Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae. In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.

scholarly journals Biogeographic Patterns in Genomic Diversity among a Large Collection of Vibrio cholerae Isolates

2009 ◽  
Vol 75 (6) ◽  
pp. 1658-1666 ◽  
Author(s):  
Daniel P. Keymer ◽  
Lilian H. Lam ◽  
Alexandria B. Boehm
Keyword(s):  
Vibrio Cholerae ◽  
Temporal Dynamics ◽  
Consensus Sequence ◽  
Regional Scale ◽  
Geographic Distance ◽  
Genomic Diversity ◽  
Central California ◽  
Biogeographic Patterns ◽  
Community Model ◽  
Environmental Similarity

ABSTRACT Vibrio cholerae strains are capable of inhabiting multiple niches in the aquatic environment and in some cases cause disease in humans. However, the ecology and biodiversity of these bacteria in environmental settings remains poorly understood. We used the genomic fingerprinting technique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) to profile 835 environmental isolates from waters and sediments obtained at nine sites along the central California coast. We identified 115 ERIC-PCR genotypes from 998 fingerprints, with a reproducibility of 98.5% and a discriminatory power of 0.971. When the temporal dynamics at a subset of sampling sites were explored, several genotypes provided evidence for cosmopolitan or geographically restricted distributions, and other genotypes displayed nonrandom patterns of cooccurrence. Partial Mantel tests confirmed that genotypic similarity of isolates across all sampling events was correlated with environmental similarity (0.04 ≤ r ≤ 0.05), temporal proximity (r = 0.09), and geographic distance (r = 0.09). A neutral community model for all sampling events explained 61% of the variation in genotype abundance. Cooccurrence indices (C-score, C-board, and Combo) were significantly different than expected by chance, suggesting that the V. cholerae population may have a competitive structure, especially at the regional scale. Even though stochastic processes are undoubtedly important in generating biogeographic patterns in diversity, deterministic factors appear to play a significant, albeit small, role in shaping the V. cholerae population structure in this system.

scholarly journals The ecology of the Drosophila-yeast mutualism in wineries

2018 ◽  
Author(s):  
Allison S. Quan ◽  
Michael B. Eisen
Keyword(s):  
Temporal Dynamics ◽  
Yeast Species ◽  
Close Association ◽  
Fruit Fly ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Spatial And Temporal Dynamics ◽  
Specific Manner ◽  
Fallen Fruit ◽  
Open Question

AbstractThe fruit fly, Drosophila melanogaster, is preferentially found on fermenting fruits. The yeasts that dominate the microbial communities of these substrates are the primary food source for developing D. melanogaster larvae, and adult flies manifest a strong olfactory system-mediated attraction for the volatile compounds produced by these yeasts during fermentation. Although most work on this interaction has focused on the standard laboratory yeast Saccharomyces cerevisiae, a wide variety of other yeasts naturally ferment fallen fruit. Here we address the open question of whether D. melanogaster preferentially associates with distinct yeasts in different, closely-related environments. We characterized the spatial and temporal dynamics of Drosophila-associated fungi in Northern California wineries that use organic grapes and natural fermentation using high-throughput, short-amplicon sequencing. We found that there is nonrandom structure in the fungal communities that are vectored by flies both between and within vineyards. Within wineries, the fungal communities associated with flies in cellars, fermentation tanks, and pomace piles are distinguished by varying abundances of a small number of yeast species. To investigate the origins of this structure, we assayed Drosophila attraction to, oviposition on, larval development in, and longevity when consuming the yeasts that distinguish vineyard microhabitats from each other. We found that wild fly lines did not respond differentially to the yeast species that distinguish winery habitats in habitat specific manner. Instead, this subset of yeast shares traits that make them attractive to and ensure their close association with Drosophila.

scholarly journals Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors

2020 ◽  
Author(s):  
Ezequiel Santillan ◽  
Hari Seshan ◽  
Stefan Wuertz
Keyword(s):  
Community Structure ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Treatment Plant ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Batch Reactors ◽  
Function Structure ◽  
Community Function ◽  
And Function

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract

scholarly journals Spatio-temporal dynamics of glacial lakes (1990-2018) in the Kashmir Himalayas, India using remote sensing and GIS

2021 ◽  
Author(s):  
Rayees Ahmed ◽  
Gowhar Farooq Wani ◽  
Syed Towseef Ahmad ◽  
Riyaz Ahmad Mir ◽  
Mansour Almazroui ◽  
...  
Keyword(s):  
Growth Rate ◽  
Temporal Dynamics ◽  
Field Studies ◽  
Rapid Expansion ◽  
Spatial Extent ◽  
Glacial Lakes ◽  
Landsat Images ◽  
Change Analysis ◽  
Study Region ◽  
Kashmir Himalayas

Abstract This study is perhaps the first attempt to use satellite data (1990–2018) to analyze spatiotemporal changes in glacial lakes over the Kashmir Himalayas supplemented by field studies. Landsat images were used to delineate the spatial extent of glacial lakes at four time points, i.e., 1990, 2000, 2010 and 2018. The total count of lakes as well as their spatial extent showed a discernible increase. The number increased from 253 in 1990 to 322 in 2018, with a growth rate of 21.4%. The area has increased from 18.84 Km2 in 1990 to 22.11 Km2 in 2018 with a growth rate of 14.7 percent. The newly formed glacial lakes, including supra glacial lakes, were greater in number than the lakes that disappeared over the study period. All glacial lakes are situated at elevations of 2700 m asl and 4500 m asl. More than 78% of lake expansion in the study region is largely due to the growth of existing glacial lakes. Through area change analysis, our findings reveal that certain lakes show rapid expansion needing immediate monitoring and observation. The analysis of the meteorological variables reveals that minimum and maximum temperatures in the Jhelum basin have shown an increasing trend. Tmax showed an increase of 1.1°C, whereas Tmin increased to 0.7°C from 1990 to 2018. On the other hand, precipitation has shown a decreasing trend, which can be attributed to one of the major causes of glacier recession and the expansion of glacial lakes in the Upper Jhelum basin. Consequently, this study could play a significant role in devising a comprehensive risk assessment plan for potential GLOFs and developing a mechanism for continuous monitoring and management of lakes in the study region.

scholarly journals Spatial and temporal dynamics of SAR11 marine bacteria sampled across a nearshore to offshore transect in the tropical Pacific Ocean

2021 ◽  
Author(s):  
Sarah J. Tucker ◽  
Kelle C. Freel ◽  
Elizabeth A. Monaghan ◽  
Clarisse E.S. Sullivan ◽  
Oscar Ramfelt ◽  
...  
Keyword(s):  
Time Series ◽  
Ribosomal Rna ◽  
Marine Bacteria ◽  
Temporal Dynamics ◽  
Amplicon Sequencing ◽  
Ecological Niches ◽  
Tropical Pacific Ocean ◽  
Time Period ◽  
Spatial And Temporal Dynamics ◽  
The Tropical Pacific

AbstractTime-series surveys of microbial communities coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāne‘ohe Bay on the island of O‘ahu, Hawai‘i, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria over a two-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and individual amplicon sequence variants (ASVs) were evaluated. On average, 77% of the SAR11 community was compromised of a small number of ASVs (7 of 106 in total), which were ubiquitously distributed across all samples collected from one or both of the end-member environments sampled in this study (coastal or offshore). SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.

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