Prevalence of a Novel Division-Level Bacterial Lineage in Lake Dhanmondi, Dhaka, Bangladesh, as Revealed by Deep Sequencing of 16S rRNA Gene Amplicons

Azmuda, Nafisa; Rahman, Mohammed Ziaur; Madsen, Marit Steine; Khan, Md. Sakirul Islam; Birkeland, Nils-Kåre

doi:10.1007/s00284-012-0165-9

Cited by 4 publications

(6 citation statements)

References 15 publications

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“…PCR amplification of the highly variable V3 region of the bacterial 16S rRNA gene was carried out in two steps using HotStar DNA polymerase (QIAGEN GmbH, Hilden, Germany), based on the universal bacterial primers, A8-28F (Edwards et al, 1989) and K517R (Muyzer et al, 1993). In the first PCR step, untagged primers were used in a 20-cycle reaction as described by Azmuda et al (2012), followed by purification of the amplicons using the GenElute PCR Clean-Up Kit (Sigma-Aldrich, Copenhagen, Denmark). The second reaction was performed with 100 ng of the purified PCR amplicons as template and primers containing the 454 FLX adaptors with sample-specific multiple identifiers ( Supplementary Table 1) using 10 PCR reaction cycles (Azmuda et al, 2012).…”

Section: S Rrna Gene Amplicon Barcoded Pyrosequencingmentioning

confidence: 99%

“…In the first PCR step, untagged primers were used in a 20-cycle reaction as described by Azmuda et al (2012), followed by purification of the amplicons using the GenElute PCR Clean-Up Kit (Sigma-Aldrich, Copenhagen, Denmark). The second reaction was performed with 100 ng of the purified PCR amplicons as template and primers containing the 454 FLX adaptors with sample-specific multiple identifiers ( Supplementary Table 1) using 10 PCR reaction cycles (Azmuda et al, 2012). The final products were purified using the Agencourt AMPure purification kit (Agencourt Bioscience Corporation (Beckman Coulter), Beverly, MA, USA) before shipment to GATC Biotech AG (Konstanz, Germany) for pyrosequencing with the GS FLX (Roche 454 Life Sciences, Branford, CT, USA) Titanium chemistry.…”

Section: S Rrna Gene Amplicon Barcoded Pyrosequencingmentioning

confidence: 99%

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Evidence for successional development in Antarctic hypolithic bacterial communities

et al. 2013

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Hypoliths (cryptic microbial assemblages that develop on the undersides of translucent rocks) are significant contributors to regional C and N budgets in both hot and cold deserts. Previous studies in the Dry Valleys of Eastern Antarctica have reported three morphologically distinct hypolithic community types: cyanobacteria dominated (type I), fungus dominated (type II) and moss dominated (type III). Here we present terminal-restriction fragment length polymorphism analyses to elucidate the bacterial community structure in hypolithons and the surrounding soils. We show clear and robust distinction in bacterial composition between bulk surface soils and hypolithons. Moreover, the bacterial assemblages were similar in types II and III hypolithons and clearly distinct from those found in type I. Through 16S rRNA gene 454 pyrosequencing, we show that Proteobacteria dominated all three types of hypolithic communities. As expected, Cyanobacteria were more abundant in type I hypolithons, whereas Actinobacteria were relatively more abundant in types II and III hypolithons, and were the dominant group in soils. Using a probabilistic dissimilarity metric and random sampling, we demonstrate that deterministic processes are more important in shaping the structure of the bacterial community found in types II and III hypolithons. Most notably, the data presented in this study suggest that hypolithic bacterial communities establish via a successional model, with the type I hypolithons acting as the basal development state.

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Section: S Rrna Gene Amplicon Barcoded Pyrosequencingmentioning

confidence: 99%

Section: S Rrna Gene Amplicon Barcoded Pyrosequencingmentioning

confidence: 99%

Evidence for successional development in Antarctic hypolithic bacterial communities

et al. 2013

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“…Along with the major permanent members, 16 phyla; the Acidobacteria, Chlorobi, Cloroflexi . Fibrobacteres, Firmicutes, Fusobacteria, Gemmatimonadetes, Lentisphaerae, Nitrospira, OD1, OP10, Planctomycetes, Spirochaetes , and the candidate phyla BRC1, LD11, SR1, and TM7 were detected occasionally in freshwater lakes (10, 11). Along with the total community profiling, seasonal variations of bacterial community structures have been already observed in different aquatic systems e.g., marine, estuarine, and freshwater ecosystems (12–14).…”

Section: Introductionmentioning

confidence: 99%

Bacterial Community Profiling of Tropical Freshwaters in Bangladesh

Azmuda

Fakruddin

Khan

et al. 2019

Front. Public Health

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Seasonal and spatial variations in the bacterial communities of two tropical freshwater sources in Bangladesh, Lake Dhanmondi in central Dhaka, and a pond in the outskirts of Dhaka, were assessed and compared using PCR-DGGE and deep sequencing of 16S rRNA genes, as well as heterotrophic enrichments using water samples collected at nine different time points during 1 year. Temporal and spatial variations of common aquatic bacterial genera were observed, but no clear seasonal variations could be depicted. The major bacterial genera identified from these two sites were members of the Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Verrucomicrobia , and Firmicutes . Among the proteobacterial groups, members of the α - , β - , and γ - Proteobacteria predominated. γ - Proteobacteria belonging to the Escherichia coli/Shigella group even the diarrheagenic pathotypes of E. coli e.g., EPEC and ETEC were detected in most samples throughout the year, with no apparent correlations with other microbial groups. The other pathotypes, EHEC, EAEC, and EIEC/ Shigella spp. were also detected occasionally. This study represents the first thorough analysis of the microbial diversity of tropical freshwater systems in Bangladesh.

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“…Bangladesh is an agricultural country that is located between the 20 • 34 and 26 • 38 N latitudes and 88 • 01 and 92 • 41 E longitudes in South Asia. Like Bangladesh, the Bay of Bengal rim region is currently under pressure due to invasion of human pollutants [7]. Wastes in this zone affect the physical, biological and chemical qualities of the water environment, and as such have negative impacts on human health for (e.g., pathogenic bacteria have caused typhoid fever and pediatric bloodstream infections in this area, which have been documented in hospitals [8]).…”

Section: Introductionmentioning

confidence: 99%

“…Among different methods, the intensive application of next-generation sequencing (NGS) helps to explore the diversity, dynamics and sensitivity of microorganisms [12,14,[16][17][18]. [7] studied the different bacterial diversities in physical ecosystems using 16S rRNA-based and independent culture studies approach where bacterial lineages were found without cultivated representatives.…”

Section: Introductionmentioning

confidence: 99%

Spatial Modelling of Bacterial Diversity over the Selected Regions in Bangladesh by Next-Generation Sequencing: Role of Water Temperature

et al. 2020

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In this study, a spatial model has been developed to investigate the role of water temperature to the distribution of bacteria over the selected regions in the Bay of Bengal, located in the southern region of Bangladesh using next-generation sequencing. Bacterial concentration, quantitative polymerase chain reactions, and sequencing were performed on water samples and identified Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The spatial model tessellated the parts of the Bay of Bengal with hexagons and analyzed the relationship between the distribution of bacteria and water temperature. A geographically weighted regression was used to observe whether water temperature contributed strongly or weakly to the distribution of bacteria. The residuals were examined to assess the model's fitness. The spatial model has the potential to predict the bacterial diversity in the selected regions of Bangladesh.

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Prevalence of a Novel Division-Level Bacterial Lineage in Lake Dhanmondi, Dhaka, Bangladesh, as Revealed by Deep Sequencing of 16S rRNA Gene Amplicons

Cited by 4 publications

References 15 publications

Evidence for successional development in Antarctic hypolithic bacterial communities

Evidence for successional development in Antarctic hypolithic bacterial communities

Bacterial Community Profiling of Tropical Freshwaters in Bangladesh

Spatial Modelling of Bacterial Diversity over the Selected Regions in Bangladesh by Next-Generation Sequencing: Role of Water Temperature

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