Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments

Danovaro, Roberto; Luna, Gian Marco; Dell’Anno, Antonio; Pietrangeli, Biancamaria

doi:10.1128/aem.01361-06

Cited by 166 publications

(124 citation statements)

References 49 publications

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“…Although the richness of the bacterial community increased from about 3000-5000 m depth, the richness of the viral community decreased over this depth range ( Figure 6). It is well documented that different fingerprinting techniques differ in their resolution resulting in different numbers of OTUs as shown for ARISA and T-RFLP (Danovaro et al, 2006). Our observed trend in bacterial and viral communities with depth, however, is most likely independent of the different resolutions of the methods used assuming similar extraction and amplification efficiencies over the depth range of the water column sampled.…”

Section: Viral and Heterotrophic Prokaryotic Productioncontrasting

confidence: 42%

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

et al. 2010

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Viral and prokaryotic abundance, production and diversity were determined throughout the water column of the subtropical Atlantic Ocean to assess potential variations in the relation between viruses and prokaryotes. Prokaryotic abundance and heterotrophic activity decreased by one and three orders of magnitude, respectively, from the epi-to the abyssopelagic layer. Although the lytic viral production (VP) decreased with depth, lysogenic VP was variable throughout the water column and did not show any trend with depth. The bacterial, archaeal and viral community composition were depth-stratified as determined by the automated ribosomal intergenic spacer analysis, terminalrestriction fragment length polymorphism and randomly amplified polymorphic DNA-PCR, respectively. Generally, the number of operational taxonomic units (OTUs) did not reveal consistent trends throughout the water column. Viral and prokaryotic abundance were strongly related to heterotrophic prokaryotic production, suggesting similar linkage strength between the viral and prokaryotic communities from the lower epi-to the abyssopelagic layer in the Atlantic Ocean. Strikingly, the prokaryotic and viral parameters exhibited a similar variability throughout the water column down to the abyssopelagic layers, suggesting that the dark ocean is as dynamic a system as is the lower epipelagic layer. It also indicates that viruses are apparently having a similar role for prokaryotic mortality in the dark oceanic realm as in surface waters. The more than twofold increase in bacterial OTUs from 2750 m depth to 45000 m depth and the concurrent decrease in viral OTUs, however, suggests that viruses might exhibit a wider host range in deep waters than in surface waters.

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Section: Viral and Heterotrophic Prokaryotic Productioncontrasting

confidence: 42%

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

et al. 2010

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“…However, this data set represents a relatively coarse taxonomic resolution (Crosby and Criddle 2003, Danovaro et al 2006, Novis et al 2007, Gao and Tao 2012, and dispersal-based metacommunity dynamics (H2) may create biogeography at a finer taxonomic resolution (i.e., species or strain).…”

Section: Total Soil Bacterial Diversity Corresponds With Broad Enviromentioning

confidence: 99%

Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains

Sokol¹,

Herbold²,

Lee³

et al. 2013

Ecosphere

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Abstract. The metacommunity concept provides a useful framework to assess the influence of local and regional controls over diversity patterns. Culture-independent studies of soil microbial communities in the McMurdo Dry Valleys of East Antarctica (778 S) have shown that bacterial diversity is related to soil geochemical gradients, while studies targeting edaphic cyanobacteria have linked local diversity patterns to dispersal-based processes. In this study, we increased the spatial extent of observed soil microbial communities to cover the Beardmore Glacier region in the central Transantarctic Mountains (848 S). We used community profiling techniques to characterize diversity patterns for bacteria and the cyanobacterial subcomponent of the microbial community. Diversity partitioning was used to calculate beta diversity and estimate among-site dissimilarity in the metacommunity. We then used variation partitioning to assess the relationship between beta diversity and environmental and spatial gradients. We found that dominant groups in the soil bacterial metacommunity were influenced by gradients in pH and soil moisture at the Transantarctic scale (800 km). Conversely, beta diversity for the cyanobacterial component of the edaphic microbial metacommunity was decoupled from these environmental gradients, and was more related to spatial filters, suggesting that wind-driven dispersal dynamics created cyanobacterial biogeography at a local scale (,3 km).

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“…This type of approach suffers from a number of methodological limitations that preclude accurate quantitative interpretation of BCC (Wintzingerode et al 1997 Newton et al 2006). The high-throughput nature of the technique makes it a valuable tool despite its established limitations (Danovaro et al 2006). Furthermore, it is encouraging that a recent comparison of ARISA peaks and quantitative data based on direct cell counts showed that quantification of certain abundant taxa by ARISA was more accurate than may be expected (Brown et al 2005).…”

Section: Discussionmentioning

confidence: 97%

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2007

Limnology & Oceanography

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We investigated patterns of intra-and interannual change in pelagic bacterial community composition (BCC, assessed using automated ribosomal intergenic spacer analysis) over six years in eutrophic Lake Mendota, Wisconsin. A regular phenology was repeated across years, implying that freshwater bacterial communities are more predictable in their dynamics than previously thought. Seasonal events, such as water column mixing and trends in water temperature, were most strongly related to BCC variation. Communities became progressively less similar across years between the months of May and September, when the lake was thermally stratified. Dissolved oxygen and nitrate + nitrite concentrations were highly correlated to BCC change within and across seasons. The relationship between BCC and seasonal drivers suggests that trajectories of community change observed over long time series will reflect large-scale climate variation.

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Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments

Cited by 166 publications

References 49 publications

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains

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