In situ transplant analysis of free-living bacteria in a lotic ecosystem

Or, Amitai; Comay, Orr; Gophna, Uri

doi:10.1016/j.resmic.2012.12.004

Cited by 4 publications

(1 citation statement)

References 42 publications

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“…Most urbanization studies on microbial communities have focused on pathogenic taxa such as fecal coliform bacteria (Nagy et al, 2012 ; Daly et al, 2013 ; Kapoor et al, 2014 ), denitrifying bacteria (Hale and Groffman, 2006 ; Knapp et al, 2009 ; Perryman et al, 2011b ; Harrison et al, 2012 ), or unicellular algae and diatoms (Hill et al, 2000 ; Elsdon and Limburg, 2008 ). The handful of studies that were not limited to coliforms, denitrifiers, or algae/diatoms have suggested a large difference between bacterial communities in biofilms (Lear and Lewis, 2009 ; Lear et al, 2011 ), streambed sediments (Jackson and Weeks, 2008 ; Perryman et al, 2011a ; Wang et al, 2011 ), and the water column (Belt et al, 2007 ; Or et al, 2013 ). This body of work provides important insights, but these studies used relatively coarse measurements of microbial diversity such as denaturing gel gradient electrophoresis (DGGE), automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (T-RFLP) analysis.…”

Section: Introductionmentioning

confidence: 99%

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

et al. 2017

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Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition of headwater streams, and suggest that processes driving these changes in urbanized water column vs. sediment environments are distinct.

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Section: Introductionmentioning

confidence: 99%

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

et al. 2017

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Investigating a lotic microbial community following a severe detergent spill

Gophna

2014

Arch Microbiol

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A large non-ionic detergent spill affected the Yarqon stream, where water sampling was performed prior to the spill as a part of the stream's routine sampling and during and after the event. Following the spill, a large foam layer was observed for about 3-4 days accompanied by death of all fauna in the stream. Despite a large quantity of freshwater that was introduced to the stream as an emergency measure, a drastic decrease in dissolved oxygen was also observed. A rapid reduction in bacterial diversity and richness, as measured by automated ribosomal intergenic spacer analysis, was also evident, as microbial assemblages changes accompanied pollutant exposure. However, this analysis showed that the microbial assemblages of the stream were quick to recover and became similar to pre-spill communities as early as a week after the spill. These findings suggest that bacterial assemblages are much more robust to large anthropogenic disturbances than expected.

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How to Deal with PCR Contamination in Molecular Microbial Ecology

Mennerat

Sheldon²

2014

Microb Ecol

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Microbial ecology studies often use broad-range PCR primers to obtain community profiles. Contaminant microbial DNA present in PCR reagents may therefore be amplified together with template DNA, resulting in unrepeatable data which may be difficult to interpret, especially when template DNA is present at low levels. One possible decontamination method consists in pre-treating PCR mixes with restriction enzymes before heat-inactivating those enzymes prior to the start of the PCR. However, this method has given contrasting results, including a reduction in PCR sensitivity. In this study, we tested the efficiency of two different enzymes (DNase 1 and Sau3AI) as well as the effect of dithiothreitol (DTT), a strong reducing agent, in the decontamination procedure. Our results indicate that enzymatic treatment does reduce contamination levels. However, DNase 1 caused substantial reductions in the bacterial richness found in communities, which we interpret as a result of its incomplete inactivation by heat treatment. DTT did help maintain bacterial richness in mixes treated with DNase 1. No such issues arose when using Sau3AI, which therefore seems a more appropriate enzyme. In our study, four operational taxonomic units (OTU) decreased in frequency and relative abundance after treatment with Sau3AI and hence are likely to represent contaminant bacterial DNA. We found higher within-sample similarity in community structure after treatment with Sau3AI, probably better reflecting the initial bacterial communities. We argue that the presence of contaminant bacterial DNA may have consequences in the interpretation of ecological data, especially when using low levels of template DNA from highly diverse communities. We advocate the use of such decontaminating approaches as a standard procedure in microbial ecology.

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In situ transplant analysis of free-living bacteria in a lotic ecosystem

Cited by 4 publications

References 42 publications

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

Investigating a lotic microbial community following a severe detergent spill

How to Deal with PCR Contamination in Molecular Microbial Ecology

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