Limits...
Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments.

Brown SM, Jenkins BD - Environ. Microbiol. (2014)

Bottom Line: The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site.Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes.Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA.

Show MeSH
Downcore abundance and nifH expression of group NB3 (related to P.carbinolicus) enumerated by quantitative PCR in 1 cm intervals from sediment samples collected at four sites, PRE (red), MNB (green), RIS2 (blue) and MP1 (purple). NB3 (A) abundance and (B) nifH expression during each sampling month as indicated by different line styles. NB3 (C) average abundance and (D) average nifH expression over the sampling time points. Graphs are plotted on a log scale and the standard error of the mean indicated by the error bars.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4231279&req=5

fig05: Downcore abundance and nifH expression of group NB3 (related to P.carbinolicus) enumerated by quantitative PCR in 1 cm intervals from sediment samples collected at four sites, PRE (red), MNB (green), RIS2 (blue) and MP1 (purple). NB3 (A) abundance and (B) nifH expression during each sampling month as indicated by different line styles. NB3 (C) average abundance and (D) average nifH expression over the sampling time points. Graphs are plotted on a log scale and the standard error of the mean indicated by the error bars.

Mentions: Changes in abundance, distribution and levels of expression of the two dominant microbial groups related to anaerobic bacteria expressing nifH, groups NB3 and NB7, were determined by qPCR. The greatest overall abundance of group NB3 was detected at site MNB at 3 to 4 cm in depth (Fig. 5A and C). Site PRE maintains the next highest levels of group NB3, with the lowest levels detected at the offshore sites RIS2 and MP1 (Fig 5A and C). One-way analysis of variance (anova) tests revealed the abundance of NB3 differed significantly among sites [F(3,20) = 20.98, P < 0.0001], with the maximum difference between site MNB and the other three sites as determined by the Tukey–Kramer honest significant difference (HSD) test (Supporting Information Table S5). The highest nifH expression of group NB3 is observed at the head of the Bay (site PRE), with a peak from 4 to 6 cm in depth during June 2010 (Fig. 5B and D). Both the abundance and nifH expression of group NB3 are lowest at the offshore sites, RIS2 and MP1 (Fig. 5). Group NB7 followed a similar distribution in the depth profile, with the greatest abundance between 3 and 6 cm in depth at site MNB (Fig. 6A and C). The abundance of group NB7 differed significantly between sites [F(3,20) = 24.1, P < 0.0001], with the greatest difference between the sites enclosed by land, PRE and MNB, versus the offshore locations, RIS2 and MP1 (Supporting Information Table S6). Highest nifH expression by group NB7 was also detected at lower depths at site PRE, with the exception of peak nifH transcripts detected at the sediment–water interface in October 2010 (Fig. 6B and D). Even though both groups NB3 and NB7 established highest abundances at site MNB, expression of nifH by these groups follows the estuarine gradient, with maximum levels observed at site PRE decreasing out to the continental shelf station, MP1 (Fig. 7). The expression of both microbial groups, NB3 and NB7, is significantly higher at site PRE compared with the other three sites [F(3,20) = 12.74, P < 0.0001 and F(3,20) = 48.19, P < 0.0001 respectively] (Supporting Information Tables S5 and S6). No statistical differences were detected in abundance or expression of groups NB3 and NB7 over the seasonal cycle or along the depth gradient at the sampling locations.


Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments.

Brown SM, Jenkins BD - Environ. Microbiol. (2014)

Downcore abundance and nifH expression of group NB3 (related to P.carbinolicus) enumerated by quantitative PCR in 1 cm intervals from sediment samples collected at four sites, PRE (red), MNB (green), RIS2 (blue) and MP1 (purple). NB3 (A) abundance and (B) nifH expression during each sampling month as indicated by different line styles. NB3 (C) average abundance and (D) average nifH expression over the sampling time points. Graphs are plotted on a log scale and the standard error of the mean indicated by the error bars.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231279&req=5

fig05: Downcore abundance and nifH expression of group NB3 (related to P.carbinolicus) enumerated by quantitative PCR in 1 cm intervals from sediment samples collected at four sites, PRE (red), MNB (green), RIS2 (blue) and MP1 (purple). NB3 (A) abundance and (B) nifH expression during each sampling month as indicated by different line styles. NB3 (C) average abundance and (D) average nifH expression over the sampling time points. Graphs are plotted on a log scale and the standard error of the mean indicated by the error bars.
Mentions: Changes in abundance, distribution and levels of expression of the two dominant microbial groups related to anaerobic bacteria expressing nifH, groups NB3 and NB7, were determined by qPCR. The greatest overall abundance of group NB3 was detected at site MNB at 3 to 4 cm in depth (Fig. 5A and C). Site PRE maintains the next highest levels of group NB3, with the lowest levels detected at the offshore sites RIS2 and MP1 (Fig 5A and C). One-way analysis of variance (anova) tests revealed the abundance of NB3 differed significantly among sites [F(3,20) = 20.98, P < 0.0001], with the maximum difference between site MNB and the other three sites as determined by the Tukey–Kramer honest significant difference (HSD) test (Supporting Information Table S5). The highest nifH expression of group NB3 is observed at the head of the Bay (site PRE), with a peak from 4 to 6 cm in depth during June 2010 (Fig. 5B and D). Both the abundance and nifH expression of group NB3 are lowest at the offshore sites, RIS2 and MP1 (Fig. 5). Group NB7 followed a similar distribution in the depth profile, with the greatest abundance between 3 and 6 cm in depth at site MNB (Fig. 6A and C). The abundance of group NB7 differed significantly between sites [F(3,20) = 24.1, P < 0.0001], with the greatest difference between the sites enclosed by land, PRE and MNB, versus the offshore locations, RIS2 and MP1 (Supporting Information Table S6). Highest nifH expression by group NB7 was also detected at lower depths at site PRE, with the exception of peak nifH transcripts detected at the sediment–water interface in October 2010 (Fig. 6B and D). Even though both groups NB3 and NB7 established highest abundances at site MNB, expression of nifH by these groups follows the estuarine gradient, with maximum levels observed at site PRE decreasing out to the continental shelf station, MP1 (Fig. 7). The expression of both microbial groups, NB3 and NB7, is significantly higher at site PRE compared with the other three sites [F(3,20) = 12.74, P < 0.0001 and F(3,20) = 48.19, P < 0.0001 respectively] (Supporting Information Tables S5 and S6). No statistical differences were detected in abundance or expression of groups NB3 and NB7 over the seasonal cycle or along the depth gradient at the sampling locations.

Bottom Line: The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site.Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes.Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA.

Show MeSH