Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean

Dong, C.; Bai, X.; Sheng, H.; Jiao, L.; Zhou, H.; Shao, Z.

doi:https://doi.org/10.5194/bg-12-2163-2015

Articles | Volume 12, issue 7

https://doi.org/10.5194/bg-12-2163-2015

© Author(s) 2015. This work is distributed under
the Creative Commons Attribution 3.0 License.

https://doi.org/10.5194/bg-12-2163-2015

© Author(s) 2015. This work is distributed under
the Creative Commons Attribution 3.0 License.

Articles | Volume 12, issue 7

Research article

|

13 Apr 2015

Research article |

| 13 Apr 2015

Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean

C. Dong, X. Bai, H. Sheng, L. Jiao, H. Zhou, and Z. Shao

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Final revised paper (published on 13 Apr 2015)
Supplement to the final revised paper
Preprint (discussion started on 29 Sep 2014)
Supplement to the preprint

Interactive discussion

Status: closed

AC: Author comment | RC: Referee comment | SC: Short comment | EC: Editor comment

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- Supplement

RC C6271: 'Solid manuscript with a few English problems', Andrew Steen, 29 Oct 2014
- AC C6939: 'Response to Dr. Andrew Steen', Chunming Dong, 23 Nov 2014
RC C7175: 'Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean_review', Kelly McFarlin, 07 Dec 2014
- AC C7560: 'Response to Dr. Kelly McFarlin FV', Chunming Dong, 21 Dec 2014
RC C8015: 'Referee Comment', Anonymous Referee #3, 12 Jan 2015
- AC C8213: 'Response to Anonymous Referee #3', Chunming Dong, 22 Jan 2015

Peer-review completion

AR: Author's response | RR: Referee report | ED: Editor decision

AR by Chunming Dong on behalf of the Authors (01 Feb 2015) Author's response Manuscript

ED: Referee Nomination & Report Request started (11 Feb 2015) by Gerhard Herndl

RR by Gonzalez Natalia (11 Feb 2015)

RR by Andrew Steen (18 Mar 2015)

Suggestions for revision or reasons for rejection

This manuscript is basically in good shape. The authors have satisfactorily addressed my previous, minor reservations. I have a couple of technical suggestions which I strongly encourage the authors to adopt.

I must apologize to the authors: one of the suggestions arises from bad advice I gave in my previous review. The authors recreated Fig 3 using code I pointed them to. However, this code produced plots with unlabeled axes, which is unacceptable. I have included revised R code below to produce similar plots, but with labeled axes. I strongly encourage the authors to use the revised code (or to produce plots with labeled axes according to their own methods - it doesn't matter how precisely they do it, but it is essential to label plot axes!).

I also encourage the authors to rebuild Fig 3 using the same code. As I mentioned previously, stacked bar graphs are commonly used in microbial ecology, but I find them to be harder to interpret than the kind of plot in Fig 2. If these plots make sense for Fig 2, they probably make sense for Fig 3 as well.

Lines 184-190 and Fig 4: I appreciate the authors including the equation for their calculation, but I still think that anything described as a "rate" needs to have units of time in the denominator. What the authors have calculated is more accurately described as "removal extent". It will be difficult to compare these data with any other experiment without dividing by the incubation time, which would give a true removal rate in units of %/hr. (If, for some reason, the authors really do not want to divide by incubation time, they should refer to the parameter they have calculated as "removal extent" and keep the units as %.)

############

R script to make better versions of Fig 2 and 3:

##########
# Timothee Poisot's original code
##########
library(RColorBrewer)

Abund = round(matrix(runif(12*13,0,1),nc=13),2)
Abund = Abund/max(Abund)

rownames(Abund) = LETTERS[c(1:nrow(Abund))]
colnames(Abund) = letters[c(1:ncol(Abund))]

pal = colorRampPalette(brewer.pal(9,'Paired'))(nrow(Abund))

###########
# My code to produce a different version of this plot
# WITH AXIS LABELS
##########

# If you don't have these packages, run the following line:
# install.packages(c("reshape2", "ggplot2", "scales", "rColorBrewer"))
library(reshape2)
library(ggplot2)
library(scales)
library(rColorBrewer)
# I'm assuming there is a row for each site and a column for each compound
Abund <- as.data.frame(Abund) # Convert to data frame
Abund$site <- rownames(Abund) # Sites must be a column of the data frame
Abund_m <- melt(Abund, id.vars="site", variable.name="compound", value.name="concentration")

# p_Abund <- ggplot(Abund_m, aes(x=site, y=concentration)) + # Use this if you don't want color
p_Abund <- ggplot(Abund_m, aes(x=site, y=concentration, fill=compound)) + # use this if you do want colors
geom_bar(stat="identity") +
coord_flip() + # This line changes vertical bars to horizontal - personal preference
scale_fill_manual(values=colorRampPalette(brewer.pal(9,'Paired'))(ncol(Abund))) + # Remove this if you don't want colors
xlab("site") +
ylab(expression(paste("concentration, ", mu, "M ", g^{-1}, " sed"))) + # I can't remember which units the authors used
facet_wrap(~compound, nrow=2) +
theme_bw() + # I prefer this background color scheme; this is pure opinion
theme(legend.position="none") + #if you want to color the bars but not include a legend
theme(axis.text.x=element_text(angle=-45, hjust=0),
text=element_text(size=9)) # Adjust the font size of the plot text as necessary
print(p_Abund)

#########
# Save the plot.
# Be sure to use the appropriate figure dimensions for the journal
#########

#For Mac
ggsave("review_plot.tiff", height=12, width=20, units="cm", type="cairo", dpi=300)
# For Windows
ggsave("review_plot.tiff", height=12, width=20, units="cm", dpi=300)

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ED: Publish subject to technical corrections (20 Mar 2015) by Gerhard Herndl

AR by Chunming Dong on behalf of the Authors (27 Mar 2015) Author's response Manuscript

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