Next Article 
Applied and Environmental Microbiology, December 2003, p. 6961-6968, Vol. 69, No. 12
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.12.6961-6968.2003
Copyright © 2003, American
Society for
Microbiology. All Rights Reserved.
Physiological and Community Responses of Established Grassland Bacterial Populations to Water Stress
Robert I. Griffiths,1,2 Andrew S. Whiteley,1* Anthony G. O'Donnell,2 and Mark J. Bailey1
Molecular
Microbial Ecology Laboratory, CEH-Oxford, Oxford OX1
3SR,1
Department of Agricultural
and Environmental Science, The University of Newcastle Upon
Tyne, Newcastle Upon Tyne NE1 7RU, United
Kingdom2
Received 19 March 2003/
Accepted 1 September 2003
 |
ABSTRACT
|
|---|
The
effects of water stress upon the diversity and culturable activity of
bacterial communities in the rhizosphere of an established upland
grassland soil have been investigated. Intact monoliths were subjected
to different watering regimens over a 2-month period to study community
adaptation to moisture limitation and subsequent response to stress
alleviation following rewetting. Genetic diversity was analyzed with
16S-based denaturing gradient gel electrophoresis (DGGE) of total
soil-extracted DNA (rRNA genes) and RNA (rRNA transcripts) in an
attempt to discriminate between total and active communities.
Physiological response was monitored by plate counts, total counts, and
BIOLOG-GN2 substrate utilization analyses. Controlled soil drying
decreased the total number of CFU on all the media tested and also
decreased the substrate utilization response. Following rewetting of
dried soil, culture-based analyses indicated physiological recovery of
the microbial population by the end of the experiment. In contrast,
DGGE analyses of community 16S rRNA genes, rRNA transcripts and
cultured communities did not reveal any changes relating to the
moisture regimens, despite the observed physiological effects. We
conclude that the imposed moisture regimen modulated the physiological
status of the bacterial community and that bacterial communities in
this soil are resistant to water stress. Further, we highlight the need
for a reexamination of rRNA transcript-based molecular profiling
techniques as a means of describing the active component of soil
bacterial
communities.
 |
INTRODUCTION
|
|---|
Bacteria play key roles in soil ecosystem processes by breaking down
plant exudates and litter and are therefore important mediators of
nutrient cycling in the plant-soil system. However, there is a lack of
understanding as to how the activity and diversity of these communities
in soils respond to perturbation. This issue needs particular attention
in threatened ecosystems, such as grasslands, due to their importance
in global carbon cycling and agricultural production. Many studies have
examined the consequences of natural and anthropogenic perturbations on
the soil microbiota, but these have mainly focused on the measurement
of total biomass or gross microbial processes in crop soils. Molecular
techniques based upon the analysis of 16S rRNA allow for assessment of
genetic diversity (23,
35), which may provide a
more sensitive and less biased indicator of changes in soil
communities. Using such methods, we have previously observed both
temporal and spatial changes in the diversity and activity of bacterial
communities in an upland grassland soil
(17). Here we extend this
research by investigating the role of soil moisture content in
regulating community structure and activity in grassland soil
ecosystems.
Soil moisture directly affects the
physiological status of bacteria
(21). Water availability
affects the osmotic status of bacterial cells and can indirectly
regulate substrate availability, diffusion of gases, soil pH, and
temperature. Further, moisture deficit will stress plants and, as a
result, may affect bacterial communities through changes in
rhizodeposition and nutrient allocation below ground
(29). Ultimately, periods
of moisture limitation may affect bacterial communities through
starvation, induced osmotic stress, and resource competition, eliciting
a strong selective pressure on the structure and functioning of soil
bacterial communities.
The involvement of soil moisture in
controlling fluxes of important greenhouse gases has been shown for
methane (19,
41), nitrous oxide
(4,
24), and carbon dioxide
(9,
12,
32,
38). While these
processes are not entirely the result of microbial activity, it has
recently been suggested that the underlying mechanisms may be due to
changes in the diversity and activity of bacterial populations
(8,
40). In bioremediation
studies, degradation rates have been correlated to the culturable
activities of specific organisms, which are in turn influenced by
moisture availability (7,
20). The role of moisture
in regulating the activity of specific culturable populations has also
been observed following inoculation of marked bacteria into soil
(31). However, such
studies on culturable bacteria may not adequately reflect changes
occurring in the total community.
Many studies have attempted to
analyze microbial responses to drying and rewetting by using chemical
determinants of biomass or microbial activities. These studies have
generally revealed that drying or drying and rewetting causes a
decrease in the total soil biomass
(5,
27,
45). Furthermore,
rewetting of dried soils is known to cause increased mineralization of
carbon (28) and nitrogen
(1,
6) coupled with a flush of
CO2 efflux
(14). The exact roles of
microbes in mediating these processes is still largely unresolved,
since biomass estimations may be hampered by methodological constraints
(13), and so it is
difficult to determine whether the effects are biological or physically
driven. However, CO2 evolution, as a general measure of
gross microbial activity, is known to reflect changes in water
potential (36). While
these studies have revealed the effect of moisture on broad-scale
microbial properties, no inference has been made to changes in
diversity of the total bacterial community which underlie these
processes. The use of molecular methodologies currently offers the most
potential for assessing the diversity of soil communities, yet only a
single article was found applying such approaches in investigating
moisture effects on soil bacterial populations
(22).
Our present
study aimed to monitor the molecular diversity and physiological status
of soil bacteria subjected to drying and rewetting in intact soil
monoliths collected from the Natural Environment Research Council
(NERC) Soil Biodiversity field site located at Sourhope (Scotland,
United Kingdom). The experimental regimen was applied to allow
examination of the bacterial community response to soil drying and
recovery following rewetting. The activity of culturable bacteria was
measured by performing plate counts on different media, and the
substrate utilization potential was assayed by using BIOLOG GN-2 plates
(15,
39). To examine
culture-independent effects on the extractable cell biomass, total cell
counts were compared by flow cytometric analysis of SYBR II-stained
cell preparations. Community structure was assessed by denaturing
gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes and
16S rRNA directly extracted from the soil
(18). It was anticipated
that the RNA transcript might be a more responsive biomarker in this
study, due to the known relationship between rRNA abundance and the
physiological status of bacterial cells
(3,
34).
 |
MATERIALS
AND METHODS
|
|---|
Experimental set-up and
sampling.
Intact grassland
monoliths were excised to a depth of approximately 15 cm from the NERC
Soil Biodiversity Program field site at Sourhope on 4 July 2001 and
transported immediately back to the laboratory. The soil is classified
as an organic rich brown forest soil (pH 4.5 to 5.0) and hosts a
diverse range of grass species typical of unimproved grazed pastures,
with the most dominant being Agrostis and Festuca
species. Monoliths were trimmed to a cylindrical core with a 45-cm
diameter and planted in close-fitting plastic pots to minimize edge
effects. Prior to planting, the pots had been customized to allow free
drainage of leachate and were filled with washed lime-free
horticultural grit to a depth that positioned the litter layer level at
the lip of the pot, thereby eliminating shading effects. Plant material
was then cropped to a height of approximately 5 cm to standardize
growth conditions at the start of the experiment.
In total, nine
microcosms were constructed, comprising three replicates of three
treatments, and maintained in the open air at Oxford. The three
treatment regimens were continual wetting (treatment A), drying
(treatment B), and drying and rewetting (treatment C). The experiment
ran for 3 months between July and October 2001, and 11 samplings were
taken in total at approximately weekly intervals (subsequently referred
to as S1 to S11). For samples 1 to 3 (S1, S2, and S3), no experimental
treatment was imposed and monoliths were exposed to natural rainfall
together with regular watering with filtered distilled water. On 14
August, UV-transparent polyethylene covers were constructed to
eliminate rainfall for experimental manipulation of water content.
Drying treatments (no watering) commenced after a final watering event
on 20 August (following S3). A watering regimen of 2 liters every 2
days (approximately) was adopted for the continually wetted treatments
to maintain water content close to field capacity. After approximately
1 month without water, treatment C (rewetted) was established by
rewatering on 18 September (following S6). This treatment was
subsequently watered with the same regimen as the continually wetted
treatment (treatment A).
All microcosms were sampled regularly to
determine the effect of the drying regimen on soil moisture content and
bacterial activity. Briefly four 1-cm-diameter cores were taken
randomly from each pot with a number 4 cork borer to a depth of
approximately 7 cm. These samples were mixed to homogeneity in plastic
bags, and large roots and plant material were extracted by hand.
Subsequently, 0.5-g (wet weight) aliquots of soil were then weighed for
dry weight determination and microbiological
analyses.
Culturability and total cell
count of bacterial community.
Soil (0.5 g wet weight) was dispersed
in 10 ml of phosphate-buffered saline (PBS) with 1.5 g of
sterile 5-mm-diameter glass beads and mixed by vortexing for 1 min.
Samples were decimally diluted, and 100-µl aliquots were spread
onto full-strength tryptic soy broth agar (TSBA; Difco,
Oxford, United Kingdom), 1/10-strength TSBA, and
pseudomonad-selective agar (PSA; Difco). All media were supplemented
with 100 µg of cycloheximide/ml to suppress fungal growth.
Plates were incubated for 10 days at 18°C prior to colony
counting. The diversity of cultured bacteria was also assayed on the
1/10-strength TSBA plates by extracting all of the colony biomass from
plates of the same dilution. Three milliliters of PBS was added to each
plate, and the biomass was dislodged with a sterile scraper.
Approximately 1.5 ml of cell suspension was then transferred to 1.5-ml
Microfuge tubes and stored at -0°C for
nucleic acid extraction.
Total bacterial cells were enumerated
according to the methods of Whiteley et al.
(46). Briefly,
0.5 g of soil was dispersed in PBS, and the resulting
supernatant was loaded onto a 1.3-g/ml Nycodenz density cushion.
Following centrifugation, cell preparations were extracted, washed, and
then fixed with a 1% final concentration of paraformaldehyde.
Cells were stained with 0.3 µl of the nucleic acid stain SYBR
Green II (Molecular Probes) for 20 min in the dark. Positively stained
bacterial cells were then enumerated with a FACSCalibur sorting flow
cytometer (Becton Dickinson Immunocytometry Systems, Oxford, United
Kingdom).
Substrate
utilization analyses.
Nine
milliliters of a 0.5% (wt/vol) soil suspension was prepared and
washed twice by dilution to 50 ml in sterile PBS, mixing, and
centrifugation (Jouan BR4i) for 5 min at 4,000 x g.
Following the cell washes, pelleted cells were resuspended in 20 ml of
sterile PBS, and 100-µl aliquots were dispensed into each of
the 96 wells of the BIOLOG-GN plates (Oxoid). Plates were incubated at
18°C and were manually scored at daily intervals to determine
the number of substrates utilized per day. For each reading, a well was
scored as positive based on visual inspection of color
change.
Statistical comparison of counts
and substrate utilization.
All quantitative data were
statistically analyzed to address three hypotheses. (i) Does short-term
drying decrease bacterial counts? (ii) Does rewetting of temporarily
dried soils reverse the effects of drying? (iii) Are there significant
differences between the three treatments at the termination of the
imposed regimens? To address the first two questions, the change over
time for each monolith was first calculated, followed by comparison of
the mean differences in change between treatments by analysis of
variance. This form of analysis was chosen to circumvent difficulties
in repeated measurement designs where there may be differences between
replicate monoliths prior to the start of the experiment. For the count
data, the estimate used to address the effects of drying was calculated
by subtracting the mean of counts from samples S2 and S3 (before
drying) from the mean of samples S5 and S6 (after drying). To test
rewetting effects, the means of samples S6 and S7 were subtracted from
the means of samples S10 and S11. For the substrate utilization data,
only rewetting effects were tested, and the change over time here was
taken to be the difference between samples S7 and S11. To assess
whether the treatments had an overall effect on culturable activity at
the end of the experiment, analysis of variance analysis was performed
on data from the final sample date (S11). Here, Fisher's
least-significant difference method was used to ascertain differences
between the three treatment means. Prior to statistical analysis, count
data were log transformed, whereas the percentages of substrates
utilized were arcsine transformed. All analyses were performed within
the MINITAB statistical software package (version 13.32; Minitab, Inc.,
State College, Pa.).
Nucleic acid
extraction and amplification.
Total nucleic acids were extracted
for DGGE analyses by the method of Griffiths et al.
(18). Briefly, 0.5 ml of
cetyltrimethylammonium bromide extraction buffer and 0.5 ml of
phenol-chloroform-isoamyl alcohol (25:24:1 [pH 8.0]) were
added to 0.5 g of soil sample or 0.5 ml of cell culture in
BIO-101 multimix bead-beating tubes. Following mechanical lysis and
subsequent solvent extraction, nucleic acids were precipitated from the
extracted aqueous layer with two volumes of 30% polyethylene
glycol 6000 (Fluka BioChemika)-1.6 M NaCl. Pelleted nucleic
acids were washed in ice-cold 70% (vol/vol) ethanol, air dried,
and resuspended in 50 µl of RNase-free Tris-EDTA buffer (pH
7.4). Extracted nucleic acids were then inspected by gel
electrophoresis prior to enzymatic separation of DNA and RNA and PCR or
reverse transcription-PCR amplification (total soil-extracted nucleic
acids only). Following DNase treatment, 16S rRNA was reverse
transcribed with the universal 16S primer 519r
(5'-GTA TTA CCG CGG CTG CTG-3') as
described previously
(18). DNA and cDNA were
then PCR amplified with the GC-clamped forward primer 338f
(5-CGC CCG CCG CGC CCC CGC CCC GGC CCG CCG CCC CCG CCC ACT
CCT ACG GGA GGC AGC-3') and 519r reverse primer
according to the method of Griffiths et al.
(18).
DGGE.
DGGE was performed by using the
De-Code system (Bio-Rad) with a 10% (wt/vol) acrylamide gel with
a 30 to 60% (wt/vol) denaturing gradient (urea and formamide)
running for 6 h at 200 V. All solutions and procedures were
standardized before the running of each gel to optimize consistency
between gels. Gels were stained with SYBR Gold (Molecular Probes, Inc.)
and visualized by UV transillumination. Gel images were analyzed
densitometrically with the Phoretix one-dimensional software package
(Nonlinear Dynamics, Newcastle upon Tyne, United Kingdom), and profiles
were compared by using the multivariate statistical package MVSP
(Kovach Computing, Anglesey, United
Kingdom).
 |
RESULTS
|
|---|
Soil
moisture content.
The effects
of the imposed watering regimen on soil moisture contents, determined
by oven drying, are shown in Fig.
1. During the experimental period, dried treatments reached a minimum of
approximately 15% moisture per g of soil (fresh weight), whereas
continually wetted pots fluctuated around 50%. For dried and
rewetted treatments, soil moisture content dropped to a minimum of
18% but subsequently recovered to 44% by the end of the
treatment regimen.
Bacterial culturability
and total cell count.
The
effect of the three treatment regimens on the total numbers of bacteria
able to form colonies (CFU) on agar plates was determined on two
nonselective media and one semiselective medium (Fig.
2). The highest overall counts were observed on 1/10 TSBA, with wetted
treatments consistently being over 108 CFU g (dry weight) of
soil-1, whereas the lowest counts were observed on
PSA. By contrasting the mean change over time between wetted and dried
treatments, soil drying up to sample S6 significantly decreased the
culturable counts on all media (P < 0.05). The effect
of drying was most pronounced for the bacteria able to grow on PSA,
where for certain sample dates, there was up to a 40-fold reduction in
CFU in dried treatments compared with the continually wetted
treatments. Rewetting caused significant increases in counts on PSA and
1/10 TSBA over time compared with the dried treatments (P
< 0.05), resulting in no significant difference between
rewetted and continually wetted mean counts at the final sampling (S11,
P > 0.05). On TSBA, the lower amount of variation
between treatments and a low count at the final sampling point
prevented us from ascertaining a significant effect of rewetting
(P = 0.066), although it is likely that recovery would
have been observed with further samplings.

View larger version (24K):
[in this window]
[in a new window]
|
FIG. 2. Responses
of culturable bacteria to moisture treatments on three different
culture media: 1/10 TSBA, TSBA, and PSA. Sampling points are indicated
at the base of the graph. Error bars represent standard errors of the
means (n = 3). Treatments are indicated by symbols as
follows: , continually wetted; , dried; ,
dried and rewetted. Jul, July; Aug, August; Sep, September; Oct,
October; Nov,
November.
|
|
A small yet
significant decrease occurred in total cell counts as a result of
drying up to sample S6. However, this effect was not consistent, since
no significant increase in rewetted samples occurred, and there was no
difference in means at the end of the experiment (sample S11).
Interestingly, total counts were consistently around 108
cells per g of soil (Table
1), which is in the same range as those observed from culturable
enumeration. While higher total cell counts would have been expected,
it is noted that this analysis was carried out on cell preparations
taken from a soil supernatant and separated by centrifugation on
Nycodenz media. It is therefore possible that this method may give an
underestimate of the total count, but the extractable count obtained
still permitted comparison between
samples.
View this table:
[in this window]
[in a new window]
|
TABLE 1. Total
cell counts for all treatments and sample dates determined by flow
cytometric counting of SYBR II-stained cells
|
|
Substrate utilization
rates.
The BIOLOG assay was
used to complement the culture assays in determining recovery of viable
bacteria following rewetting of the dried soils. The rate at which the
bacterial communities utilized each of the 95 substrates was assayed
for all samples following the rewetting event on 18 September 2001
(samples S7 to S11). Characteristic sigmoid responses were observed,
with substrate utilization appearing to proceed at a lower rate in
dried treatments than in the continually wetted treatments (data not
shown). The rates of substrate utilization also appeared to increase in
the rewetted treatments with continued water application. To assess the
effect of the moisture treatments on substrate utilization, the
percentage of substrates utilized after 4 and 7 days of incubation were
plotted and are shown in Fig. 3a and
3b, respectively. These plots reveal that immediately following rewetting
(sample S7) wetted samples appear to utilize more substrates regardless
of incubation time. Continued rewetting increased the number of
substrates utilized between sample dates S7 and S11 compared to
continually dried monoliths (P < 0.05). However, full
recovery at the final time point (S11) could only be ascertained when
plate readings after 7 days of incubation were compared. This may be
due to the decreased sensitivity of the assay for detecting differences
between samples when longer incubations are
used.
DGGE.
DGGE profiling of 16S rRNA was used to
assess moisture-induced changes in eubacterial community structure. In
total, nine gels were run encompassing the three different treatments
and the nature of template nucleic acid (DNA extracted from soil, RNA
extracted from soil, and DNA extracted from 1/10 TSBA culture plates).
The DGGE profiles from total soil-extracted rRNA genes and rRNA were
extremely complex, yet no obvious changes were observed in the
predominant bands as a result of the imposed moisture regimens.
Furthermore, no major differences were apparent between RNA- and
DNA-based profiles from the same treatment. In contrast, DGGE analysis
of bacteria cultured on 1/10 TSBA revealed highly variable profiles
between both treatment replicates and sample dates. However,
densitometric profiling and multivariate analysis
(17) of all gels failed
to detect any consistent variation in profiles which could be
attributed to the moisture treatments (data not shown). For
illustrative purposes, gels are only presented for the rewetted
treatment, since they encompass stages of continual wetting, drying,
and rewetting for each of the three templates (Fig.
4).

View larger version (107K):
[in this window]
[in a new window]
|
FIG. 4. DGGE
analyses of total extracted rRNA genes (a), rRNA transcripts (b), and
total culturable bacteria (c) for the dried and rewetted treatment
only. Sampling points are indicated above each gel, and the three lanes
for each time point represent the individual profiles obtained from
each replicate pot. Marker lanes comprising amplicons from bacterial
isolates are located at either side of each
gel.
|
|
 |
DISCUSSION
|
|---|
Culture-based methods
indicated that microbial physiological response was modulated by
moisture content, with total culturability and substrate utilization
response being maintained in continually wetted treatments, depressed
in dried treatments, and cycled between these extremes with the drying
and rewetting regimen. Previous studies on unplanted sieved soils found
drying and rewetting to significantly reduce microbial biomass to a
greater degree than observed in our study
(5,
27). The less-pronounced
effect observed here may be due to more-gradual soil drying
(44), as would be the
case in the environment, and/or the free draining system preventing
cell death caused by rapid changes in moisture potential
(21). Our data therefore
implicate the inherent resistance of natural grassland-soil bacterial
communities to environmentally realistic gradual changes in moisture
content.
In contrast to the physiological methods, no
moisture-related changes were observed following molecular profiling of
the culturable diversity or total nucleic acids extracted from soil.
The lack of change in diversity profiles is surprising in light of the
effect of moisture upon the community physiology discussed above. For
the analysis of culturable diversity, moisture perturbation may not
have sufficiently impacted the total community to influence the
reported high variation in species assembly on agar plates
(11). The absence of
change in community profiles based upon extracted rRNA genes or the
rRNA transcripts may be partly explained by the large genotypic
diversity of bacteria present in soil
(42) and the fact that
only the dominant templates are detected in DGGE profiles
(16). Assuming the total
diversity to be log normally distributed
(10), it is conceivable
that variation within diverse populations of low numerical abundance
may not be detected by primers targeting the whole community. This may
have been the case for the rRNA gene-based analysis, since no
consistent changes in total cell counts were observed, indicating
negligible cell growth or death in response to the moisture treatments
(as was found in reference
47).
The similarity
of rRNA transcript-based community profiles cannot be explained by the
lack of variation in total cell counts, since rRNA transcript
concentrations should vary independently of biomass and in relation to
cellular physiological state
(34) and growth stage
(3). However, aside from
pure culture studies, there is little information on the variation of
rRNA content in bacterial cells present in natural environments such as
soils. Therefore, it may be possible that small increases in the rRNA
content of active cells are masked by more abundant rRNA from quiescent
cells. Furthermore, recent research on marine isolates has revealed
that RNA levels may not always relate to growth rate, especially during
non-steady-state growth
(26). Additionally,
RNA/DNA ratios have been shown to not always relate to microbial
activity in heterogeneous environmental samples such as sediment
(25). These findings
therefore raise questions on the relative advantages of using rRNA
transcript analysis over rRNA gene analysis as a more-responsive
biomarker to study soil bacterial communities.
Despite these
methodological constraints, our data enforce the belief that soil
bacteria may be preadapted to resist moisture variations by regulation
of cellular activity
(31). The ability of soil
bacteria to withstand such perturbations may relate to the so-called
starvation state (2). This
state is thought to represent a survival strategy for bacterial
persistence in harsh, low-nutrient environments and may be mediated by
starvation gene expression, cell shrinkage, or sporulation. Specific
responses to osmotic stress include sensing mechanisms coupled with the
uptake or synthesis of compatible solutes to reestablish cell turgor
pressure (33,
48). If our diversity
assessments are representative, then it may be that the predominant
soil community responds to moisture availability in the same manner,
i.e., all the dominant bacterial species are equally capable of
surviving drying and no competition occurs after rewetting. While this
does not agree with the concepts of copiotrophy and oligotrophy
(43), it does reinforce
the idea that soil bacteria are able to cope with both high and low
nutrient conditions equally well
(34).
To conclude,
our data implicate the marked resistance of soil bacteria to water
stress based upon physiological criteria (culturability and substrate
utilization analyses). However, we did not observe significant changes
within the total community from a molecular standpoint when directing
the analyses at the population level, with both rRNA gene- and rRNA
transcript-based 16S profiling. Under the experimental regimen employed
(controlled slow perturbation), these latter approaches may lead to an
unrepresentative picture of what is occurring in the natural
environment. This is likely to be a facet of the large diversity
present within these environments, diversity changes occurring within
small fractions of the community, and potential physiological
adaptations which have yet to be resolved. Indeed, we have recently
shown that differences could be detected in the community structure of
active cells by prior isolation by using cell sorting of
5-cyano-2,3-ditolyl tetrazolium chloride (CTC)-stainedcells (46). It may
therefore be likely that changes occurring in these operationally
defined active communities may be more relevant in terms of ecosystem
functioning. Further, technologies which directly link the activity of
microbes with ecosystem processes, such as the labeling of plant
material with 13CO2
(37) and phylogenetic
analysis of isotopically enriched rRNA
(30), may be a more
appropriate way of subdividing the community for more-resolved analyses
of the response to perturbation.
 |
ACKNOWLEDGMENTS
|
|---|
This work was supported as
part of the NERC Soil Biodiversity thematic program through grant
GST/32/2136 (to M.J.B., A.S.W., and A.G.O.) and an associated
studentship (to R.I.G.).
We thank Damien Mayoux and Graham
Burt-Smith for help with sample collection and Nick Ostle and Niall
McNamara for advice on setting up the mesocosms. We extend our
gratitude to David Elston and an anonymous reviewer for suggestions
which improved the statistical
analysis.
 |
FOOTNOTES
|
|---|
* Corresponding
author. Mailing address: IVEM, CEH-Oxford, Mansfield Rd., Oxford OX1
3SR, United Kingdom. Phone: 44 0 1865 281686. Fax: 44 0 1865 281696.
E-mail:
whiteley{at}molbiol.ox.ac.uk. 
 |
REFERENCES
|
|---|
- Appel,
T. 1998. Non biomass soil organic N-the substrate for
N mineralization flushes following soil drying-rewetting and for
organic N rendered CaCl2-extractable upon soil drying.Soil Biol. Biochem.
30:1445-1456.[CrossRef]
- Bakken,
L. R. 1997. Culturable and nonculturable
bacteria in soil, p. 47-62.
In J. D. van Elsas, J. T. Trevors, and
E. M. H. Wellington (ed.), Modern soil
microbiology. Marcel Dekker, New York,
N.Y.
- Binder,
B. J., and Y. C. Liu. 1998. Growth
rate regulation of rRNA content of a marine Synechococcus
(Cyanobacterium) strain. Appl. Environ. Microbiol.
64:3346-3351.[Abstract/Free Full Text]
- Bollmann,
A., and R. Conrad. 1998. Influence of O2
availability on NO and N2O release by nitrification and
denitrification in soils. Glob. Change Biol.
4:387-396.[CrossRef]
- Bottner,
P. 1985. Response of microbial biomass to alternate
moist and dry conditions in a soil incubated with 14C
labeled and 15N labeled plant material. Soil Biol.
Biochem.
17:329-337.[CrossRef]
- Cabrera,
M. L. 1993. Modeling the flush of nitrogen
mineralization caused by drying and rewetting soils. Soil Sci.
Soc. Am. J.
57:63-66.
- Cattaneo,
M. V., C. Masson, and C. W. Greer.1997
. The influence of moisture on microbial transport,
survival and 2, 4-D biodegradation with a genetically marked
Burkholderia cepacia in unsaturated soil columns.Biodegradation
8:87-96.[CrossRef][Medline]
- Conrad,
R. 1996. Soil microorganisms as controllers of
atmospheric trace gases (H2, CO, CH4, OCS,
N2O, and NO). Microbiol. Rev.
60:609-640.[Abstract/Free Full Text]
- Craine,
J. M., D. A. Wedin, and P. B. Reich.2001
. The response of soil CO2 flux to changes
in atmospheric CO2, nitrogen supply and plant diversity.Glob. Change Biol.
7:947-953.[CrossRef]
- Curtis,
T. P., W. T. Sloan, and J. W.
Scannell. 2002. Estimating prokaryotic diversity and
its limits. Proc. Natl. Acad. Sci. USA
99:10494-10499.[Abstract/Free Full Text]
- Duineveld,
B. M., A. S. Rosado, J. D. van Elsas, and
J. A. van Veen. 1998. Analysis of the
dynamics of bacterial communities in the rhizosphere of the
chrysanthemum via denaturing gradient gel electrophoresis and substrate
utilization patterns. Appl. Environ. Microbiol.
63:4950-4957.
- Frank,
A. B., M. A. Liebig, and J. D.
Hanson. 2002. Soil carbon dioxide fluxes in northern
semiarid grasslands. Soil Biol. Biochem.
34:1235-1241.[CrossRef]
- Franzluebbers,
A. J., R. L. Haney, C. W. Honeycutt,
H. H. Schomberg, and F. M. Hons.2000
. Flush of carbon dioxide following rewetting of dried
soil relates to active organic pools. Soil Sci. Soc.
Am. J.
64:613-623.[Abstract/Free Full Text]
- Franzluebbers,
A. J., R. L. Haney, F. M. Hons, and
D. A. Zuberer. 1996. Determination of
microbial biomass and nitrogen mineralization following rewetting of
dried soil. Soil Sci. Soc. Am. J.
60:1133-1139.[Abstract/Free Full Text]
- Garland,
J. L., and A. L. Mills. 1991.
Classification and characterization of heterotrophic microbial
communities on the basis of patterns of community-level
sole-carbon-source-utilization. Appl. Environ.
Microbiol.
57:2351-2359.[Abstract/Free Full Text]
- Gelsomino,
A., A. C. Keijzer-Wolters, G. Cacco, and J. D. van
Elsas. 1999. Assessment of bacterial community
structure in soil by polymerase chain reaction and denaturing gradient
gel electrophoresis. J. Microbiol. Methods
38:1-15.[CrossRef][Medline]
- Griffiths,
R. I., A. S. Whiteley, A. G.
O'Donnell, and M. J. Bailey. 2003.
Influence of depth and sampling time on bacterial community structure
in an upland grassland soil. FEMS Microbiol. Ecol.
43:35-43.[CrossRef]
- Griffiths,
R. I., A. S. Whiteley, A. G.
O'Donnell, and M. J. Bailey. 2000.
Rapid method for coextraction of DNA and RNA from natural environments
for analysis of ribosomal DNA- and rRNA-based microbial community
composition. Appl. Environ. Microbiol.
66:5488-5491.[Abstract/Free Full Text]
- Gulledge,
J., and J. P. Schimel. 1998. Moisture
control over atmospheric CH4 consumption and CO2
production in diverse Alaskan soils. Soil Biol. Biochem.
30:1127-1132.[CrossRef]
- Han,
S. O., and P. B. New. 1994. Effect
of water availability on degradation of 2, 4-dichlorophenoxyacetic acid
(2, 4-D) by soil microorganisms. Soil Biol. Biochem.
26:1689-1697.[CrossRef]
- Harris,
R. F. 1981. Effect of water potential on
microbial growth and activity, p.23
-95. In J. F.
Parr, W. R. Gardner, and L. F. Elliott (ed.), Water
potential relations in soil microbiology. Soil Science Society of
America, Madison,
Wis.
- Hastings,
R. C., C. Butler, I. Singleton, J. R. Saunders, and
A. J. McCarthy. 2000. Analysis of
ammonia-oxidizing bacteria populations in acid forest soil during
conditions of moisture limitation. Lett. Appl.
Microbiol.
30:14-18.[CrossRef][Medline]
- Head,
I. M., J. R. Saunders, and R. W.
Pickup. 1998. Microbial evolution, diversity, and
ecology: a decade of ribosomal RNA analysis of uncultivated
microorganisms. Microb. Ecol.
35:1-21.[CrossRef][Medline]
- Hutchinson,
G. L., W. D. Guenzi, and G. P.
Livingston. 1993. Soil water controls on aerobic soil
emission of gaseous nitrogen oxides. Soil Biol. Biochem.
25:1-9.
- Jeffrey,
W. H., R. VonHaven, M. P. Hoch, and R. B.
Coffin. 1996. Bacterioplankton RNA, DNA, protein
content and relationships to rates of thymidine and leucine
incorporation. Aquat. Microb. Ecol.
10:87-95.
- Kerkhof,
L., and P. Kemp. 1999. Small ribosomal RNA content in
marine Proteobacteria during non-steady-state growth. FEMS
Microbiol. Ecol.
30:253-260.[CrossRef][Medline]
- Kieft,
T. L., E. Soroker, and M. K. Firestone.1987
. Microbial biomass response to a rapid increase in
water potential when dry soil is wetted. Soil Biol.
Biochem.
19:119-126.
- Lundquist,
E. J., L. E. Jackson, and K. M. Scow.1999
. Wet-dry cycles affect dissolved organic carbon in
two California agricultural soils. Soil Biol. Biochem.
31:1031-1038.[CrossRef]
- Lynch,
J. M., and J. M. Whipps. 1990.
Substrate flow in the rhizosphere. Plant Soil
129:1-10.
- Manefield,
M., A. S. Whiteley, R. I. Griffiths, and
M. J. Bailey. 2002. RNA stable isotope
probing, a novel means of linking microbial community function to
phylogeny. Appl. Environ. Microbiol.
68:5367-5373.[Abstract/Free Full Text]
- Meikle,
A., S. Aminhanjani, L. A. Glover, K. Killham, and
J. I. Prosser. 1995. Matric potential and
the survival and activity of a Pseudomonas fluorescens
inoculum in soil. Soil Biol. Biochem.
27:881-892.[CrossRef]
- Mielnick,
P. C., and W. A. Dugas. 2000. Soil
CO2 flux in a tallgrass prairie. Soil Biol.
Biochem.
32:221-228.[CrossRef]
- Miller,
K. J., and J. M. Wood. 1996.
Osmoadaptation by rhizosphere bacteria. Annu. Rev.
Microbiol.
50:101-136.[CrossRef][Medline]
- Morita,
R. Y. 1993. Bioavailability of energy and
the starvation state, p. 1-24.
In S. Kjelleberg (ed.), Starvation in bacteria. Plenum Press,
New York,
N.Y.
- O'Donnell,
A. G., and H. E. Gorres. 1999. 16S
rDNA methods in soil microbiology. Curr. Opin.
Biotechnol.
10:225-229.[CrossRef][Medline]
- Orchard,
V. A., and F. J. Cook. 1983.
Relationship between soil respiration and soil moisture. Soil
Biol. Biochem.
15:447-453.
- Ostle,
N., P. Ineson, D. Benham, and D. Sleep. 2000. Carbon
assimilation and turnover in grassland vegetation using an in situ
13CO2 pulse labelling system. Rapid
Commun. Mass Spectrom.
14:1345-1350.[CrossRef][Medline]
- Ouyang,
Y., and C. Zheng. 2000. Surficial processes and
CO2 flux in soil ecosystem. J. Hydrol.
234:54-70.[CrossRef]
- Preston-Mafham,
J., L. Boddy, and P. F. Randerson. 2002.
Analysis of microbial community functional diversity using
sole-carbon-source utilisation profiles-a critique. FEMS
Microbiol. Ecol.
42:1-14.[CrossRef]
- Schimel,
J. P., and J. Gulledge. 1998. Microbial
community structure and global trace gases. Glob. Change
Biol.
4:745-758.[CrossRef]
- Schnell,
S., and G. M. King. 1996. Responses of
methanotrophic activity in soils and cultures to water stress.Appl. Environ. Microbiol.
62:3203-3209.[Abstract]
- Torsvik,
V., J. Goksoyr, and F. L. Daae. 1990. High
diversity in DNA of soil bacteria. Appl. Environ.
Microbiol.
56:782-787.[Abstract/Free Full Text]
- van
Elsas, J. D., and L. S. van Overbeek.1993
. Bacterial responses to soil stimuli, p.55
-80. In S. Kjelleberg
(ed.), Starvation in bacteria. Plenum Press, New York,
N.Y.
- Vangestel,
M., J. N. Ladd, and M. Amato. 1992.
Microbial biomass responses to seasonal change and imposed drying
regimes at increasing depths of undisturbed topsoil profiles.Soil Biol. Biochem.
24:103-111.
- Vangestel,
M., R. Merckx, and K. Vlassak. 1993. Microbial biomass
and activity in soils with fluctuating water contents.Geoderma
56:617-626.[CrossRef]
- Whiteley,
A. S., R. I. Griffiths, and M. J.
Bailey. 2003. Analysis of the microbial functional
diversity within water stressed soil communities by flow cytometric
analysis and CTC+ cell sorting. J. Microbiol.
Methods
54:257-267.[CrossRef][Medline]
- Winding,
A., S. J. Binnerup, and J. Sorensen. 1994.
Viability of indigenous soil bacteria assayed by respiratory activity
and growth. Appl. Environ. Microbiol.
60:2869-2875.[Abstract/Free Full Text]
- Wood,
J. M. 1999. Osmosensing by bacteria: signals
and membrane-based sensors. Microbiol. Mol. Biol. Rev.
63:230-262.[Abstract/Free Full Text]
Applied and Environmental Microbiology, December 2003, p. 6961-6968, Vol. 69, No. 12
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.12.6961-6968.2003
Copyright © 2003, American
Society for
Microbiology. All Rights Reserved.
This article has been cited by other articles:
-
Vriezen, J. A. C., de Bruijn, F. J., Nusslein, K.
(2007). Responses of Rhizobia to Desiccation in Relation to Osmotic Stress, Oxygen, and Temperature. Appl. Environ. Microbiol.
73: 3451-3459
[Full Text]
-
Nakatsu, C. H.
(2007). Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis. Soil Sci.
71: 562-571
[Abstract]
[Full Text]
-
DeSantis, T. Z. Jr, Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y. M., Phan, R., Andersen, G. L.
(2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.. Nucleic Acids Res
34: W394-W399
[Abstract]
[Full Text]
-
Castaldini, M., Turrini, A., Sbrana, C., Benedetti, A., Marchionni, M., Mocali, S., Fabiani, A., Landi, S., Santomassimo, F., Pietrangeli, B., Nuti, M. P., Miclaus, N., Giovannetti, M.
(2005). Impact of Bt Corn on Rhizospheric and Soil Eubacterial Communities and on Beneficial Mycorrhizal Symbiosis in Experimental Microcosms. Appl. Environ. Microbiol.
71: 6719-6729
[Abstract]
[Full Text]