50 M.-E. P. Papadimitropoulos and M. I. Klapa
is even greater in the coastal areas, where the seawater enters the aquifer, increas-
ing thus the soil salinity in intensively cultivated areas (Mahajan and Tuteja 2005 ).
As the growing of hydroponic cultures in greenhouses gains momentum as a means
for consistent plant and product quality independently of the place of plant growth
around the globe (Jones 2005 ), this trend has also contributed in the past decade to
an increase in the studies about the effect of varying water salinity on plant growth.
On the other hand, considering the elevation of the CO 2 concentration in the envi-
ronment due to the greenhouse effect, which can drastically change the physiology
of the plants and the quality of crop production in the future (Solomon et al. 2007 ),
the particular stress has been the subject of molecular plant physiology studies for
many years. This is also due to the fact that CO 2 is the major carbon source for the
plants and its increase at moderate levels and for moderate durations has been shown
to be beneficial for the plant growth, especially when the plants are also under the
influence of other stresses, including salinity (Takagi et al. 2009 ; Geissler et al. 2010 ;
Kanani et al. 2010 ; Perez-Lopez et al. 2012 ; Ratnakumar et al. 2013 ). Therefore, the
combined effect of high soil, but mainly water, salinity, and elevated CO 2 on plants
has been under investigation by agricultural engineers and plant physiologists not
only in the context of the greenhouse effect but also for the development of plant
growth optimization strategies in the presence of salinity stress.
In the system biology era, the investigation of the molecular mechanisms underly-
ing plant growth and response under various stresses has been enhanced by the high-
throughput biomolecular (i.e., omic) analyses. The latter enable the simultaneous
quantification of the concentration of tens to hundreds to thousands of molecular
quantities from the RNA to protein to small molecule (i.e., metabolic) level. How-
ever, these are new technologies, most at the stage of standardization, and the current
number of omic analyses in plants is not extensive, especially in the case of inte-
grated analyses at various molecular levels of cellular function. Moreover, the inves-
tigation of intact plants using omic analyses presents unique challenges over similar
investigations in cell cultures or other biological systems, among which are the cur-
rent lack of full genome sequence information for most plants, long life cycles, and
poorly controlled conditions in field experiments. In this chapter, we present the tran-
scriptomic and metabolomic studies of salinity and elevated CO 2 stresses in plants,
applied individually or in combination, emphasizing on the integrated analyses of
both levels of cellular function. The specifications of the experimental design for the
plant growth and the omic analyses, the challenges of such experiments, the acquired
results, and future directions for research and practice are also discussed.
3.2 Physiological Characteristics of the Plant Response
to High Salinity and/or Elevated CO 2
3.2.1 High Soil and/or Water Salinity
High soil salinity can affect plants in multiple ways. High salt depositions in the
soil generate low water potential in the root zone, making it difficult for the plants