Influence of salinity and water content on soil microorganisms

Abstract

Salinization is one of the most serious land degradation problems facing world. Salinity results in poor plant growth and low soil microbial activity due to osmotic stress and toxic ions. Soil microorganisms play a pivotal role in soils through mineralization of organic matter into plant available nutrients. Therefore it is important to maintain high microbial activity in soils. Salinity tolerant soil microbes counteract osmotic stress by synthesizing osmolytes which allows them to maintain their cell turgor and metabolism. Osmotic potential is a function of the salt concentration in the soil solution and therefore affected by both salinity (measured as electrical conductivity at a certain water content) and soil water content. Soil salinity and water content vary in time and space. Understanding the effect of changes in salinity and water content on soil microorganisms is important for crop production, sustainable land use and rehabilitation of saline soils. In this review, the effects of soil salinity and water content on microbes are discussed to guide future research into management of saline soils.

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International Soil and Water Conservation Research 3 (2015) 316– 323
Influence of salinity and water content on soil microorganisms
Nan Yan
a,b,
n
, Petra Marschner
c
, Wenhong Cao
a,b
, Changqing Zuo
a,b
, Wei Qin
a,b
a
Department of Sediment Research, China Institute of Water Resources and Hydropower Research, Beijing 100048, China
b
Research Centre on Soil and Water Conservation of the Ministry of Water Resources, Beijing 100048, China
c
School of Agriculture, Food & Wine, The Waite Research Institute, The University of Adelaide, Adelaide, SA 5005, Australia
Received 10 October 2015; received in revised form 30 November 2015; accepted 30 November 2015
Available online 2 December 2015
Abstract
Salinization is one of the most serious land degradation problems facing world. Salinity results in poor plant growth and low soil
microbial activity due to osmotic stress and toxic ions. Soil microorganisms play a pivotal role in soils through mineralization of organic
matter into plant available nutrients. Therefore it is important to maintain high microbial activity in soils. Salinity tolerant soil microbes
counteract osmotic stress by synthesizing osmolytes which allows them to maintain their cell turgor and metabolism. Osmotic potential is a
function of the salt concentration in the soil solution and therefore affected by both salinity (measured as electrical conductivity at a certain
water content) and soil water content. Soil salinity and water content vary in time and space. Understanding the effect of changes in salinity
and water content on soil microorganisms is important for crop production, sustainable land use and rehabilitation of saline soils. In this
review, the effects of soil salinity and water content on microbes are discussed to guide future research into management of saline soils.
& 2015 International Research and Training Center on Erosion and Sedimentation and China Water and Power Press. Production and
HostingbyElsevierB.V.Thisisanopenaccess article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/ ).
Keywords: Salinity; Water content; Soil microorganism
Contents
1. Introduction .......................................................................317
2. The importance of soil microorganisms for nutrient cycling ....................................... 317
3. Soil salinity .......................................................................317
3.1. Soil salinity definition . . ..........................................................317
3.2. Effects of salinity on microorganisms .................................................318
4. The effects of soil water availability on microorganisms .........................................319
4.1. Forms of water in soils . ..........................................................319
4.2. Effect of water content on microbes ..................................................319
4.3. Effect of fluctuating water content on soil microorganisms . . .................................320
www.elsevier.com/locate/iswcr
http://dx.doi.org/10.1016/j.iswcr.2015.11.003
2095-6339/& 2015 International Research and Training Center on Erosion and Sedimentation and China Water and Power Press. Production and
Hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
n
Corresponding author at: China Institute of Water Resources and Hydropower Research, Beijing 100048, PR China. Fax: +86 68416371.
E-mail address: yannan8521@sina.com (N. Yan).
Peer review under responsibility of IRTCES and CWPP.

5. Conclusion. . . .....................................................................320
Acknowledgments. .....................................................................320
References ...........................................................................320
1. Introduction
It is predicted that the human population will reach 8 billion in 2025. To avoid or minimize food shortage, saline
soils have to be rehabilitated and managed to meet the food demand of an ever growing human population (Ladeiro,
2012). Soil microorganisms constitute less than 0.5% (w/w) of the soil mass, but they play a key role in soil
properties and processes. Salinity affects plants and microbes via two primary mechanisms: osmotic effect and
specific ion effects (Oren, 1999; Chhabra, 1996). Another factor influencing plants and microbes is soil water
content. Soil water potential which relates to the energy level by which the water is held in the soil also closely
related to soil salinity, it is influenced by osmotic potential in the soil solution.
2. The importance of soil microorganisms for nutrient cycling
Soil microorganisms constitute less than 0.5% (w/w) of the soil mass, but they play a key role in soil properties
and processes. Soil microbes include bacteria, archaea, fungi, protozoa and viruses (Tate, 2000). Microorganisms
participate in oxidation, nitrification, ammonification, nitrogen fixation, and other processes which lead to
decomposition of soil organic matter and transformation of nutrients (Amato & Ladd, 1994), they can also store
C and nutrients in their biomass which are mineralized after cell death by survi ving microbes (Anderson & Domsch,
1980). Our understanding of these processes increased considerably in recent years with advances in molecular and
analytical methodologies which have led to more successful strategies to modify them for a range of ecosystem
services (Frey, Six, & Elliott, 2003; Gessner et al., 2010; Rillig & Mummey, 2006).
Nutrient cycling is the flux of nutrients within and between the various biotic or abiotic pools in which nutrients
occur in the soil environment (Brady & Weil, 2002). Microorganisms have a major impact on the cycling of
elements, most of which are essential for the growth of living organisms. Bacteria, archaea and fungi, in particular,
are crucial for the cycling of several important inorganic nutrients in soils. Through oxidation, ammonification,
nitrogen fixation and other processes, organic materials are decomposed, releasing essential inorganic plant nutrients
to the soil. Nitrate (through nitrification), sulfate (through sulfur oxidation), phosphate (through phosphorus
mineralization) are present in soils primarily due to the action of microorganisms. Therefore, microbes are essential
to maintain a productive and valuable soil system. Disturbance of the soil environment, such as land use change or
soil cultivation, can shift microbial communities and can have detrimental effects on soil nutrient cycling (French et
al., 2009).
In addition, the emission of CO
2
from soils, which includes respiration from soil organisms and roots, contributes
approximately 10% to atmospheric CO
2
(Raich & Potter, 1995). Microbes also play an essential role in the formation
of humic substances which are stable forms of organic C and critical for organic C sequestration in soils (Burns et al.,
1986). ( Fig. 1).
3. Soil salinity
3.1. Soil salinity definition
A soil that contains excess salts so as to impair its productivity is called a salt-affected soil. Salt in the soil can
influence soil processes through the salt concentration in the soil solution (salinity) which determines the osmotic
potential and the concentration of sodium on the exchange complex of the soil (sodicity) which influences soil
structural stability. Salinity can, over time, lead to sodicity. The major soluble salts in soils are the cations Na
þ
(sodium), Ca
2 þ
(calcium), Mg
2 þ
(magnesium) and K
þ
(potassium), and the anions Cl

(chloride), SO
2
4
(sulfate),
HCO

3
(bicarbonate), CO
2
3
(carbonate) and NO

3
(nitrate) (Shi & Wang, 2005). There are several classification
systems for salt-affected soils in the world, for example the USDA system, the USSR system and the Australian
N. Yan et al. / International Soil and Water Conservation Research 3 (2015) 316–323 317

system (Chhabra, 1996). The USDA system classifies soils in three distinct categories (saline, sodic and saline–sodic
soils). Saline soils have an electrical conductivity of the saturated paste (EC
e
)4 4dSm
 1
, ESP o 15 or SARo 13
and pHo 8.5. Sodic soils have an ESP 4 15 or SAR4 13. Soils that have both detrimental levels of neutral soluble
salts (EC
e
4 4dSm
 1
) and a high-proportion of sodium ions (ESP4 15 or SAR 4 13) are classified as saline–sodic
soils (Brady & Weil, 2002; CISEAU, IPTRID, AGLL, & FAO, 2005)(Table 1). Salt-affected soils can be classified
according to how the salinity developed: primary salinity which occurs naturally where the soil parent material is rich
in soluble salts, or geochemical processes result in salt-affected soil. Secondary salinity is salinization of land and
water resources due to human activities. Human activities which can induce salinization include poor irrigation
management; insufficient drainage; improper cropping patterns and rotat ions; chemical contamination (Oldeman,
Hakkeling, & Sombroek, 1990; UNEP, 2007).
3.2. Effects of salinity on microorganisms
High-concentrations of soluble salts affect microbes via two primary mechanisms: osmotic effect and specific ion
effects.
Soluble salts increase the osmotic potential (more negative) of the soil water, drawing water out of cells which may
kill microbes and roots through plasmolysis. Low osmotic potential also makes it more difficult for roots and
microbes to remo ve water from the soil (Oren, 1999). Plants and microbes can adapt to low osmotic potential by
accumulating osmolytes, however, synthesis of osmolytes requires large amounts of energy and this results in
reduced growth and activity (Oren, 1999; Wichern, Wichern, & Joergensen, 2006). At high-concentrations, certain
ions, including Na
þ
,Cl

, and HCO

3
HCO
3

, are toxic to many plants (Chhabra, 1996).
Table 1
Classification of salt-affected soils.
Salt-affected soil
classification
EC
e
(dS m
 1
)
pH Sodium
adsorption
ratio
Soil
physical
condition
Saline 4 4.0 o 8.5 o 13 Normal
Saline–sodic 4 4.0 o 8.5 4 13 Normal
Sodic o 4.0 4 8.5 4 13 Poor
Animal Biomass
Plant+Animal
Residues+Exudates
Plant Biomass
CO
2
Soil CO
2
Microbial Biomass
Abiontic Residues
Humic Substances
Soil CO
2
Fig. 1. Conceptual model of carbon cycle emphasizing transfers between major soil organic matter pools (Tate, 2000).
N. Yan et al. / International Soil and Water Conservation Research 3 (2015) 316–323318

Many studies showed that salinity reduces microbial activity, microbial biomass and changes microbial
community structure (Andronov et al., 2012; Batra & Manna, 1997; Pathak & Rao, 1998; Rousk, Elyaagubi,
Jones, & Godbold, 2011; Setia, Marschner, Baldock, Chittleborough, & Verma, 2011 ). Salinity reduces microbial
biomass mainly because the osmotic stress results in drying and lysis of cells (Batra & Manna, 1997; Laura, 1974;
Pathak & Rao, 1998; Rietz & Haynes, 2003; Sarig, Fliessbach, & Steinberger, 1 996; Sarig & Steinberger, 1994;
Yuan, Li, Liu, Gao, & Zhang, 2007a). Some studies showed that soil respiration decreased with increasing soil EC
(Adviento-Borbe, Doran, Drijber, & Dobermann, 2006; Wong, Dalal, & Greene, 2009; Yuan et al., 2007b). Setia,
Marschner, Baldock, and Chittleborough (2010) found that soil respiration was reduced by more than 50% at
EC
1:5
Z 5.0 dS m
 1
. However, Rietz and Haynes (2003) reported that soil respiration was not significantly correlated
with EC, but as EC increased, the metabolic quotient (respiration per unit biomass) increased. The sensitivity of soil
enzyme activities to salinity varies: activities of urease, alkaline phosphatase, β-glucosidase were strongly inhibited
by salinity (Frankenberger & Bingham, 1982; Pan, Liu, Zhao, & Wang, 2013), whereas dehydrogenase and catalase
were less affected (Garcia & Hernandez, 1996).
As explained above, microorganisms have the ability to adapt to or tolerate stress caused by salinity by
accumulating osmolytes (Del Moral, Quesada, & Ramos-Cormenzana, 1987; Quesada, Ventosa, Ramoscormenzana,
& Rodriguezvalera, 1982; Sagot et al., 2010; Zahran, Moharram, & Mohammad, 1992). Proline and glycine betaine
are the main organic osmolytes and potassium cations are the most common inorganic solutes used as osmolyte s
accumulated by salinity tolerant microbes (Csonka, 1989). However, the synthesis of organic osmolytes requires
high-amounts of energy (Killham, 1994; Oren 2001). Accumulation of inorganic salts as osmolytes can be toxic
therefore it is confined to halophytic microbes which evolved salt tolerant enzymes to survive in highly saline
environments. Fungi tend to be more sensitive to salt stress than bacteria (Gros, Poly, Monrozier, & Faivre, 2003;
Pankhurst, Yu, Hawke, & Harch, 2001; Sardinha, Muller, Schmeisky, & Joergensen, 2003; Wichern e t al., 2006),
thus the bacteria/fungi ratio can be increased in saline soils. Differences in salinity tolerance among microbes results
in changes in community structure compared to non-saline soils (Gros et al., 2003; Pankhurst et al., 2001 ).
4. The effects of soil water availability on microorganisms
4.1. Forms of water in soils
Substantial volumes of water are commonly stored in soils. For example, 1ha of medium textured soil (1 m deep)
with a water content at field capacity of 20% can store 8.0  10
5
L water (Or & Wraith, 2000). Plants and organisms
rely heavily on water in soils and water is essential for nutrient cycling. However, soil water content varies both in
time and in space which not only influences water availability to plants and microbes but also has a major effect on
the rate of diffusion of solutes and gases (Adl, 2003).
The status of soil water can be described in two ways: the soil water content, which indicates how much water is
present, and soil water potential, which relates to the energy level by which the water is held in the soil. The water
potential is the amount of pressure that needs to be applied to transport a solution of known molarity from a
referenced elevation to that of pure water (McKenzie, 2002), mainly including matric, osmotic and gravitational
potential. Processes dealing with water balance are usually more related to water content; whereas processes related
to water movement are mainly related to soil water potential (Warrick & Or, 2007).
4.2. Effect of water content on microbes
Water is not only an essential transport medium for substrates, it is also an important participant in hydrolysis
processes. Therefore soil water content controls microbial activity and is a major factor that determines the rates of
mineralization (Paul et al., 2003). However, excess soil water content results in limited O
2
diffusion because O
2
diffusion in water is much lower (about 10
4
times) than in air which will reduce the activity of aerobic
microorganisms (Kozlowski, 1984; Skopp, Jawson, & Doran, 1990), but could increase the activities of anaerobes.
Lack of water reduces microbial activity and growth (Bottner, 1985; Kieft, Soroker, & Firestone, 1987), C and N
mineralization (Pulleman & Tietema, 1999; Sleutel et al., 2008) and shifts microbial community structure (Hueso,
Garcia, & Hernandez, 2012; Sorensen, Germino, & Feris, 2013). Cells retain sufficient water for cell turgor and
metabolism by maintaining a higher osmotic potential (more negative) in the cytoplasm than that of the surrounding
N. Yan et al. / International Soil and Water Conservation Research 3 (2015) 316–323 319

environment (Martin, Ciulla, & Roberts, 1999). At low water content (high water potential), soil microbes c an
accumulate organic and inorganic compounds which increases the osmotic potential inside their cells. Therefore the
principal tolerance mechanism for low water conten t and high-salinity is the same: accum ulation of osmolytes.
Further as soils dry out, substrate supply becomes incre asingly limited because the pores drain and water films
around aggregates become thinner and disconnected (Ilstedt, Nordgren, & Malmer, 2000; Stark & Firestone, 1995).
Fungi, Gram-positive bacteria and archaea can better tolerate high matric potential than Gram-negative bacteria
because they have stronger cell walls (Fierer, Schimel, & Holden, 2003; Martin et al., 1999; Schimel, Balser, &
Wallenstein, 2007; Vasileiadis et al., 2012).
4.3. Effect of fluctuating water content on soil microorganisms
Soil moisture and the distribution of water within a soil profile vary with seasonal cycles of rainfall, irrigation
periods (farm lands) and temperat ure. In semi-arid and Mediterranean ecosystems, surface soils frequently experience
long dry periods followed by a relat ively rapid wetting (Fierer & Schimel, 2002). The effects of drying and rewetting
on soil microbial processes have been studied (Griffiths, Whiteley, O'Donnell, & Bailey, 2003; Herron, Stark, Holt,
Hooker, & Cardon, 2009; Ilstedt et al., 2000; Schimel et al., 2007; Xiang, Doyle, Holden, & Schimel, 2008). The
concentration of available substrate and microbial activity peak in the first 24 h after rewetting (Fierer & Schimel,
2003). This is because, upon rewetting, cells of sensitive microbes lyse, whilst other microbial genotypes release the
organic solutes they accumulated during the dry phase (Halverson, Jones, & Firestone, 2000). Furthermore, soil
aggregates break down and their previously protected organic matter is exposed and can then be decomposed.
Microbial biomass, activity and nitrification decrease with increasing number of dry and rewetting cycles (Mikha,
Rice, & Milliken, 2005; Nelson, Ladd, & Oades, 1996; Wu & Brookes, 2005). The decrease in microbial biomass
with increasing number of drying and rewetting cycles may be due to the higher microbial biomass turnover (Van
Gestel, Merckx, & Vlassak, 1993) and the loss of C during the flush in respiration upon rewetting (Fierer & Schimel,
2003). However, the response of microbial activity to drying and rewetting varies with soil type (Jin, Haney, Fay, &
Polley, 2013 ) which may be due to the interaction of soil moisture and soil type, aggregation and the concentration of
potentially bioavailable soil organic matter (Anderson & Ingram, 1993). However, drying and rewetting can also kill
some microbes and change microbial community structure which, in turn, could influence nutrient cycling (Fierer et
al., 2003; Schimel et al., 2007). Butterly, Bunemann, McNeill, Baldock, and Marschner (2009) found that drying and
rewetting induced a reduction in fungi and an increase in Gram-positive bacteria (Butterly et al., 2009).
5. Conclusion
Soil salinity is a threat world-wide to agricultural production and ecosystems because it reduces plant growth and
microbial functioning. The effects of salinity and soil water content on soil microbes have been studied extensively, but
usually separately, in saline soils, the water content also influences the salt concentration in the soil solution (osmotic
potential), the study of interaction between soil water content and salinity on soil microbes is needed. Further in the field,
soil salinity and water conten t are not constant in time and space. Therefore, experiments are needed to better understand
the effect of fluctuating salinity and so il water content on soil microbe s. Synthesis of osmolytes requires large amounts of
energy. Therefore addition of organic materials such as plant residues or manures as nutrient sources for microbes may be
an important strategy to ameliorate saline soils. Future research could investigate the effect the properties of organic
materials such as decomposability and nutrient content on microbial tolerance to osmotic stress.
Acknowledgments
This project was funded by the Non-Profit Special Fund of the Ministry of Water Resources, China (Grant no.
201501045) and the Special Fund of the China Institute of Water Resources and Hydropower Research.
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