a foundation to achieve food security for
the growing population and restore soil fer-
tility ( 48 ). Indeed, next to soil chemical and
soil physical parameters, microbial soil in-
dicators have been used as a proxy to mea-
sure soil fertility and soil health levels more
generally ( 19 ).
Remediation of saline soils
Each year, around 1 to 2% of fertile soils are
being degraded worldwide as a consequence
of salinity ( 111 ), and about 20% of irrigated
land is currently already affected by saliniza-
tion ( 112 ). Soil salinity can be due to cations
such as sodium (Na+) and anions such as
chloride (Cl–), among others. Exposure to sa-
linity increases the concentrations of Na+
and Cl–ions and decreases the availability of
other ions such as potassium (K+)toplants.
Sodium ions not only cause plant cell injury
but also degrade soil structure. By contrast,
K+is essential to plant cells as a major inor-
ganic nutrient and an osmotic regulator ( 113 ).
Along with ionic imbalance, long-term salin-
ity reduces the ability of plants to extract wa-
ter from the soil, making the salt and drought
problems of plants closely related ( 113 ). Sa-
linity occurs in agricultural soils in the arid
and semi-arid regions of the world, but also
in some coastal regions (e.g., the Netherlands)
as a result of rising seawater level. Consequent-
ly, interest in salinity-tolerant plants and sus-
tainable methods for the bioremediation of
saline soils is also growing ( 111 ).
Biological remediation by the application
of salt-tolerant, or halophilic, PGPR and AMF
is a sustainable alternative to conventional
physical and chemical treatments of saline
soil ( 111 , 114 , 115 ). Halophilic PGPR can re-
mediate saline soils directly via improving
nutrient status, soil structure, organic mat-
ter, pH, electrical conductivity, and deposi-
tion of ionic salts in soil ( 116 ). These PGPR
are increasingly seen as an efficient tool to
mitigate salinity stress in plants through mech-
anisms stimulating multidirectional physio-
logical, biochemical, and molecular responses.
In particular, inoculation with halophilic PGPR
and AMF increases K+/Na+ratios, which are
beneficial in maintaining ionic homeostasis
in the cytoplasm or Na+efflux from plants
( 114 , 115 ). Lately, the application of halophilic
PGPRs from the rhizosphere of halophilic plant
species has been actively explored as a means
to stimulate plant growth and increase the salt
tolerance of nonhalophytic crops ( 111 , 117 ).
Recent studies on the underlying mechanisms
have shown that halophilic PGPR can modify
the expression in plants of several genes re-
sponsible for the amelioration of salinity stress
( 118 , 119 ). The connection among plant stress
responses, signaling molecules, and micro-
biome assembly can be used to modify the
phytomicrobiome for the benefit of stressed
plants and can be explored further for the
development of stress-resilient“smart agri-
culture”( 120 – 122 ).Soil contamination
Soil can become contaminated by chemicals
originating from various sources, including
agricultural and industrial activities, dump-
ing waste, and urbanization. Soil pollution
can produce negative agricultural, industrial,
urban, and environmental effects such as re-
duced soil fertility, water pollution, reduced
plant growth, and modified soil biodiversity.
These can cause subsequent soil erosion and
degradation, ultimately changing the whole
ecosystem ( 123 ). Information about the global
extent of soil pollution is lacking, as only some
countries undertake national surveys of soil
pollution ( 124 ). However, the information that
is available is cause for concern. For example,
China has categorized 16% of all its soils as
polluted ( 125 ). Among physical, chemical, and
biological approaches for remediation, inter-
est in the latter has amplified in recent years
as societies turn to sustainable and green so-
lutions to solve environmental problems ( 126 ).
Bioremediation of contaminated soils refers to
the degradation of pollutants through micro-
bial metabolic activities by mostly indigenous
microorganisms ( 102 ). PGPR also have an indi-
rect positive impact on removal of contaminants
by plants (phytoremediation)—for example,
by stimulating plant growth and increasing
contaminant bioavailability—and this role
can be manipulated to improve the efficacy
of phytoremediation ( 127 ). Microbe-assisted
phytoremediation has shown to be efficient in
restoring sites contaminated by heavy metals,
pesticides, and hydrocarbons ( 128 ). This bio-
technology can kick-start further recovery of
degraded ecosystems, leading to much faster
biodiversity restoration ( 128 ). For example,
inoculation of contaminated soil with fungi
when reintroducing vegetation not only en-
hances the extraction of heavy metals from the
polluted soils but also enables the plants to es-
tablish themselves on degraded soil and there-
by improve soil quality and health ( 129 , 130 ).
The effects of remediation on the restora-
tion of biodiversity remains to be explored fur-
ther. For example, one recent study considers
how the composition and structure of fungi
after phytoremediation are driven by the plant
species present ( 131 ). A wide variety of micro-
organisms and metabolites that can degrade
pollutants are still largely unexplored, and
better understanding of their metabolism will
enable their use in bioremediation. Recently,
the potential of extremophiles that survive in
environments with high concentrations of me-
tals, radionuclides, or other pollutants has been
explored ( 132 , 133 ). Next-generation sequenc-
ing approaches can help to discover micro-
bial diversity and metabolic functions thatpredict the presence and extent of contam-
ination, characterize the process of natural
attenuation by unculturable microbes, and
clarify the impact of biostimulation on micro-
bial communities ( 134 ).Effects of microorganisms on soil
physical properties
Microbes affect soil structure by direct and in-
direct processes, including (i) moving pri-
mary particles along cell or hyphal surfaces;
(ii) adhering particles together by their se-
cretions, such as EPSs; (iii) enmeshing and
binding aggregates by fungal hyphae and
actinomycete filaments; and (iv) producing
hydrophobic compounds that coat pore walls,
particularly in fungi. A major factor in soil
structure formation and stabilization is the
soil organic matter, which increases soil ag-
gregation. Microbes, including their remains
or necromass, can make up more than half of
soil organic carbon ( 135 , 136 ), highlighting the
role of microbes along with macroorganisms
and plants in strongly related soil physical prop-
erties, such as porosity and aggregate stability.
Soil aggregates support root growth, resist-
ance to erosion, carbon storage, and water-
holding capacity ( 137 ), and a well-aggregated
soil structure is fundamental to ensure healthy
functioning of soil ( 43 ). Bacteria and fungi
excrete mucilages that play important roles
in soil microaggregate stabilization by gluing
soil particles together ( 110 , 137 ). They also take
part in macroaggregate stabilization by en-
tangling particles within the hyphae network
and through production of EPSs ( 110 , 137 ). Also,
AMF are known to produce glomalin-like pro-
teins that play an important role in soil stabi-
lization, carbon storage, and soil aggregate
stability and thereby decrease soil suscepti-
bility to erosion ( 138 ). Although the role of
bacteria and fungi in soil aggregate forma-
tion and stability is established, experimental
studies on the application of microorgan-
isms for soil structure improvement are scarce
( 139 , 140 ).Effects of microorganisms on soil
hydraulic properties
Aggregate stability, soil structure, organic mat-
ter, and microtopography are all attributes
associated with soil hydraulic properties. Micro-
organisms affect soil hydraulic properties at
the pore scale in multiple ways (Fig. 4): by bio-
film formation, EPS excretion, exudation of
binding agents (e.g.,glomalin-like proteins),
particle enmeshment by fungi, production of
water-repellent compounds, and alteration
of soil surface microtopography.
Biofilms are aggregations of microorgan-
ismswhosecellsadheretoeachotherortoa
surface, often embedded within a self-produced
matrix of EPS ( 141 ). Biofilms can form as a
response to an environmental stress, enablingCobanet al.,Science 375 , eabe0725 (2022) 4 March 2022 5 of 10
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