Groups of microorganisms used in restoring
degraded lands
Restoration of degraded ecosystems can be
slow and unsuccessful if conditions are un-
favorable for the development of soil biota
( 26 ). Because soil biota is an important driver
of plant community development ( 27 , 28 ),
the successful restoration of terrestrial eco-
systems may depend on the manipulation of
soil organisms ( 21 ). With respect to their im-
pact on plant growth, nutrient cycling, and
soil structure, three main groups of benefi-
cial microorganisms can be distinguished:
plant growth–promoting rhizobacteria (PGPR),
nitrogen-fixing bacteria, and arbuscular my-
corrhizal fungi (AMF) together with ectomy-
corrhizal fungi (EMF). As a possible fourth
group, cyanobacteria in biological soil crusts
(BSCs)areabletoincreasesoilnutrientavail-
ability by fixing nitrogen and improving soil
structure at the surface ( 29 , 30 ). Examples of
beneficial microorganisms as remediation
agents are shown in Fig. 1.
PGPR are loosely defined as soil bacteria
that colonize the plant roots and enhance plant
growth. Enhancement can occur in a direct
or indirect way, and only some of the mech-
anisms involved have been characterized so
far ( 31 ). Among direct mechanisms are nitro-
gen fixation, solubilization of minerals (e.g.,
phosphorus) and enhancement of their uptake
by plants, synthesis of phytohormones, and
chelation of metals to make them available
to plant roots. The addition of PGPR has also
been shown to increase crop yield by protecting
plants from pests, parasites, or diseases ( 32 ).
Agricultural yields are often limited by N
availability, and the natural N input into the
biosphereismostlyprovidedbybiologicalN
fixation by bacteria and archaea. Nitrogen-
fixing organisms or diazotrophs can be free-
living or exist in a symbiotic relationship with
their host plant ( 33 ). Among different forms
of association, symbioses in which rhizobacte-
ria live within root nodules are the most ef-
ficient in terms of making N available to the
plant. Root nodule symbioses between legu-
minous crops and rhizobia result in particu-
larly high rates of N fixation (50 to 465 kg N
ha–^1 year–^1 ) and can occur in nearly all cropping
systems ( 34 ). The world’s main cereal crops
(rice, wheat, and maize) do not associate with
rhizobia, and associative N fixation in cereals
is often considered insignificant in comparison
to nodulated symbiotic N-fixing plants ( 35 ).
Manipulating bacteria to increase biological
N fixation in nonleguminous plants has been
a long-standing pursuit ( 36 ), but the expan-
sion of symbiotic associative N fixation to other
crops has been hindered by poor understand-
ing of the genetic requirements that allow
the host plant to associate with and benefit
from diazotrophs ( 37 ). Technological advances
during the past two decades, including next-
generation sequencing, gene editing, and syn-
thetic biology, enable genetic manipulation
of plants and microbes at an unprecedented
scale. However, it is expected that the develop-
ment of nodulation in non-nodulating crops
will still take a few decades ( 33 , 38 ).
EMF form symbiotic structures with the
roots of woody plants and drive the nutrient
cycle in forest ecosystems. In addition to nu-
trient supply, EMF have been shown to en-
hance water transfer between plants through
their hyphal network, thereby increasing plant
survival during drought periods ( 39 ). AMF
form symbioses with the roots of ~80% of vas-
cular plant species, helping them to acquire
soil nutrients (especially phosphorus) in re-
turn for plant carbohydrates ( 40 ). In some
cases, AMF provide most of the plant’s phos-
phorus needs, and all its phosphorus uptake
may be of hyphal origin ( 41 ). Phosphorus is
needed for all major metabolic processes (photo-
synthesis, respiration, energy transfer), and seedformation and root strength depend on it.
Associations between AMF and bacteria are
important in the symbiosis with the plant
roots because of the critical role they play in
mycorrhizal functions ( 42 , 43 ). Disentangling
the very complex ecological roles of AMF re-
quires a collaborative effort involving physiol-
ogists, molecular biologists, and ecologists.
Recent advances in molecular genetics are
helping to decipher the morphological, phys-
iological, and genetic characteristics of AMF
and to understand the molecular mechanisms
of symbiosis among AMF, bacteria, and plants
( 44 ). Stable isotope probing (SIP), for example,
makesitpossibletostudytheinterrelatedef-
fects of structure and function of the symbiont
organisms ( 45 , 46 ).Plant-microbe interactions
Plants in natural environments coexist with
a wide variety of microbes (archaea, bacteria,
fungi, viruses, and protists), collectively called
the microbiome. The microbiome is vital to
plant growth, productivity, and plant overall
condition ( 47 ). The interactions can be patho-
genic, commensal, or beneficial, depending
on such factors as plant species, soil type, and
environmental conditions ( 31 ). Plant-microbiome
engineering aims to direct the interactions
toward increasing crop yield. The understand-
ing of plant-microbiome interactions remains
rudimentary ( 31 ), but it has become clear that
thereisconsiderablescopeformanipulation.
In recent years, research into the application
of microorganisms as biocontrol, biostimu-
lant, and bioremediation agents has expanded
( 48 – 50 ). In agriculture, the primary research
foci are product reliability and consistency
( 48 ). Better understanding of the mechanisms
of plant-microbial interactions is key to in-
creasing the benefits to be gained from their
exploitation ( 51 ).
Major developments in plant-microbe inter-
actions have occurred in recent years thanks
to advances in techniques for genomic studies
and the increased availability of genomic in-
formation ( 52 , 53 ). Such developments provide
a basis for exploring plant-microbe interac-
tions across chemical, molecular, metagenomic,
and exometabolomic scales ( 54 ). For example,
progress is being made toward large-scale
microbial isolation and the synthetic produc-
tion of communities ( 55 ). Next-generation se-
quencing techniques provide a necessary basis
for the preparation of bacterial isolates that
are further inoculated in germ-free plants.
Systematic microbiota culture collections can
be used in microbiota reconstitution experi-
ments with germ-free plants to investigate the
principles underlying community assembly
and to identify microbiota-mediated func-
tions important for plant health ( 56 ). Further-
more, novel methods of exometabolomics can
help to unravel the mechanisms underlyingCobanet al.,Science 375 , eabe0725 (2022) 4 March 2022 2 of 10
Fig. 1. Land degradation types and examples of beneficial microorganisms acting as remediation agents.
RESEARCH | REVIEW