grazing) are sufficient to facilitate unassisted
recovery. For severely degraded ecosystems,
in particular when soil hydrology is affected
( 167 ), greater efforts may be needed to accel-
erate and influence the successional trajec-
tory of recovery. Given the spread of land use
and change by humans globally, we need ap-
proaches that return healthy soil ecosystems
in more timely and steady trajectories than are
achieved with the methods that are currently
available ( 168 ). In agricultural systems, land
use and management strategies critically af-
fect the rate and trajectory of recovery ( 168 ).
Agricultural practices such as reduced till-
age, crop rotation, organic amendments, and
reduced fertilizer use where there was overuse
can help prevent disruption of beneficial plant
root symbioses, such as with N-fixing bacteria
and mycorrhizal fungi, and entire microbial
communities.Although beneficial soil-borne organisms
are already naturally present, the aim in soil
restoration is to enhance their abundance and
activity by either inoculation or enhancement
of their growth. Direct injections of bacteria
together with growth substrates into the soil
has disadvantages, such as clogging of the
soil pore spaces and higher concentrations
of organisms and substrates near the injec-
tion points ( 169 ). Furthermore, a single micro-
bial species is not likely to adapt and survive in
all soil environments ( 170 ) and thus geograph-
ical differences in microbial soil composition
should be considered ( 171 ). Furthermore, com-
mercially available PGPR may affect the na-
tive microbial population, unlike indigenous
bacteria that are well adapted to the local en-
vironment ( 100 ). Instead, a strategy more likely
to be successful is to introduce microorganisms
as a part of a healthy soil inoculum as an aid
to plant community reestablishment, espe-
cially in conditions where the topsoil has been
replaced ( 26 , 110 , 172 ).
Another way to stimulate the establishment
of healthy soil microbiomes in degraded soils
is through amendments with (noncontami-
nated) sewage sludge ( 173 ) or another organic
substrate that matches the needs of the de-
graded soil. Given the risks to human health
from pathogenic microbes of such organic
materials as manure and sewage biosolids
( 174 ), alternative approaches to enhance soil
quality are needed. Novel amendments are
currently being developed that are free of
such risks and are still able to enhance soil
hydraulic properties, while at the same time
stimulating microbial growth and increas-
ing soil organic matter content ( 175 ). The long-
term effects of these amendments on soil
properties and on entire microbial communi-
ties remain to be studied. Before upscaling such
approaches, detailed and systematic studies are
needed in which a particular microorganism
is enriched in living soil and its long-term
effects on soil properties and soil microbial
communities are tracked; such studies are
entirely lacking at present.
Given the critical role of freshwater availa-
bility in terrestrial life and the paucity of studies
on hydrological restoration, we especially ad-
vocate for research on the hydrological resto-
ration of degraded soil using microorganisms.
We propose that microorganisms can improve
soil hydraulic properties such as water infil-
tration and water retention and reduce soil
hydrophobicity. Along with new organic mat-
ter derived from microbes, this will promote
plant growth and facilitate further ecosystem
restoration. Such a restoration strategy requires
collaboration across the research fields of soil
microbiology and soil hydrology, of which
there has been very little to date ( 176 ). Under-
standing the interaction between soil micro-
bial and hydrological dynamics will create theCobanet al.,Science 375 , eabe0725 (2022) 4 March 2022 7 of 10
Box 1. Methodological challenges.Although a number of studies have explored the role of biofilms in soil physical processes, most of
these studies face methodological issues. Methodological needs are summarized below.Setting proper scientific controls
In studies ( 142 , 180 , 181 ) investigating effects of a microorganism on soil hydraulic properties, the control
group did not include all of the constituents of the media that had been used along with the microorganism
in the treatment group. Considering that soil additives have been shown to affect soil hydrology ( 182 ),
a lack of the proper negative control prohibits distinguishing effects of the tested microorganism from
the effects of media.Combining microbiological and hydrological methodologies
For measurements of soil hydrophysical properties that may take weeks, the laboratory needs to be
temperature- and humidity-controlled. Low temperature is important for minimizing microbial growth that
could alter hydraulic parameters while these measurements take place. Although some studies use elevated
temperature settings for stimulation of evaporation in order to reduce the required duration of the ex-
periment ( 180 ), use of lower-humidity settings is recommended over increasing temperature in such
experiments ( 181 ).Standardizing the hydrological methodology
Standardization of methodological procedures is vital for cross-comparison of data from different ex-
periments, consistency between replicates, and minimizing risk of procedural bias. Soil compaction has
been shown to affect bacterial abundances in inoculated soil ( 142 ) and also strongly affects soil hydraulic
properties via changes of bulk density ( 183 ). For soil sterilization, double sterilization or gamma-radiation
appear to be most efficient ( 184 , 185 ), although their alteration of soil chemical and physical properties
shouldbeconsidered( 186 ). Also, a temperature dependence of water retention curves for various types of
soils has been shown ( 187 ), and comparisons between different studies would be facilitated by the use of
low temperature (as explained above).Monitoring of microbial growth
Hydrological methodologies require a substantial amount of time (e.g., several days or even weeks), and
microbial growth should be evaluated and reported. A study ( 181 ) showed that carbon deficit assessment
demonstrated more consistent results than cell counting, a method used in most similar experiments
( 64 , 142 ); therefore, careful consideration should be given to the choice of monitoring method. How
microbial abundance affects soil hydraulic properties remains to be tested.Microorganism addition to a sterilized, not living soil
“Proof of concept”studies evaluating the effect of a single microorganism in sterilized soil are useful for
early investigational stages ( 65 , 180 , 181 ). The next step for such studies should be focused on approaches
to enrich a microorganism in field soil and investigation of the effects of such enrichment on the entire
microbial community.Finding suitable microorganism(s)
Reports on enhancement of soil hydraulic properties after incubation with microorganisms are scarce in
the current literature. Effects on soil hydraulic properties of only a few bacterial species ( 142 , 180 , 181 ),
fungi ( 188 ), and algae ( 64 , 65 ) have been reported. In addition to these, several studies on arid and
semi-arid land restoration using biological crusts are available ( 71 , 161 , 189 ). We also suggest exploring
the synergistic effects of consortia of microorganisms that can provide additional benefits for improving
soil quality by means of, for example, N fixation and soil structure formation.RESEARCH | REVIEW