P ac ical applica ions o soil mic obio a
o imp o e ecosys em es o a ion: cu en
knowledge and u u e di ec ions
Shawn D. Peddle
1,
*,Riley J. Hodgson
1
,Ryan J. Bo e
2
,S ella B achmann
3
,
Ta yn C. Da ies
1
,Todd E. E ickson
4,5
,C aig Liddicoa
1
,
Mi iam Muñoz-Rojas
6,7
,Jake M. Robinson
1
,Ca l D. Wa son
1
,
Sieg ied L. K auss
4,8
and Ma in F. B eed
1
1
College o Science and Enginee ing, Flinde s Uni e si y, S u Road, Bed o d Pa k, Sou h Aus alia 5042, Aus alia
2
SoilsWes , Cen e o Sus ainable Fa ming Sys ems, Food Fu u es Ins i u e, Mu doch Uni e si y, 90 Sou h S ee , Mu doch,
Wes e n Aus alia 6150, Aus alia
3
Uni e si y o Waika o Te Wha e Wananga o Waika o Ga e 1, Knigh on Road, Hamil on 3240, New Zealand
4
Depa men o Biodi e si y, Conse a ion and A ac ions, Kings Pa k Science, Ka idj Close, Kings Pa k, Wes e n Aus alia 6005, Aus alia
5
Cen e o Enginee ing Inno a ion, School o Ag icul u e and En i onmen , The Uni e si y o Wes e n Aus alia, S i ling Highway, C awley,
Wes e n Aus alia 6009, Aus alia
6
Depa men o Plan Biology and Ecology, Uni e si y o Se ille, C. San Fe nando, Se illa, Spain
7
School o Biological, Ea h and En i onmen al Sciences, Cen e o Ecosys em Science, Uni e si y o New Sou h Wales, Sydney,
New Sou h Wales 2052, Aus alia
8
School o Biological Sciences, The Uni e si y o Wes e n Aus alia, S i ling Highway, C awley, Wes e n Aus alia 6009, Aus alia
ABSTRACT
Soil mic obio a a e impo an componen s o heal hy ecosys ems. G ea e conside a ion o soil mic obio a in he es o a ion o
biodi e se, unc ional, and esilien ecosys ems is equi ed o add ess he win global c ises o biodi e si y decline and clima e
change. In his e iew, we discuss a ailable and eme ging p ac ical applica ions o soil mic obio a in o (i) es o a ion planning,
(ii) di ec in e en ions o shaping soil biodi e si y, and (iii) s a egies o moni o ing and p edic ing es o a ion ajec o ies. We
show how be e planning o es o a ion ac i i ies o accoun o soil mic obio a can help imp o e p og ess owa ds es o a ion
a ge s. We show how planning o embed soil mic obio a expe imen s in o es o a ion p ojec s will pe mi a mo e igo ous
assessmen o he e ec i eness o di e en es o a ion me hods, especially when complemen ed by s a is ical modelling
app oaches ha capi alise on exis ing da a se s o imp o e causal unde s andings and p io i ise esea ch s a egies whe e
app op ia e. In addi ion o eco e ing belowg ound mic obio a, es o a ion s a egies ha include soil mic obio a can imp o e
he esilienceo wholeecosys ems.Fundamen ally, es o a ionplanning should iden i y app op ia e e e ence a ge ecosys em
a ibu es and – om he pe spec i e o soil mic obio a –comp ehensibly conside po en ial physical, chemical and biological
influences on eco e y. We iden i y ha inocula ing ecologically app op ia e soil mic obio a in o deg aded en i onmen s can
suppo a ange o es o a ion in e en ions (e.g. a ge ed, b oad-spec um and cul u ed inocula ions) wi h p omising esul s.
Such inocula ions howe e a e cu en ly unde u ilised and knowledge gaps pe sis su ounding success ul es ablishmen in
ligh o communi y dynamics, including p io i y e ec s and communi y coalescence. We show how he ecological ajec o ies
o es o a ion si es can be assessed by cha ac e ising mic obial di e si y, composi ion, and unc ions in he soil. Ul ima ely, we
highligh p ac ical ways o apply he soil mic obio a oolbox ac oss he planning, in e en ion, and moni o ing s ages o eco-
sys em es o a ion and add ess pe sis en open ques ions a each s age. Wi h con inued collabo a ions be ween esea che s and
p ac i ione s o add ess knowledge gaps, hese app oaches can imp o e cu en es o a ion p ac ices and ecological ou comes.
Key wo ds: ecosys em es o a ion, imp o ed ecological ou comes, posi i e soil legacy, eco e y ajec o y, es o a ion
genomics, es o a ion me hods.
*Au ho o co espondence (Tel.: +61 8 8201 2113; E-mail: shawn.peddle@flinde s.edu.au).
Biological Re iews (2024) 000–000 © 2024 The Au ho (s). Biological Re iews published by John Wiley & Sons L d on behal o Camb idge Philosophical Socie y.
This is an open access a icle unde he e ms o he C ea i e Commons A ibu ion License, which pe mi s use, dis ibu ion and ep oduc ion in any medium,
p o ided he o iginal wo k is p ope ly ci ed.
Biol. Re . (2024), pp. 000–000. 1
doi: 10.1111/b .13124
CONTENTS
I. In oduc ion .........................................................................2
II. Soil mic obio a in es o a ion planning .....................................................3
(1) Conside ing soil mic obio a and es o a ion goal se ing ................................... 4
(2) When o p io i ise in es men in soil mic obio a ......................................... 5
(3) Imp o ing conclusions on causa ion in soil mic obio a es o a ion ........................... 5
(4) Embedding soil mic obio a expe imen s ............................................... 6
(5) Modelling app oaches o asce ain causa ion ............................................ 6
III. Res o a ion in e en ions ha di ec ly a ge soil mic obio a ....................................7
(1) Whole-soil ansloca ions and mic obial inocula ions ..................................... 8
(2) Seed enhancemen s ha con ain mic obial addi i es ...................................... 9
(3) Mic obial cul u es and suspensions .................................................. 10
(4) Ta ge ing specific mic obio a ...................................................... 10
(5) P omo ing posi i e soil legacies ..................................................... 11
IV. Moni o ing soil mic obio a o es o a ion .................................................11
(1) Moni o ing mic obial di e si y, composi ion, and unc ion ................................ 11
(2) Moni o ing es o a ion ajec o ies wi h soil mic obio a .................................. 13
V. Conclusions .........................................................................14
VI. Acknowledgemen s ...................................................................14
VII. Au ho con ibu ions ..................................................................14
VIII. Re e ences ..........................................................................14
I. INTRODUCTION
O e exploi a ion o na u al sys ems has led o he biodi e -
si y c isis (Ceballos e al., 2015; Di zo & Ra en, 2003) and
as a eas o deg aded ecosys ems (Gibbs & Salmon, 2015).
While conse ing emnan ecosys ems is a p io i y, he e is
also a need o es o e deg aded a eas o biodi e se and unc-
ioning ecosys ems (Higgs e al., 2018; Pe ing, E ickson &
B ancalion, 2018; Mo eno-Ma eos e al., 2020). Acco dingly,
he e is a ma ked inc ease in ecosys em es o a ion globally,
wi h a ge s o es o e mo e han 350 million hec a es unde
The Bonn Challenge and he Uni ed Na ions decla ing
2021–2030 he Decade on Ecosys em Res o a ion. Howe e ,
he e is conside able oom o imp o e he success o es o a-
ion p ojec s (C ouzeilles e al., 2016; Wo ley, He o &
Howes, 2013).
The essen ial ole o soil in ecosys em es o a ion is
ecognised, mainly by conside ing soil physical and chemical
p ocesses in ecosys em eco e y (Cos an ini e al., 2016;
Muñoz-Rojas, 2018; Pe ing e al., 2015). O e he las
15 yea s howe e , inc eased a en ion has been gi en o soil
mic obio a – he communi ies o bac e ia, a chaea, ungi,
i uses and p o is s wi hin soils –and hei in e ac ions in
he soil sys em and wi h abo eg ound bio a due o hei
essen ial unc ional oles (Ha is, 2009; McKinley, 2019;
Eisenhaue e al., 2017). Soil mic obio a a e among he mos
biodi e se and unc ionally impo an ecosys em compo-
nen s and a e essen ial o many biogeochemical p ocesses.
Fo example, biological ni ogen fixa ion by diazo ophs,
ni ogen-fixing bac e ia and a chaea o ms he ounda ion
o Ea h’s e es ial p oduc i i y (Zhu e al., 2022; Vi ousek
e al., 2013) and cyanobac e ia (ca bon and ni ogen fixe s)
combine wi h ungi, bac e ia, lichens, and o he o ganisms
o o m biological soil c us s (“bioc us s”) which can s abilise
soil landscapes and enhance wa e a ailabili y (Webe
e al., 2022; Yan-Gui e al., 2013). Fu he mo e, soils a e
home o o e hal o Ea h’sbiodi e si y(An hony,
Bende & an de Heijden, 2023) and belowg ound mic o-
bial biomass is o en compa able in scale o abo eg ound
plan o animal biomass (Fie e , 2017). Soil mic obio a
also in e ac wi h abo eg ound ecosys em componen s
and a e in ima ely in ol ed in plan and animal
heal h, and ice e sa. Fo example, he ela ionship
be ween plan s and a buscula myco hizal ungi is one
o he oldes e es ial symbio ic in e ac ions (Field &
P essel, 2018;Tisse an e al., 2013) whe e plan s depend
on ungi o ga he essen ial nu ien s in exchange o ca -
bohyd a es. Consequen ly, we can expec ecip ocal shi s
in abo e- and belowg ound ecosys em componen s
(Ka dol & Wa dle, 2010;P obe e al., 2015). The e o e,
imp o ing he in eg a ion o soil mic obio a and associ-
a ed mic obial ecology in o ecosys em es o a ion will
ha e conside able benefi s ac oss es o a ion planning,
in e en ion, and moni o ing phases (Fig. 1).
His o ically, scien is s aced echnological challenges in
quan i ying and g asping he di e si y and composi ion o
soil mic obio a, as adi ional cul u e-dependen me hods
we e only able o g ow <1% o mic obial axa (Ali isa os
e al., 2015; Va oukian, Palme & Wade, 2010). Howe e ,
mode n sequencing echnologies enable a de ailed axo-
nomic and unc ional unde s anding o soil mic obio a. Fo
example, he now ou ine high- h oughpu amplicon
sequencing o DNA ex ac ed om soil samples can p o ide
a de ailed axonomic iew o he mic obio a wi hin a gi en
sample (Be g e al., 2020; Fie e , 2017). These amplicon da a
se s can hen be associa ed wi h spa ial, land-use,
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2Shawn D. Peddle and o he s
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en i onmen al condi ion and/o es o a ion-in e en ion
da a o answe ecological ques ions (Tede soo e al., 2019;
Thomsen & Wille sle , 2015; B eed e al., 2019).
Ad ances in DNA-based echnologies and imp o emen s
in ou unde s anding o plan –soil–ecosys em in e ac ions
a e enhancing ou abili y o use soil mic obio a in es o a ion
(Moh e al., 2022). Indeed, he e a e se e al e iews on soil
mic obio a in a es o a ion con ex , and mos ha e ocused
on heo e ical aspec s o including soil mic obio a in es o a-
ion o ele an echnological ad ancemen s (Coban, De
Deyn & an de Ploeg, 2022; Con os e al., 2021; Rawa
e al., 2022). He e, we complemen hese p e ious e iews
by ocussing on he p ac ical in e ace o soil mic obio a
and ecosys em es o a ion and highligh key knowledge gaps
ha a e limi ing e ec i e in eg a ion o soil mic obio a in o
es o a ion. We highligh whe e and how he in eg a ion o
soil mic obio a has success ully occu ed and iden i y oppo -
uni ies and challenges o imp o ed in eg a ion o enhance
es o a ion ou comes.
II. SOIL MICROBIOTA IN RESTORATION
PLANNING
Planning a es o a ion p ojec equi es se ing ealis ic goals,
making in o med choices o in e en ions, and deciding on
indica o s o moni o p og ess owa ds s a ed goals
(Hobbs & No on, 1996; Collen & Nicholson, 2014; Suding
e al., 2015). Un o una ely, despi e eno mous g ow h in he
scope and scale o es o a ion globally, many p ojec s ail o
achie e hei s a ed goals despi e he g owing scien ific igou
o es o a ion p ac ice (C ouzeilles e al., 2016; Wo ley
e al., 2013; Sun e al., 2017). The easons o hese sho alls
a e nume ous and include insu ficien conside a ion o soil
mic obio a (Heneghan e al., 2008; Ka dol & Wa dle, 2010;
Fa ell e al., 2020). Acco dingly, es o a ion p ojec s should
ou inely conside soil mic obio a ea ly as pa o hei modus
ope andi – oge he wi h mo e adi ional a ge s and assess-
men s o flo a and auna. These p ojec s will hen be in a
be e posi ion o de e mine hei ecological s a ing place,
Fig. 1. The Socie y o Ecological Res o a ion (SER) eco e y wheel (Gann e al., 2019) and how imp o ed in eg a ion o soil
mic obio a in o he planning, in e en ion, and moni o ing phases o ecosys em es o a ion p ojec s could con ibu e o each o he
six eco e y ou come hemes.
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Soil mic obio a and ecosys em es o a ion 3
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ajec o y and a ge –all componen s o bes -p ac ice
es o a ion (Ka dol & Wa dle, 2010; Heneghan e al., 2008;
Gann e al., 2019). He e, we ou line how and when es o a-
ion p ojec s should plan o inco po a e soil mic obio a om
he ou se o maximise benefi s o ecological ou comes while
a oiding was ed esou ces. We also highligh ha imp o ing
ou unde s anding o how specific es o a ion in e en ions
a ec soil mic obio a is needed o plan es o a ion e ec i ely.
(1) Conside ing soil mic obio a and es o a ion goal
se ing
Quan i ying he se e i y o he deg ada ion o an ecosys em is
c ucial in de e mining he le el o in e en ion equi ed o
mee a ge s (Heneghan e al., 2008; Chazdon, 2008). Fo
example, when a es o a ion si e is deple ed o myco hizal
ungi equi ed by a a ge plan species (e.g. mixo ophic
o chid species a e en i ely dependen on o chid myco hiza
o ge mina ion), he e is li le sense in in es ing esou ces
o es ablish he plan wi hou simul aneously add essing he
lack o symbio ic ungi (Koziol, C ews & Be e , 2020).
Fu he mo e, in asi e plan species in a deg aded landscape
can modi y soil mic obio a o he poin ha he soil en i on-
men is in an al e na e s a e o dynamic equilib ium (Suding,
G oss & Houseman, 2004; Go nish e al., 2020). He e,
emo ing he in asi e plan s and e ege a ing he landscape
elies on he soil mic obio a o mo e owa ds a s a e ha is
mo e suppo i e o he eco e ing na i e plan communi y
which is by no means gua an eed (Ha is, 2009). A
e ege a ion-only app oach may no o e come pe sis en soil
legacies (i.e. al e ed nu ien le els om e ilise use, al e ed
soil s uc u e om compac ion, in asi e species, undesi able
biological communi ies) and isks pe pe ual s a es o ecologi-
cal in asion (An hony e al., 2019; Bell, Siciliano &
Lamb, 2020). As a esul , specific in e en ions ha add ess
in asi e plan s and al e ed soil mic obio a (see Sec ion III)
need o be pa o he es o a ion planning phase. Mo eo e ,
majo dis u bance o soil physical and chemical condi ions
(e.g. om mining, e osion, compac ion, excess nu ien s) will
al e he ounda ional habi a o soil mic obio a, so add es-
sing limi ing abio ic ac o s also ep esen s a key p io i y in
es o a ion planning (Robinson e al., 2024). The e is
immense alue in se ing ea ly goals o unde s and soil mic obial
ecology a he ini ial s ages o a es o a ion p ojec . This goal-
se ing p ocess will help he es o a ion p ac i ione o quan i y
and p e-emp bio ic and abio ic cons ain s o oppo uni ies
(e.g. a lack o myco hizal ungi, plan -associa ed pa hogens
o s uc u ing plan communi ies, al e ed soil physical o
chemical p ope ies).
I ba ie s o eco e y a e no iden ified as pa o he plan-
ning s age, ecosys em eco e y will likely be inhibi ed
(Hobbs & No on, 2004). P ac i ione s should add ess hese
cons ain s in a es o a ion p ojec by, o example, using
knowledge o plan –soil eedbacks in he planning phase.
Res o a ion p ojec s could p omo e nega i e eedbacks
be ween plan and soil communi ies by, o example, inocu-
la ing si es wi h la e-succession soil mic obio a ha
encou ages ege a ion di e si y in he ea ly eco e y phase
(Ca bajo e al., 2011; Ka dol, Ma ijn Bezeme & Van De
Pu en, 2006). This can lead o myco hizal ungi ou pacing
bac e ial pa hogens, po en ially p omo ing communi y e en-
ness in la e-succession plan s (Fie e , 2017; Ka dol &
Wa dle, 2010). In eg a ing soil mic obial ecology knowledge
in o p edic i e ecological amewo ks (e.g. modelling di e -
en en i onmen al change scena ios, including mic obio a
assembly and unc ional dynamics) could u he allow a -
ge ed si e-specific es o a ion plans (E ine & Hawkes, 2008).
Re e ence si e selec ion and assessmen s a e cen al ele-
men s o planning and defining goals in a es o a ion p ojec
(Gann e al., 2019). Soil physical and chemical condi ions,
oge he wi h plan di e si y and o he ac o s in e e ence
si es, shape mic obio a de elopmen (Fie e , 2017). While
e e ence si e soil mic obio a a e inc easingly used in es o a-
ion moni o ing (see Sec ion IV), hey a e no ou inely
assessed du ing he planning phase. Gaining in o ma ion
on he composi ion, and e en unc ional cha ac e is ics, o
mic obio a in bo h deg aded and a ge e e ence si es will
posi ion p ojec s be e o ailo hei in e en ions o add ess
a ied le els o deg ada ion in he whole ecosys em. Soil
mic obio a a e highly he e ogeneous ac oss e en small
(<1cm
2
) spa ial scales (Fie e , 2017) and he e o e e e ence
si e selec ion and sampling design a e c ucial o cap u e a -
ia ion adequa ely ( an de Heyde, Bunce & Ne ill, 2022;
Liddicoa e al., 2022). This high le el o spa ial a ia ion
can impac assessmen s o communi y composi ion and unc-
ion and dis o in e p e a ions o he e e ence communi y
(Peddle e al., 2022).
The numbe s and loca ions o e e ence si e samples
should accoun o ege a ion and soil he e ogenei y o p o-
ide he bes possible pic u e o mic obio a a ge s (Peddle
e al., 2022; an de Heyde e al., 2022). One op ion is o
implemen a s a ified andom sampling scheme. This
app oach in ol es di iding he s udy a ea in o dis inc s a a
based on ele an ac o s influencing biodi e si y dis ibu-
ion, such as ege a ion and soil ypes o opog aphical ea-
u es. Wi hin each s a um, andom sampling poin s a e
selec ed o ensu e ep esen a i e co e age o he a ea while
minimising bias and dis o ions caused by he e ogenei y.
Addi ionally, employing sys ema ic sampling echniques,
such as g id o ansec sampling o pooling samples o
accoun o landscape he e ogenei y (Bisse e al., 2016) can
u he enhance spa ial ep esen a i eness and accu acy o
biodi e si y assessmen s.
A key open ques ion in in eg a ing soil mic obio a in o es-
o a ion is: wha do “good”soil mic obial communi ies look
like in e ms o species composi ion and/o unc ionali y?
The composi ion o soil mic obio a will a y g ea ly in di e -
en con ex s and en i onmen s wi h no single “ideal”mic o-
bial communi y (Fie e , Wood & de Mesqui a, 2021).
Gene ally speaking, he mic obial communi y composi ion
mos sui ed o any gi en es o a ion si e should be in o med
by sui able e e ence si es. Howe e , unde s anding he spe-
cific elemen s o mic obial communi ies and d i e s o
mic obial di e si y, composi ion and unc ion ha can be
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gene alised ac oss en i onmen s will imp o e how and
whe e we in eg a e mic obio a in o es o a ion (Liddicoa
e al., 2024). In some cases, desi able mic obio a cha ac e -
is ics migh be in o med by highe -le el unc ional ou comes
(e.g. es ablishmen o sensi i e plan s, nu ien cycling, disease
supp ession). Va ious mic obial axa ha e seen inc eased
esea ch ocus on hei uses o es o ing pa icula ecosys em
p ocesses o connec ions. Fo example, plan g ow h-
p omo ing hizobac e ia ha e po en ial o hei abili y o
imp o e plan g ow h (Radhap iya, Ramachand an &
Palani, 2018; Solans, Pelliza & Tadey, 2022) and enhance ge -
mina ion (Domínguez-Cas illo e al., 2021), and a buscula
myco hizal ungi can p omo e eco e y o na i e ege a ion
ia mechanisms ha enhance phospho us up ake in plan s
(Koziol e al., 2018) and imp o e soil physicochemical p ope -
ies (Willis, Rod igues & Ha is, 2013).
While he e a e “good”membe s o mic obial comm-
uni ies, he e a e also pa hogens ha can be ha m ul o
mic obial communi ies and o he ecosys em componen s
(e.g. Phy oph ho a cinnamomi is a soil-bo ne plan pa hogen)
(Mansfield e al., 2024) and es o a ion plans need ca e ully
o conside he isks o inad e en ly sp eading ha m ul pa h-
ogens. Impo an ly howe e , plan –pa hogen in e ac ions
may be beneficial in es o a ion as hey also play a significan
ole in shaping plan di e si y and communi y dynamics.
Pa hogens can influence plan di e si y h ough a ious
mechanisms, including selec ion p essu e on hos species
and acili a ion o compe i i e in e ac ions (Be e , Mangan
& Alexande , 2015), which may impac plan and soil com-
muni y s abili y.
(2) When o p io i ise in es men in soil mic obio a
Ano he key ques ion ha needs o be add essed o ensu e
es o a ion is as e ficien and e ec i e as p ac ically possible
is: when will he inclusion o soil mic obial da a imp o e es-
o a ion success? While he explici conside a ion o soil
mic obio a in es o a ion could a guably p o ide benefi s o
all p ojec s, i does come wi h addi ional cos s (e.g. soil sam-
pling, DNA ex ac ion and sequencing, complex bioin o -
ma ics) and po en ial isks (e.g. in oduc ion o ha m ul
pa hogens, public o policymake scep icism om undesi -
able ou comes) ha need o be conside ed o maximise posi-
i e es o a ion ou comes and a oid was ed esou ces. Soil
ecosys ems a e complex and highly a iable bo h wi hin
and ac oss si es which means a one-size-fi s-all ecommenda-
ion is p oblema ic. Fu he mo e, soil mic obio a a e unlikely
o be he only ac o hinde ing es o a ion ou comes. Res o-
a ion p ojec s should he e o e include isk assessmen s and
cos –benefi analyses on a case-by-case basis o de e mine i ,
and o wha ex en , soil mic obio a should be included. The
inclusion o soil mic obio a in any gi en es o a ion p ojec
and any de e mina ion on he likelihood o ha inclusion
ansla ing in o cos -e ec i e imp o ed es o a ion ou comes
will be la gely dependen on he p ojec ’s goals and le el o
deg ada ion o dis u bance o soil physical, chemical, and
biological p ope ies.
Decisions on including soil mic obio a in es o a ion plans
and in e en ions should be in o med la gely by he impac
ha deg ading p ocesses ha e had on soils and he le el o
in es men ha is a ailable. E en sho - e m dis u bances
o ege a ion communi ies wi h minimal dis u bance o soils
can cause shi s in soil mic obial di e si y and composi ion
(Na a e e e al., 2015;Que al., 2024). Howe e , i soil phys-
ical and chemical p ope ies emain simila o an undis-
u bed s a e, a ocus on es o ing ege a ion communi ies
alone may be su ficien o see he eco e y o soil mic obio a.
On he con a y, i deg ading p ocesses ha e subs an ially
modified soil physical o chemical p ope ies, hen soil bio-
logical p ope ies will mos likely be impac ed as well. Fo
example, es o a ion si es ha we e p e iously used o ag i-
cul u e wi h ex ensi e e ilise applica ions can ha e long-
las ing nu ien legacies ha pe sis o decades o millennia
(Tu ley e al., 2020; Pa khu s , S andish & P obe , 2022).
These pe sis en land-use legacies can hen ac as an abi-
o ic ba ie and impede he eco e y o soil mic obio a and
p esen si ua ions whe e es o a ion should plan in e en-
ions ha specifically seek o o e come hese abio ic con-
s ain s (Peddle e al., 2024). Addi ionally, al e a ions in soil
pH, mois u e, and s uc u e esul ing om deg ada ion can
also influence mic obial communi y composi ion and ac i -
i y, u he emphasising he ele ance o soil physicochemical
assessmen s in guiding he inclusion o soil mic obio a in es-
o a ion ini ia i es. Physical and chemical condi ions a e gen-
e ally easie o obse e and es han soil mic obio a and
should be conside ed o p o ide as nea -op imal condi ions
as possible wi h e e ence si es as a guide. This se s he oun-
da ion o de elopmen o biological communi ies (Robinson
e al., 2024). Res o a ion planning can, o cou se, conside
“in-p inciple”influences on (and ia) mic obio a, howe e ,
p ac i ione s will be blind o ac ual e ec s and eco e y i el-
e an a ibu es o mic obio a emain uncha ac e ised. By
in eg a ing assessmen s o soil physical, chemical, and biolog-
ical p ope ies, es o a ion p ac i ione s can ailo decisions
on he inclusion o mic obio a-based in e en ions (see
Sec ion III) o he specific needs o deg aded ecosys ems,
acili a ing mo e e ec i e es o a ion ou comes.
(3) Imp o ing conclusions on causa ion in soil
mic obio a es o a ion
To de e mine be e he le el o e o equi ed o a ec
eco e y o soil mic obio a i is impo an o imp o e ou
unde s anding o how soil mic obio a esponds ollowing a-
di ional es o a ion in e en ions such as e ege a ion. I
e ege a ion alone la gely leads o eco e y o soil mic o-
bio a, hen cos ly assessmen s and in e en ions ocussed on
mic obio a a e p obably no needed. Howe e , a ibu ing
soil mic obial eco e y solely o e ege a ion wi hou
p ope ly asce aining causa ion will lead o soil mic obio a
being o e looked and isks missing oppo uni ies ei he o
add ess his c ucial ecosys em componen di ec ly (Lem
e al., 2022) o o u ilise soil mic obio a mo e as d i e s o
change as opposed o solely passenge s (Ha is, 2009).
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Soil mic obio a and ecosys em es o a ion 5
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Obse a ional s udies o soil mic obio a ollowing e ege a-
ion o en indica e ha soil mic obio a in es o a ion si es
esemble e e ence si es mo e closely wi h inc easing ime
since es o a ion (Ba be e al., 2017; Gellie e al., 2017; Klop
e al., 2017; Ngugi e al., 2018; Pa sons e al., 2020; Sun
e al., 2017; Yan e al., 2019; Banning e al., 2011). These s ud-
ies a e o en used o in e ha he es o a ion in e en ion
(e.g. na i e plan e ege a ion) is causing he es o a ion o soil
mic obio a bu u he igou is needed o imp o e ou
knowledge o causal mechanisms a ec ing he eco e y o soil
mic obio a.
Obse a ional ch onosequence-based s udies o en su e
om unmeasu ed o unaccoun ed ac o s ha can con ound
esul s and cloud conclusions. O he soil cha ac e is ics (bo h
bio ic and abio ic), clima e, abo eg ound biological influences
(e.g. ege a ion, land-managemen his o y), opog aphic elie ,
pa en geological ma e ials, age o de elopmen , and spa ial
loca ion (e.g. p oximi y o ex e nal influences) will influence
soil mic obio a composi ion (Delgado-Baque izo e al., 2020;
McB a ney, San os & Minasny, 2003; Pino e al., 2019) and
may a y independen ly o a es o a ion in e en ion.
Fu he mo e, es o a ion me hods may change o e ime;
o example, an unp edic able supply o seed esou ces may
cause empo al a ia ion in e ege a ion (B oadhu s
e al., 2016; Ladouceu e al., 2018), o he e may be in e -
seasonal changes in clima e, o changes in e ege a ion
p ac ices o plan ing c ew. These ime-dependen changes
o es o a ion p ac ice can in oduce uncon olled a ia ion
ac oss he ch onosequence and mus be conside ed du ing
ch onosequence s udies. In many si ua ions, collec ing su fi-
cien co a ia e da a o explain ully (o de elop models o
accoun o ) soil mic obio a spa ial au oco ela ions is
imp ac ical. The e o e, ensu ing ha hese unmeasu ed o
unaccoun ed influences do no comp omise expe imen al
designs and sampling plans by ha ing app op ia ely designed
s udies is necessa y.
Despi e hei limi a ions, ch onosequence designs a e use-
ul o in e ing ecological esponses o es o a ion in e en-
ions h ough ime wi hou long- e m sampling o
con olled expe imen s (Walke e al., 2010). Howe e ,
explici ly planning o embed good quali y expe imen s –such
as hose wi h adequa e eplica ion, con ols and
andomisa ion –in o es o a ion p ojec s will help o alle ia e
issues wi h spa ial au oco ela ion ( an de Heyde e al., 2022)
o pseudo- eplica ion (i.e. ea men N=g oups o 1) and
assis in minimising he e ec s o con ounding ac o s
(e.g. changes in es o a ion plan ing me hods, seed supply,
clima e a ia ion, spa ial loca ion). Howe e , i should be
no ed ha uly longi udinal and/o manipula i e s udies
a e needed o p oduce high-quali y e idence and conclusi e
suppo on causa ion (Lem e al., 2022) (see Sec ion II.5).
(4) Embedding soil mic obio a expe imen s
By planning o embed well-designed expe imen s in o es o-
a ion p ojec s, p ac i ione s and esea che s could o m
pa ne ships o add ess many o he limi a ions o
ch onosequence (i.e. space- o - ime) designs (B oadhu s
e al., 2023). Embedded expe imen s could nes eplica ed soil
mic obio a in e en ions (e.g. di e en soil inocula ion
me hods o e ege a ion echniques) wi hin e e ence and
es o a ion si es o include spa ially independen and epli-
ca ed es o a ion in e en ions ac oss a p ojec (Fig. 2). Such
an app oach will imp o e he e idence base o he e ec o
specific es o a ion in e en ions on he eco e y o soil
mic obio a and hei associa ed unc ions.
Adequa ely eplica ed, andomised, con olled and com-
pa able es o a ion si es a e no o en ou inely p esen in es-
o a ion p ojec s unless planned o om he ou se . This lack
o co e scien ific design p inciples in sys ems ha a e o en
used in obse a ional s udies limi s conclusions ha can be
d awn om such esea ch. Fo his eason, es o a ion p o-
jec s could imp o e ou e idence base by collabo a ing wi h
esea che s and embedding mic obio a- ocussed expe i-
men s in o es o a ion p ojec s. Well-designed longi udinal
s udies ha epea edly sample he same es o a ion si es
h ough ime will p o ide mo e obus e idence on cause–
e ec ela ionships han c oss-sec ional ch onosequence
s udies alone (Ch is ie e al., 2019; Lem e al., 2022). Embed-
ding expe imen s would also help close c i ical es o a ion
knowledge gaps, such as knowing when a ocus on soil
mic obio a will subs an ially imp o e es o a ion success.
Howe e , by hei e y na u e, longi udinal s udies equi e
yea s o esea ch and gi en he u gency equi ed o add ess
he biodi e si y c isis, s a is ical modelling me hods
(e.g. s uc u al–causal modelling, see Sec ion II.5) will be use-
ul o help unde s and he key knowledge gaps ha need o be
add essed wi h on-si e long- e m expe imen s and wha can
be sol ed wi h obse a ional s udy designs alone.
(5) Modelling app oaches o asce ain causa ion
Whe e pa icula mic obio a-o ien ed ou comes a e desi ed,
bu es o a ion ac i i y canno wai o defini i e expe imen-
ally de i ed knowledge on cause–e ec ela ionships, ce ain
modelling app oaches may help o dis il in o ma ion om
ele an exis ing mic obio a- es o a ion da a se s. Tech-
niques such as s uc u al–causal modelling, s uc u al
equa ion modelling and pa h analysis can be applied o
es hypo heses using obse a ional c oss-sec ional da a
(A i & MacNeil, 2023; G ace & I ine, 2020). These
app oaches in ol e speci ying a heo e ical model ha
eflec s likely causal ela ionships among a iables o in e -
es , including bo h obse ed and la en (i.e. unmeasu ed)
a iables. Then, he hypo heses a e es ed by speci ying
di ec ional pa hs ha ep esen he assumed causal ela-
ionship be ween a iables in he model. Using he
obse ed da a, pa ame e s (i.e. coe ficien s) o he specified
model a e es ima ed. These es ima es assess he s eng h o
he hypo hesised causal/di ec ional ela ionships and
goodness o fi me ics indica e how well he model aligns
wi h he da a, e en in he absence o expe imen al e i-
dence (Eisenhaue e al., 2015), acili a ing in o med deci-
sion making in es o a ion planning.
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6Shawn D. Peddle and o he s
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As a specific example, we could conside a scena io whe e
a es o a ion in e en ion aims o enhance soil e ili y and
plan g ow h by in oducing specific mic obial species o
communi ies. By using s uc u al causal modelling,
esea che s can cons uc a heo e ical model ha includes
a iables ela ed o soil mic obio a composi ion and unc-
ion, soil e ili y, and plan pe o mance. They can hypo he-
sise di ec ional pa hs be ween hese a iables ep esen ing
he assumed causal ela ionships. Th ough analysis o obse -
a ional c oss-sec ional da a om simila es o a ion p ojec s
and con olling o co a ia es, esea che s can es ima e he
pa ame e s o he model and assess he s eng h and di ec ion
o he hypo hesised causal ela ionships. Fo ins ance, i
migh be ha ce ain mic obial axa o unc ional genes a e
s ongly associa ed wi h inc eased soil e ili y, which in u n
posi i ely impac s plan g ow h.
While s uc u al–causal modelling wi h c oss-sec ional
da a is powe ul, i has limi a ions. I canno es ablish causal-
i y as defini i ely as con olled o longi udinal expe imen s,
and causali y may be mo e challenging o in e in he p es-
ence o unobse ed con ounde s especially in sys ems such
as soil wi h housands o dis inc axa and many unc ional
g oups (Eisenhaue e al., 2022). Howe e , i allows
esea che s o speci y, es ima e and e alua e complex causal
models p o iding insigh s in o causal ela ionships (e.g. he
ela i e oles o physical, chemical and biological p ope ies
o soil in limi ing soil ecosys em eco e y; he acili a ion o
ollowing oles o soil bio a and abo eg ound plan and ani-
mal communi ies du ing es o a ion; he influence o clima e
change and o he majo global deg ading o ces on limi ing
he eco e y o soil ecosys ems) wi hou he need o expe i-
men al o longi udinal designs. Fu he mo e, he s eng h
o causal claims should always be conside ed in he con ex
o he s udy’s design and he po en ial p esence o unob-
se ed con ounding a iables.
III. RESTORATION INTERVENTIONS THAT
DIRECTLY TARGET SOIL MICROBIOTA
I is possible o manipula e soil mic obio a o assis in he
eco e y o deg aded ecosys ems by ein o cing beneficial
in e ac ions be ween plan species and soil mic obio a los
Fig. 2. Embedding soil mic obio a expe imen s in o es o a ion si es. (A) A soil mic obio a ansloca ion field expe imen embedded
in o an ongoing es o a ion p ojec in Wes e n Aus alia (pho og aph c edi : Shawn Peddle). (B) Embedded soil mic obio a
expe imen s in a es o a ion si e in he M Lo y Ranges, Sou h Aus alia (pho og aph c edi : Ta yn Da ies). Designing and
embedding expe imen s in o es o a ion p ojec s will allow o imp o ed causal conclusions in es ing mic obio a- ocussed hypo heses.
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Soil mic obio a and ecosys em es o a ion 7
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h ough deg ada ion (Aghili e al., 2014; an de Pu en
e al., 2016; Albo noz e al., 2022). Soil mic obio a- ocussed
in e en ions can imp o e plan species p ospec s by imp o -
ing plan g ow h, and depending on he ecological sys em,
di e se soil mic obio a ha e also been shown o media e eg-
e a ion communi y di e si y and imp o e ecosys em p oduc-
i i y (Naeem e al., 1994; Yang e al., 2021). In o med by
mechanisms o ecosys em eco e y and species-specific
esponses, soil mic obio a in e en ions can ad ance es o a-
ion objec i es and es o e he diminished capaci y o
impac ed ecosys ems o eco e na u ally. In his sec ion, we
e iew mo e es ablished (e.g. soil inocula ions) and
less well-es ablished (e.g. specific mic obial cul u es, seed
enhancemen s) ways o manipula e soil mic obio a o imp o e
es o a ion ou comes. We no e ha ob ious abio ic ba ie s o
he de elopmen o si e-specific a ou able soil mic obial com-
muni ies (e.g. soil subs a e p oblems, excess nu ien s, low pH,
high salini y) should be iden ified and add essed be o e
a emp ing di ec manipula ion o soil mic obio a.
(1) Whole-soil ansloca ions and mic obial
inocula ions
T ansloca ing whole soil communi ies –whe he in he o m
o in ac u s o homogenised bulk soil –is one way o inoc-
ula ing soil mic obio a in o deg aded ecosys ems o shi he
mic obial communi y owa ds one ha is mo e ep esen a-
i e o a a ge ecosys em. This essen ially in ol es collec ing
soil om a e e ence ecosys em and ansloca ing i di ec ly
in o a es o a ion si e (Koziol e al., 2018; Wubs e al., 2016;
Ca bajo e al., 2011). Inocula ing deg aded si es wi h e e -
ence ecosys em soil and associa ed bio a has been shown o
imp o e he g ow h and es ablishmen o desi able na i e
plan s and exclude weeds in bo h g eenhouse and field condi-
ions (Koziol e al., 2018; Wubs e al., 2016; Fahey &
Flo y, 2022). Fo example, Wubs e al.(2019a) showed ha
soil inocula ions can ha e ecosys em legacy e ec s ha s ee
successional changes and can las o a leas wo decades.
Impo an ly, howe e , Ge i s e al.(
2023) highligh how
he di ec ionali y o his legacy e ec depends on he sui abil-
i y o fi o ansloca ed soil o he ecipien si e, wi h mis-
ma ches s ee ing communi ies in he w ong di ec ion.
Simila in e en ions can also shi he di ec ion o he de el-
opmen o ege a ion communi ies (Wubs e al., 2016) and
imp o e p ospec s o na i e ege a ion success (Wubs
e al., 2019b). Howe e , while esea ch has shown a benefi
o he es o a ion o ege a ion, ew s udies ha e ocussed
on he e ficacy o soil ansloca ions o shi ing whole mic o-
bial communi ies hemsel es.
Subs an ial knowledge gaps emain on he e ec i eness o
soil ansloca ions, including: wha me hods a e mos e ec-
i e (e.g. bulk soil, in ac u s, olumes equi ed), o wha
ex en do soil physical and chemical p ope ies in ecipien
si es impac es ablishmen , how do p io i y e ec s impac
on mic obial communi y eco e y (i.e. es ablishmen may
be dependen on he o de o a i al o specific axa), and,
how does he coalescence o dis inc ly di e en soil communi ies
impac success ul es ablishmen ? As such, u he esea ch on
whole-soil ansloca ions and inocula ions should ocus on
add essing hese knowledge gaps ia embedded expe imen s
o unde s and be e how soil olume, ansloca ion me hod,
and communi y coalescence dynamics a ec mic obial com-
muni y assembly ac oss a ied ecosys ems and soil ypes.
Add essing hese knowledge gaps will hen enable he
esea ch communi y o de elop decision-suppo amewo ks
o help de e mine when whole-soil ansloca ions will p o ide
es o a ion benefi s ha a e commensu a e wi h cos .
Ano he c i ical open ques ion ela ing o soil ansloca-
ion is: how can we minimise he impac s soil ansloca ions
ha e on dono ecosys ems? While soil ansloca ions may
be e ec i e, soil collec ion can impac emnan habi a s and
conside a ion is needed o limi impac s o emnan si es
while p o iding a benefi o deg aded si es. Solu ions a e
needed o scale up soil ansloca ions ou side si ua ions whe e
soil can be ha es ed because exis ing emnan habi a is
al eady being clea ed. As such, decisions on in e en ions
impac ing emnan habi a will need o weigh ac o s such
as he con ibu ion o emnan habi a o suppo he in eg-
i y and iabili y o es o a ion o conse a ion e o s
(Tulloch e al., 2016; Win le e al., 2019), o i a deg ee o
des uc i e ha es ing o soil esou ces om emnan si es
can p o ide es o a ion benefi s ha ou weigh impac s o
emnan habi a . To add ess he need o eliable seed sou c-
ing in es o a ion o e ege a ion, seed-p oduc ion a eas a e
being es ablished ins ead o elying on sou cing seeds om
emnan habi a s (i.e. a ge plan s a e g own ex-si u “en
masse” o p oduce seed s ock) (Zinnen e al., 2021). This con-
cep could po en ially be applied o soil mic obio a wi h soil
mic obio a p oduc ion a eas, al hough a ious open ques-
ions (i.e. how do we cul i a e whole a ge mic obial com-
muni ies, can we subse communi ies o ocus on pa icula
axa, and wha is he “ideal”composi ion o hese communi-
ies) need o be add essed be o e soil mic obio a p oduc ion
a eas can be e ec i ely implemen ed a scale.
Despi e hese knowledge gaps, whole-soil ansloca ions
a e inc easingly used in la ge-scale es o a ion p ojec s whe e
opsoil is sal aged as pa o he ini ial dis u bance (e.g. su -
ace s ip mining) and hen eins a ed du ing es o a ion
(Tibbe , 2010; Schmid e al., 2020; Liddicoa e al., 2022).
The objec i e o opsoil ans e is o p ese e he soil-s o ed
seedbank a he han he soil mic obio a pe se. S ill, benefi s
om he ese oi o mic obio a con ained in hese opsoils
p esen an oppo uni y o imp o e es o a ion ou comes.
Limi ing he amoun o ime o which soils a e s ockpiled
be o e ansloca ion is c ucial as s ockpiling can dis up
biological in eg i y and impac mic obial di e si y and com-
posi ion (He nandez e al., 2024; Vallie e e al., 2022). In bes -
p ac ice cases, he di ec e u n o ha es ed opsoil o nea by
es o a ion si es will limi he physical and biological deg a-
da ion o soil om long- e m s ockpiling (Rokich
e al., 2000; Peddle e al., 2022). Howe e , he impac o he
collec ion and homogenisa ion o e ical soil p ofiles du ing
he ans e p ocess on soil mic obio a is likely de imen al
bu s ill poo ly unde s ood.
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An eme ging app oach ha a oids b oadac e sp eading o
whole soil is he a ge ed use o mic obio a om local soils ia
ex uded pelle s o coa ings as a essel o seed deli e y
(Go nish, A nold & Fehmi, 2019; Madsen e al., 2016)
(Fig. 3). This me hod is designed o imp o e he p ecision
o seed deli e y in la ge-scale es o a ion e o s ha simul a-
neously p o ide beneficial soil mic obio a and he a ge
seeds. Such an app oach can educe he demand o soil by
100- old (S ock e al., 2020). Howe e , simila ques ions o
hose iden ified ea lie in ela ion o whole-soil inocula ions
a e s ill un esol ed and applicable he e. Fo example: how
do he mechanical and chemical dis u bances o c ea ing
he pelle s a ec mic obial communi y composi ion, and
how well can a ge ed mic obial communi ies in ex uded
pelle s be es ablished wi hin dono soils wi h as ly di e en
mic obial communi ies o physicochemical p ope ies?
(2) Seed enhancemen s ha con ain mic obial
addi i es
Seed enhancemen s ha add specific mic obial inoculan s in
a es o a ion con ex can imp o e he ge mina ion and
g ow h o desi able plan species (Chua e al., 2019; Dadzie
e al., 2023;O’Callaghan, 2016). Seed coa ing in ol es he
p ecise applica ion o binde s and mine al powde s o seeds
o c ea e a hin a ificial laye o ma e ial capable o al e ing
he physical shape o seeds and/o ca ying beneficial p od-
uc s such as mic obio a (Fig. 3A–C) (B own e al., 2021;
E ickson e al., 2021). Simila ly, ex uded pelle s made ia
ex usion o moulding echnologies can make la ge seed-soil
ma ices while o e ing he same mic obial inocula ion
oppo uni ies. Fo ins ance, mic obio a can be added o he
seed coa and/o in o ex uded pelle ing edien s ei he d y
wi hin he powde o we ia he binde (Al onze i e al., 2023;
Dadzie e al., 2023;Mun oe al., 2024). Al e na i ely, seed p im-
ing in ol es imme sing seeds in wa e -based (i.e. hyd o-p im-
ing) o osmo ically con olled (i.e. osmo-p iming) solu ions o
soil ma ix (i.e. ma ix-p iming) o commence he p ocess o
ge mina ion unde con olled condi ions, ollowed by a e-
d ying s ep (B own e al., 2021; Madsen e al., 2018). Once
sown, p imed seeds show a much highe and mo e apid ge -
mina ion po en ial, ec ui men synch onici y and seedling
igou . P iming wi h addi i es like mic obial suspensions
can acili a e he up ake o beneficial mic obio a di ec ly on o
and po en ially in o he seeds (O’Callaghan, 2016; Muñoz-
Rojas, 2018). Consequen ly, he a ge ed mic obio a will be
es ablished di ec ly in he soil nea he ge mina ing seed o
wi hin he seedling issue i sel (O’Callaghan, 2016; Chua
e al., 2019).
The e ha e been success ul implemen a ions o na u ally
ob ained mic obio a ha benefi key es o a ion plan
species by seed enhancemen s (including ex uded seed
pelle ing and/o hyd o-p iming wi h mic obial addi i es)
(Muñoz-Rojas e al., 2018;Dadziee al., 2022). The
imp o ed accessibili y and e ec i eness o hese echni-
ques ep esen a aluable oppo uni y o es o a ion.
C
B
#
F
%
A
DE
Fig. 3. Manipula ing soil mic obio a as pa o es o a ion in e en ions. Eucalyp us seeds (A) be o e and (B) a e coa ing wi h
myco hizae inoculan s (pho og aph c edi : Todd E ickson). (C) Seedlings ge mina ed om ex uded seed pelle s con aining li e
soil (pho og aph c edi : Todd E ickson). (D) Con ol (sand +ben oni e, le ) and cyanobac e ia encapsula ed pelle s ( igh )
(pho og aph c edi : Mi iam Muñoz-Rojas). (E, F) Whole soil ansloca ion expe imen wi h (E) ansloca ed in ac soil co e and (F),
esampling 1 yea a e ansloca ion o assess es ablishmen and dispe sal o soil mic obio a (pho og aph c edi : Shawn Peddle).
Biological Re iews (2024) 000–000 © 2024 The Au ho (s). Biological Re iews published by John Wiley & Sons L d on behal o Camb idge Philosophical Socie y.
Soil mic obio a and ecosys em es o a ion 9
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