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Functional diversity of soil microbial communities inresponse to tillage and crop residue retention in aneroded Loess soilQ. Yang a b , X. Wang a b , Y. Shen a b & J.N.M. Philp ca State Key Laboratory of Grassland Agro-ecosystems , Lanzhou , 730020 , Chinab Lanzhou University, College of Pastoral Agriculture Science and Technology , Lanzhou ,730020 , Chinac University of Western Sydney, School of Natural Sciences , Sydney , AustraliaPublished online: 01 Aug 2013.

To cite this article: Q. Yang , X. Wang , Y. Shen & J.N.M. Philp (2013) Functional diversity of soil microbial communities inresponse to tillage and crop residue retention in an eroded Loess soil, Soil Science and Plant Nutrition, 59:3, 311-321, DOI:10.1080/00380768.2013.775004

To link to this article: http://dx.doi.org/10.1080/00380768.2013.775004

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ORIGINAL ARTICLE

Functional diversity of soil microbial communities in response totillage and crop residue retention in an eroded Loess soil

Q. YANG1,2, X. WANG1,2, Y. SHEN1,2 and J.N.M. PHILP3

1State Key Laboratory of Grassland Agro-ecosystems, Lanzhou, 730020, China, 2Lanzhou University, College of PastoralAgriculture Science and Technology, Lanzhou, 730020, China and 3University of Western Sydney, School of Natural Sciences,Sydney, Australia

Abstract

This study reports the effects of a long-term tillage and crop residue experiment on the soil microbial ecology ofa Loess soil located in Gansu Province, western China. Tillage and residue management treatments wereimposed on a nine-year continuous rotation of maize (Zea mays L. cv Zhongdan No. 2), winter wheat(Triticum aestivum L. cv Xifeng No. 24) and soybean (Glycine max L. cv Fengshou No. 12). After nineyears, there were significant effects on topsoil (0–10 cm) carbon, nitrogen, microbial activity, microbialcomposition and function. The retention of crop residues compared to residue removal significantly improvedall measures of chemical and biological soil fertility. The values of average well color development (AWCD), ameasure of the metabolic utilization of organic compounds, for the residue retention treatments were alwayshigher than those with residue removal treatments, and the differences increased with increasing incubationtime. Principal component analysis indicated that crop residue retention significantly altered topsoil microbialactivity and community functional diversity. Our research clearly demonstrates that retention of crop residuessignificantly enhances soil microbial metabolic capacity, compared to no tillage, and can therefore contribute tosustainable agriculture on the Loess Plateau. Promotion of conservation agriculture has the potential torehabilitate soil fertility and improve agricultural sustainability and food security on the region.

Key words: functional diversity, Loess Plateau, microbial community, no tillage, residue retention.

INTRODUCTION

The Loess Plateau of western China has the unenviablereputation as one of the worst examples of soil erosion inthe world (Shi and Shao 2000). The combination of highlyerodible soil, variable rainfall and intensive cultivation hasresulted in severe soil erosion. Currently, the rate of soilerosion is in the range of 5000 to 25,000 t km−2 y−1 (Fu etal. 2005). The traditional practice of intensive cultivationinvolving several deep ploughings and complete removal ofcrop residues has resulted in soils low in organic matter, ofpoor fertility and very susceptible to erosion. Althoughwellestablished in other parts of China, conservation agricul-ture, particularly the combination of no tillage and stubble

retention, is very rarely practised on the Loess Plateau. Thisis because both farmers and local extension agents holdstrong beliefs that crop residues are in demand as livestockfeed and as fuel for heating or cooking (Lal et al. 2000).Elsewhere in the world conservation agriculture has beenfound to increase crop yield, improve water use efficiency,reduce energy inputs, and improve soil fertility (Lal et al.1980; Buerkert et al. 2000; Al-Kaisi andYin 2005; Thomaset al. 2007; Rahman et al. 2008). Retention of crop resi-dues increases soil organic carbon (C) and nitrogen (N)stocks (Govaerts et al. 2006; Ke and Scheu 2008), and thereduction or elimination of tillage reduces soil respiration,resulting inmore C in the soil (Brady andWeil 1999; Dolanet al. 2006; Jacobs et al. 2009). In all ecosystems, soilmicrobes play key roles in the decomposition of organicmatter, in nutrient cycling and in altering the availability ofnutrients to plants (Pankhurst et al. 1995; Loranger-Merciris et al. 2006). The soil microbe community is animportant indicator of sustainable land use as it is sensitive

Correspondence: Y. SHEN, Lanzhou University, College ofPastoral Agriculture Science and Technology, 768 JiayuguanWest Road, Lanzhou, China. Email: yy.shen@lzu.edu.cnReceived 22 August 2012.Accepted for publication 6 February 2013.

Soil Science and Plant Nutrition (2013), 59, 311–321 http://dx.doi.org/10.1080/00380768.2013.775004

© 2013 Japanese Society of Soil Science and Plant Nutrition

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to changes in the soil’s chemical properties (Pankhurst et al.2002; Hamer et al. 2009). Both the absolute quantity andthe composition and function of soil microbial commu-nities have been shown to change under conservation agri-culture (Rahman et al. 2007; Xu et al. 2008; González-Chávez et al. 2010; Nautiyal et al. 2010).However, little is known to distinguish tillage and

residue retention effects on the soil microbial commu-nities, especially in highly erodible soil. The aims of ourresearch are to quantify impacts of tillage and cropresidue management on surface soil C, N, microbial Cand N, and microbial activity and function, and todevelop a basic understanding of changes in soil micro-bial ecology that occur under local soil, climate andmanagement conditions, when conservation agricultureis applied for several years. This improved understandingmay contribute to wider efforts to promote the adoptionof conservation agriculture on the Loess Plateau.

MATERIALS AND METHODS

Site descriptionThe study site is located at the Qingyang Loess Plateau fieldresearch station of Lanzhou University (35°39′N, 107°51′E), on the western reaches of the Loess Plateau withinChina’s Gansu province. The altitude is approximately1297 m above sea level with a cool continental climate.The annual mean temperature range is from 8°C to 10°Cand mean annual accumulated temperature is 3446°C days.Rainfall is most abundant from July to September. Annualprecipitation during the 9-y trial reported here was between480 mm and 660 mm. The growing season is 255 d with110 frost-free days. The dominant soil type isHeilu (ChineseSoil Taxonomy Cooperative Research Group 1995), asandy loam of low fertility. The soil corresponds most clo-sely to Kastanozems in the Food and AgricultureOrganisation’s (FAO) soil classification system or Mollisolsunder the United States Department of Agriculture (USDA)soil taxonomy (Zhu et al. 1983). The field site had beensown with tall fescue (Festuca arundinacea Schreb.) for 3 yand then left fallow for 1 y before the long-term conserva-tion tillage experiments commenced in 2001.

Experimental designThe trial involved a phased rotation of three crops from2001 to 2009. The crop sequence was maize (Zea mays L.cv Zhongdan No. 2), winter wheat (Triticum aestivum L.cv Xifeng No. 24) followed by soybean (Glycine max L. cvFengshouNo. 12) the following summer. Themaize-winterwheat-soybean rotation cycle was completed every 2 y.A factorial of treatments was set as follows: Treatment

1 (T0 R0), no tillage (no soil disturbance except for crop

planting) and no retention of previous crop residues;Treatment 2 (T1 R0), conventional tillage (conventionalploughing of the surface 20 cm in April before maizesowing, and ploughing again in September before wheatsowing, or in October after soybean harvest) withremoval of all crop residues; Treatment 3 (T0 R1), notillage with retention of the previous crop’s residues;Treatment 4 (T1 R1), conventional tillage as above butwith retention of the previous crop’s residues.Four treatments were replicated four times each in a

randomised complete block design with a total of 16plots. Each plot was 52 m2 (4 m × 13 m) in area.There were 2-m spaces between each pair of blocks and1-m spaces between the plots of each block.Maize was sown in April each year, with 38 cm

between rows and 44 cm between plants, and harvestedin mid-September each year. Winter wheat was sownimmediately after the maize harvest with 15 cm betweenrows at a sowing rate of 187 kg ha−1. After winter wheathad been harvested in late June or early July the follow-ing year, soybean was sown with 25-cm spacing betweenrows and plants, and harvested in mid-October. Aftersoybean harvest six months’ bare fallow followed, afterwhich maize was sown for the start of a new cycle. Afterthe winter wheat was harvested, 15 cm of standingstubble remained and all the threshed crop residue wasspread uniformly across the plots for the treatments thatincluded residue retention. After the maize was har-vested, 50% of the maize residues was chopped into20 cm lengths and spread uniformly across the plots inthe residue retention treatments. After the soybean har-vests all crop residues were retained in the plots with theexception of the pods which were removed by hand.All three crops were sown using a small no-till seeder

(5–6 rows in 1.2-m width) designed by the ChinaAgricultural University. The no-till seeder, drawn by a13.4 kW (18 hp) tractor, was designed to place fertilisersbelow the seeds using narrow points followed by con-cave rubber press wheels in one operation.Fertilisation of winter wheat was done before sowing

with 300 kg ha−1 diammonium phosphate, (DAP,equivalent to 72.4 kg ha−1 N and 80.2 kg ha−1 P), andat the jointing stage with N at 69 kg ha−1 as urea. Beforesowing maize, 300 kg ha−1 DAP was applied and138 kg N ha−1 as urea was applied at the bootingstage. Before sowing soybean, 27.7 kg ha−1 of phos-phorus was added but no additional N fertiliser wasapplied. Weeds in the plots were removed by hand.

Soil samplingAfter the harvest of maize in September of 2009, soilsamples were collected from each of the 16 plots of thefour treatments. In each plot one composite soil samplewas

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obtained, consisting of three random subsamples takenfrom a depth of 0–10 cm, with all surface litter removed.During collection all fresh samples were sieved (< 2 mm).Biolog assays were performed immediately on fresh soil oron soil that had been stored at 4°C for no more than oneweek. For analysis of soil chemical properties, subsampleswere dried at 40°C for 48 h in an oven.

Crop yieldYields were determined by manual harvesting, threshingand air-drying grain with the exclusion of the twoperipheral rows to minimise edge effects. From 2001 to2009, the average grain yields and average residue yieldsof the three crops under the maize-winter wheat-soybean rotation were calculated.

Microbial biomass C and NMicrobial biomass carbon (SMB-C) and microbial bio-mass nitrogen (SMB-N) were estimated using the fumi-gation extraction method (Brookes et al. 1985; Vanceet al. 1987). Two 25-g portions of fresh soil were takenfrom each of the 16 original soil samples and placed inbrown glass tubes. Samples were dampened to approxi-mately 50% of water holding capacity and then incu-bated in the dark at 25°C for 10 d to allowequilibration of the soil microbial biomass(Franzluebbers et al. 1996). One portion of each samplewas then fumigated for 24 h at 25°C in the dark withethanol-free chloroform, while the other portion servedas the control. Following fumigant removal both fumi-gated and non-fumigated samples were extracted with100 mL of 0.5 M potassium sulphate (K2SO4) by hor-izontal centrifugation and filtration. Organic C in theextracts was measured using the dichromate oxidationmethod and total N by the improved Kjeldahl method.Values were calculated as:

SMB� C ¼ EC=KEC (1)

SMB�N ¼ EN=KEN (2)

where EC and EN are the differences between the C and Nconcentrations in fumigated and non-fumigated extracts,and KEC = 0.38 and KEN = 0.54 (Brookes et al. 1985).

Soil respirationSoil respiration was defined as the amount of carbondioxide (CO2) released from the soil and measuredusing a LI-COR 6400 portable photosynthesis systemfitted with a soil respiration chamber (6400–09, LI-COR, USA). Two polyvinyl chloride (PVC) rings(10 cm in diameter, 5 cm high) were randomly

distributed in each plot at maize crop maturity andpressed 2 cm into the soil. Litter and living plants insidethe collars were removed at least 1 d before the measure-ment to reduce errors. Data were recorded at 3-s inter-vals. Soil temperatures for 0–10 cm were obtained usinga soil temperature probe inserted in the soil beside eachPVC collar. Daily soil respiration measurements wereundertaken between 8:00 a.m. and 10:00 a.m. onSeptember 26, 27 and 28, 2009, with clear weatherconditions prevailing. Maize harvest was undertakenon September 29, 2009. Soil respiration values reportedin this article are the arithmetic average value of the 3 don which they were sampled.The respiration intensity per unit of soil microbial bio-

mass, which is the ratio of soil respiration intensity toSMB-C, was expressed as soil metabolic quotient (qCO2).

Soil microbial communityBiolog-ECO microplate (Biolog Inc., Hayward, CA,USA) substrate utilization systems were used to give anindication of the ability of soil microbes to utilize variousC sources and to characterise community-level physiolo-gical profiles (CLPP), following a procedure adaptedfrom Garland and Mills (1991). Each microplate con-tained 96 holes with three replicates of 31 different singleC sources and one blank well per replicate. The 31 Csources substrates represented six classes of organic com-pounds: amino acids, amines, polymers, carboxylic acid,carbohydrate and miscellaneous (Insam 1997).Three replicates of fresh soil from each treatment (each

about 10 g in dry weight) were centrifuged with 100 mLof autoclave-sterilised saline solution [0.85% sodiumchloride (NaCl), weight/volume] in a 250-mL flask for30 min and a final dilution of 10−3 was used to inoculatethe Biolog-ECO microplates. Aliquots (150 µL) of thesuspension were inoculated into the Biolog-ECO platesand incubated in the dark at 25°C for 10 d. The colordevelopment was read as the absorbance of each of thewells at 590 nm after incubation for 0, 24, 48, 72, 96,120, 144, 168, 192, 216 and 240 h. The average wellcolor development (AWCD) reflects the individual Csource utilization ability of the soil microbial communityand was used accordingly as an indicator of total micro-bial activity (Zabinski 1997; Classen et al. 2003). In thisstudy, the AWCD was calculated as:

AWCD ¼X

Ci� Rð Þ=31 (3)

where Ci refers to the 31 absorbance values of the dif-ferent C sources and R is the absorbance reading of theassociated blank well.In this study, the four treatments had different AWCD

curves as incubation time increased from 0 to 240 h;

Soil biological properties of conservation tillage 313

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however, the rate of increase slowed after 144 h in alltreatments. The AWCD curve in the R0 treatmentincreased sharply before 144 h, and then increasedslowly after 144 h, indicating that measurement at144 h of incubation time would permit better discrimi-nation of individual C source utilization amongst thedifferent soil samples. Previous studies using Biologassay have reported results at 144 h (Castaldi et al.2009) and 72 h (Larkin 2003; Zhou et al. 2008) undersimilar criteria. Therefore, the AWCD values at 144 hwere used for the following indices and substrate utiliza-tion calculations.Shannon’s diversity index (H) is often used to describe

the variety indices of a biocommunity, as a measure ofactual richness and evenness of bacterial populations(Garland 1996). It was calculated according to the fol-low equation (Zak et al. 1994):

H ¼ �X

Pi � lnPi (4)

where Pi is the proportional optical density value of eachwell where

Pi ¼ Ci� R=X

Ci� Rð Þ (5)

Substrate richness (S) is the number of positive(AWCD is equal to or greater than 0.2) wells on theBiolog-ECO plate, which can reflect the total number ofC substrates utilized in general and is defined as thenumber of different microorganisms present (Cai et al.2010).

The McIntosh diversity index (U) is used to describethe evenness of soil microbe response, and can reflect theconformance of microbial activity (Xu et al. 2008). Itwas calculated as:

U ¼ pXCi� Rð Þ2 (6)

Statistical analysisGrain yield, SMB-C, SMB-N, soil respiration and micro-bial community data were analysed statistically. Thesignificances of the no tillage (T0) and tillage (T1) andcrop residue removal (R0) and residue retention (R1)main effects and their interactions were tested by two-way analysis of variance (ANOVA) using GenstatDiscovery Edition. Principal component analysis (PCA)of single C source utilization patterns by topsoil micro-organisms at 144 h of incubation time across two cropresidue treatments was performed.

RESULTS

Crop yieldTable 1 shows the average grain and residue yields of thethree crops from 2001 to 2009. Maize mean grain yieldswere significant influenced by tillage and residue manage-ment. Tillage resulted in larger (P < 0.05) meanmaize grainyields (9113 kg ha−1) than no tillage (8550 kg ha−1), andretention of the preceding crop’s residues also significantly(p < 0.05) increased mean maize grain yields, from 8573 to9090 kg ha−1.Mean soybean grain yields were significantly

Table 1 Average grain yield (kg ha−1 y−1) and residue yield (kg ha−1 y−1) of maize (Zea mays L. cv Zhongdan No. 2), wheat(Triticum aestivum L. cv Xifeng No. 24) and soybean (Glycine max L. cv Fengshou No. 12) under different tillage and crop residuetreatments, from 2001 to 2009 on the Loess Plateau, China

Maize Wheat Soybean

TreatmentGrain yield(kg ha−1)

Residue yield(kg ha−1)

Grain yield(kg ha−1)

Residue yield(kg ha−1)

Grain yield(kg ha−1)

Residue yield(kg ha−1)

No tillage 8550 ± 193 6807 ± 219 3161 ± 42 4551 ± 111 885 ± 130 939 ± 79Tillage 9113 ± 170 6434 ± 225 3245 ± 89 4615 ± 224 905 ± 64 1411 ± 143Tillage Effect * ns ns ns ns *

Residue removal 8573 ± 175 6356 ± 163 3135 ± 70 4343 ± 113 743 ± 72 1092 ± 117Residue retention 9090 ± 198 6885 ± 249 3271 ± 63 4823 ± 183 1046 ± 95 1257 ± 164Residue Effect * ns ns ns * nsTillage × Residue ns ns ns ns ns ns

The cropping system was a maize–winter wheat-soybean rotation with one rotation completed every two years from 2001 to 2009. The grain and residue yieldvalues are the average yield of maize, winter wheat and soybean for the 9 years.No tillage: no soil disturbance except for crop planting; tillage: conventional tillage (tilled twice a year to 20 cm); residue removal: all residues removed after cropharvest; residue retention: all the wheat and soybean residues, 50% maize residues were retained after crop harvest.Mean values for replicates ± standard error.ns, not significant (P > 0.05).* Significance level: P ≤ 0.05.** Significance level: P ≤ 0.01.*** Significance level: P ≤ 0.001.

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(p < 0.05) increased by retaining the preceding crop’s resi-dues, from 743 to 1046 kg ha−1, and tillage had largersoybean residue yields (1411 kg ha−1) compared to notillage (939 kg ha−1), however, the average grain and resi-due yields of the winter wheat from 2001 to 2009 were notinfluenced by tillage and residue treatments. There was nosignificant interaction between tillage and residue manage-ment for the average grain and residue yields over the 9-yperiod. Overall, tillage resulted in a significant but smallyield benefit compared to no tillage, and residue retentionincreased average grain yields except for winter wheat inthis rotation.

Soil chemical and biological propertiesAfter 9 y, the tillage and residue treatments had signifi-cant effects on the chemical and biological properties ofthe topsoil (Table 2). TN, OC, MB-N and MB-C signifi-cantly decreased when the soil was tilled compared to theno-tillage treatment (P < 0.01). These soil propertieswere significantly increased by retaining previous cropresidues (p < 0.05).However, withholding tillage and retaining crop resi-

dues significantly decreased soil respiration rate, qCO2

and soil temperature in 0–10 cm (Table 2). There was atrend for increased soil respiration under tillage, being31% higher under tillage compared to no-tillage treat-ments, whereas residue retention reduced the respirationrate 10.9% compared to residue removal. No tillage andcrop residue retention had significant interaction effectson soil respiration rate (P < 0.05). Soil respiration ratewas significantly lower under conventional tillage withresidue retention treatment.

Soil microbial community functional propertiesDuring the first 24 h of incubation, the values of AWCDunder different managements were small with all absor-bencies being below 0.4 (Fig. 1). Their values increasedrapidly with incubation time increasing for all treatmentsreflecting the microbial utilization of each group of sub-strate. There was a significant effect of crop residueretention, but no significant difference between tillagetreatments for incubation times > 24 h (P < 0.01). Thevalues of AWCD for the residue retention treatmentswere always higher than with crop residue removal treat-ments and the difference increased with increasing incu-bation time; the largest difference of AWCD valuereached 1.15 (p < 0.001) (Fig. 1b).Retention of crop residues significantly (P < 0.01)

increased the Shannon, substrate richness andMcIntosh indices of microbial community functionaldiversity. Differences in microbial community functionaldiversity were not significant between conventionalT

able

2Two-way

analysisof

varian

ce(A

NOVA)forallsoilc

hemical

andbiolog

ical

prop

erty

parametersan

alyzed

intopsoilu

nder

differenttilla

gean

dcrop

residu

etreatm

ents

sampled

atmaize

harvestin

a9-year

maize

(Zea

may

sL.cv

Zho

ngda

nNo.

2)-w

heat

(Triticum

aestivum

L.cv

XifengNo.

24)-soyb

ean(G

lycine

max

L.cv

Feng

shou

No.

12)

rotation

ontheLoess

Plateau,

China

Treatment

TN

(gkg

−1)

OC

(gkg

−1)

MB-N

(mgkg

−1)

MB-C

(mgkg

−1)

Soilrespirationrate(μmolCO

2m

−2s−

1)

qCO

2(m

gCO

2g−

1M

B-C

d−1)

Soiltemperature(°C)

Notilla

ge0.79

±0.01

9.37

±0.26

72.20±2.22

170.30

±12

.96

1.51

±0.03

43.61±4.45

15.33±0.37

Tillag

e0.68

±0.03

8.35

±0.26

63.90±2.66

128.70

±10

.56

1.98

±0.09

78.47±13

.31

16.08±0.21

Tillag

eEffect

***

***

****

***

***

***

Residue

remov

al0.70

±0.03

8.23

±0.21

63.50±2.83

130.70

±13

.64

1.84

±0.13

73.99±10

.03

15.88±0.54

Residue

retention

0.77

±0.02

9.49

±0.23

72.60±1.76

168.30

±10

.77

1.64

±0.07

48.08±6.23

15.53±0.32

Residue

Effect

****

***

**

***

Tillag

e×Residue

nsns

nsns

*ns

ns

TN:totalnitrog

en;OC:organiccarbon

;MB-N

:microbial

biom

assnitrog

en;MB-C

:microbial

biom

asscarbon

;qC

O2:soilmetab

olic

quotient;no

tilla

ge:no

soildisturba

nceexcept

forcrop

plan

ting

;tilla

ge:

conv

ention

altilla

ge(tilled

twiceayear

to20

cm);residu

eremov

al:a

llresidu

esremov

edaftercrop

harvest;residu

eretention:

allthe

wheat

andsoyb

eanresidu

es,5

0%maize

residu

eswereretained

aftercrop

harvest.

Meanvalues

forreplicates

±stan

dard

error.

ns,no

tsign

ificant

(P>0.05

).*Sign

ificancelevel:P≤0.05

.**

Sign

ificancelevel:P≤0.01

.**

*Sign

ificancelevel:P≤0.00

1.

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tillage and no tillage except for the McIntosh index;there was no interaction effect to be found for allindices (Table 3).The utilization of amino acids, amines, polymers,

carboxylic acids, and carbohydrates by topsoil micro-organisms was significantly (P <0.05) greater withcrop residue retention than those with residuesremoved, with increases of 58%, 237%, 38%, 45%and 108%, respectively (Table 4). The utilization ofcarbohydrates was also affected by tillage manage-ment and a significant interaction effect of the cropresidues and tillage managements was found(P < 0.05). There was no significant tillage effect onthe utilization of the other five C source groups. Theutilization of miscellaneous sources was not signifi-cantly changed by applying tillage and residuemanagements.The C source utilization patterns of soil microorgan-

isms were measured by PCA, using the AWCD at 144 hof incubation (Fig. 2). For the tillage management sam-ples, PCA could not clearly separate the tillage and no-tillage samples (Fig. 2a). For the residue managementsamples, PC1 and PC2 accounted for 35% and 16% ofthe total variation in AWCD, respectively. The residuesretention treatments were distributed on the positive axisof PC1, compared to the residue removal treatments onthe negative axis, which clearly divides substrate utiliza-tion patterns of the microbial community under the tworesidues treatments (Fig. 2b). The score coefficients ofPC1 and PC2 showed significant differences betweentwo treatments (P < 0.001). The substrate types thathad loading coefficients of PC1 and PC2 greater thanor equal to 0.80 were obtained using the dependencymatrix of the PCA. The variability in PC1 was explainedby the utilization of carbohydrates and polymers, (N-acetyl-D-glucosamine, Tween 80, D-Mannitol). The

a

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

0 24 48 72 96 120 144 168 192 216 240

0 24 48 72 96 120 144 168 192 216 240

Incubation time (h)

AW

CD

T0 T1

b

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

Incubation time (h)

AW

CD

R0 R1

Figure 1 Variation of average well color development (AWCD)values for (a) no tillage (T0) and tillage (T1) and (b) residue removal(R0) and residue retention (R1) as a function of incubation time,from topsoil sampled at maize harvest after 9-year maize (ZeamaysL. cv Zhongdan No. 2)-wheat (Triticum aestivum L. cv Xifeng No.24)-soybean (Glycine max L. cv Fengshou No. 12) rotation on theLoess Plateau, China. T0: no soil disturbance except for crop plant-ing; T1: conventional tillage (tilled twice a year to 20 cm); R0: allresidues removed after crop harvest; R1: all the wheat and soybeanresidues, 50% maize residues were retained after crop harvest.Error bars indicate standard error of replicates.

Table 3 Topsoil microbial community functional indices of average well color development (AWCD) at 144 h incubation of soilextracts, under different tillage and crop residue treatments sampled at maize harvest in a 9-year maize (Zea mays L. cv ZhongdanNo. 2)-wheat (Triticum aestivum L. cv Xifeng No. 24)-soybean (Glycine max L. cv Fengshou No. 12) rotation on the Loess Plateau,China

Treatment Shannon’s diversity index(H) Substrate richness(S) McIntosh index(U)

No tillage 3.17 ± 0.02 26 ± 1 6.67 ± 0.57Tillage 3.16 ± 0.03 27 ± 1 7.21 ± 0.64Tillage Effect ns ns *

Residue removal 3.12 ± 0.01 25 ± 0 5.36 ± 0.13Residue retention 3.20 ± 0.02 28 ± 1 8.52 ± 0.17Residue Effect ** *** ***Tillage × Residue ns ns ns

No tillage: no soil disturbance except for crop planting; tillage: conventional tillage (tilled twice a year to 20 cm); residue removal: all residues removed after cropharvest; residue retention: all the wheat and soybean residues, 50% maize residues were retained after crop harvest.Mean values for replicates ± standard error.ns, not significant (P > 0.05).* Significance level: P ≤ 0.05.** Significance level: P ≤ 0.01.*** Significance level: P ≤ 0.001.

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variability in PC2 was explained by the utilization ofpolymers, (a-cyclodextrin and Tween 40).

DISCUSSION

Retention of crop residues significantly increased soilmicrobial activity and functional diversity compared tocrop residue removal, indicating that residue retentionis the key to improving soil biological fertility on thisLoess soil rather than the elimination of tillage. Thetendency was also found on crop yield, which is areasonable hypothesis that enhanced soil conditionsfor increased microbial community function contributeto increased crop yield (Zhang et al. 2012). This con-clusion was further reinforced by the similar perfor-mance of the crop residue removal treatments withand without tillage, indicating that under these soilsand management conditions tillage per se was not asignificant influence on soil functionality microbialecology.

Effect on soil C, N fertilityBoth residue retention and no-tillage practices increasedsoil total N and organic C, with an observed increase ofup to 15% soil N under no-tillage compared to that intillage treatments, and a 9.6% increase in soil N underresidue retention compared to residue removal. Previousstudies have consistently demonstrated that residueretention increases soil C and N stocks and that conser-vation tillage can also minimise soil N losses (Govaerts etal. 2006; Ke and Scheu 2008). Furthermore, Dolan et al.(2006) reported that after 23 y of no tillage or residueretention practices, that soil N in the 0–20 cm layer wasincreased compared with conventional tillage in a silt

loam, demonstrating the long-term advantages of con-servation tillage on soil N content.SMB-N and SMB-C are sensitive indicators of soil

quality and are closely related to soil fertility. HigherSMB-C in soils can be explained with high organic C inthe soil (Flieβbach and Mäder 2000). SMB-N effectivelypredicts overall fertility and productivity of a croppingsystem (Bending et al. 2004). Tillage significantlyreduced SMB-C in the topsoil compared with that inthe no-tillage treatments, although other research indi-cates that there is little change in available C as a sourcefor microbial use after soil disturbance (Calderón et al.2000; Spedding et al. 2004). The treatments in whichresidues were retained contained significantly moreSMB-C and SMB-N. It corresponded with higher soilmicrobial activity and high grain yields in a maize-wheat-soybean rotation system (Nair and Ngouajio2012). The result is due to the favourable conditionsfor microbial growth, as residue retention provides anincreased supply of energy, nutrients and water (Zhouet al. 2007), and previous research supports this conclu-sion (Spedding et al. 2004).It was found that no tillage and residue retention both

significantly decreased soil respiration rate. Especially,soil respiration rate was significantly lower under tillagewith residue retention treatment, suggesting that residueretention mainly alleviates soil respiration and promotesC storage. Soil respiration rates are influenced by a rangeof factors, including soil temperature, soil water content,vegetation types, topography, soil texture (Li et al. 2008)and soil microorganisms (Kuzyakov 2006), of which soiltemperature was the most influential (Laganière et al.2012). The positively exponential correlation betweensoil temperature and respiration has been demonstratedpreviously (Chen et al. 2000; Laganière et al. 2012). It

Table 4 Six types of substrate-utilisation of topsoil microbial communities at 144 h incubation under different tillage and cropresidue treatments sampled at maize harvest in a 9-year maize (Zea mays L. cv Zhongdan No. 2)-wheat (Triticum aestivum L. cvXifeng No. 24)-soybean (Glycine max L. cv Fengshou No. 12) rotation on the Loess Plateau, China

Treatment Amino acids Amines Polymers Miscellaneous Carboxylic acids Carbohydrates

No tillage 1.15 ± 0.12 0.83 ± 0.21 1.23 ± 0.13 0.63 ± 0.08 0.87 ± 0.09 1.12 ± 0.18Tillage 1.28 ± 0.16 0.75 ± 0.23 1.10 ± 0.08 0.69 ± 0.13 0.97 ± 0.10 1.27 ± 0.20Tillage Effect ns ns ns ns ns ***

Residue removal 0.94 ± 0.09 0.36 ± 0.02 0.98 ± 0.08 0.54 ± 0.09 0.75 ± 0.05 0.78 ± 0.03Residue retention 1.48 ± 0.06 1.22 ± 0.16 1.35 ± 0.08 0.78 ± 0.10 1.09 ± 0.07 1.61 ± 0.07Residue Effect ** ** * ns ** ***Tillage × Residue ns ns ns ns ns *

No tillage: no soil disturbance except for crop planting; tillage: conventional tillage (tilled twice a year to 20 cm); residue removal: all residues removed after cropharvest; residue retention: all the wheat and soybean residues, 50% maize residues were retained after crop harvest.Mean values for four replicates ± standard error.ns, not significant (P > 0.05).* Significance level: P ≤ 0.05.** Significance level: P ≤ 0.01.*** Significance level: P ≤ 0.001.

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has been described extensively that soil temperatureexerted dominant control over variations of soil respira-tion when soil moisture was relatively stable (Fang andMoncrieff 2001; Li et al. 2010). The residue retentionand no-tillage treatments reduced soil temperatures com-pared to residue removal and tillage treatments,

consistent with reports from previous studies (Licht andAl-Kaisi 2005; Wang et al. 2012). qCO2 represented soilC availability to microorganisms, which depends on soilnutrient status (Wardle and Ghani 1995). No tillage andresidue retention both decreased qCO2, which is attrib-uted to higher nutrient availability for microorganisms(Li et al. 2007). It may improve soil fertility, which isconsistent with the findings by Wang et al. (2008). It alsomay be due to the fact that the no-tillage and residueretention treatment had a higher efficiency of substrate Cuse by fungal flora in comparison with bacterial flora(Sakamoto and Oba 1994).

Effect on soil microbiologyAWCD is an important indicator of net soil microbialcommunity activity reflecting the utilization ability ofsingle C sources. The high AWCD value under cropresidue retention treatments indicates that this practicecan increase total microbial activity in the top layer ofLoess soil. Residue retention benefits the soil by moder-ating moisture and temperature variation across seasonsand has been reported to be favourable to microbialgrowth in soil (Mendham et al. 2003; O’Connell et al.2004). The Shannon (H) and McIntosh indices (U) canprovide an indication of the soil microbial biocommunityand biodiversity while the richness (S) index providesinsight into the diversity of microorganisms. It wasfound that all three indices were increased by crop resi-due retention, suggesting that the structure of the soilmicrobial communities may be altered by residueretention.Retaining residue on the soil surface significantly

increases most C sources, reflecting organic C accumula-tion and the provision of increased substrate supply formicroorganisms. Other studies have also shown thatapplying conservation management practices increasedmicrobial diversity as a result of increased organic Cfrom retaining residues (Entry et al. 2004). Similarly,regular addition of soil organic matter may increasebackground levels of microbial activity, increase nutrientcycling, decrease the concentrations of easily availablenutrient sources and increase microbial diversity (vanBruggen et al. 2006). Usability of soil carbohydrates isa useful indicator of changes in soil organic matter status(Hu et al. 1995), and it has been reported that carbohy-drates may represent up to 75% of the total organic C ofthe soils in some environments and are a key componentof the C cycle (Mager 2010). As such, when the soilmicrobial community is provided with increased carbo-hydrates from residue retention, activity and functionaldiversity increases with adaptations for greater carbohy-drate utilization, leading to increased C cycling and soilfertility.

Figure 2 Principal component analysis of single carbon sourceutilisation patterns by topsoil microorganisms at 144 h incubationtime for (a) no tillage (T0) and tillage (T1) and (b) residue removal(R0) and residue retention (R1) at maize harvest after 9-year maize(Zeamays L. cv ZhongdanNo. 2)-wheat (Triticum aestivum L. cvXifeng No. 24)-soybean (Glycine max L. cv Fengshou No. 12)rotation on the Loess Plateau, China. The percentage of variationis expressed along the two main principal component axes. PC1:the first principal component; PC2: the second principal compo-nent. T0: no soil disturbance except for crop planting; T1: conven-tional tillage (tilled twice a year to 20 cm); R0: all residues removedafter crop harvest; R1: all the wheat and soybean residues, 50%maize residues were retained after crop harvest.

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The positional differences of various samples in thePCA of Biolog-ECO metabolic fingerprints are relatedto the ability of soil microorganisms to use C substrates(Garland and Mills 1991). Residue retention treatmentswere distributed on the positive axis compared to theresidue removal treatments on the negative axis, with thescore coefficients being significantly different, whichlikely occurred as a result of crop residue retentiongreatly contributing to topsoil nutrients by microbialdecomposition. This result supports the hypothesis thatthe use of crop residues would significantly impact top-soil microbial function. The outcome is consistent withMyers et al. (2001), who stated that differences in micro-bial functional diversity could be attributed to variationsin plant litter quality and substrate inputs to the soil inforest ecosystems. The abundant resources and fastnutrient turnover in residue retention treatments mightcontribute to the changes in microbial functional diver-sity (van Bruggen et al. 2006), and suggest that themicrobial decomposition pathway is relatively moreimportant in the presence than in the absence of residue.In this study, the levels of carbohydrate and polymerutilization (PC1 values), including D-Mannitol, N-acetyl-D-glucosamine and Tween 80, were higher withresidue retention. D-Mannitol constitutes half of thehemicellulose monomer, which is the major constituentof plant cell walls, widely distributed in plant residues ofnatural ecosystems, whereas Tween 80 is a kind of lipid.High lipid content in soils has been previously linked tohigher soybean grain yields (Zhang et al. 2009). Thismight be part of the explanation for the advantage ofsoybean and maize grain yields under residue retentionin this study, driven by enriched carbohydrates and poly-mers from residue retention.There was no significant tillage effect on soil micro-

bial activity and functional diversity, although no til-lage significantly improved soil chemical properties,consistent with the crop yield performance in this rota-tion system.The average grain yield of maize and soybean after 9 y

had a positive response to residue retention, althoughno-tillage treatments had no beneficial effect. A previouslong-term study elsewhere reported a much larger yieldpenalty of 30% after 14 y of no tillage compared toconventional tillage (Heenan et al. 1995). This suggeststhat the positive response of yield to conservation tillagewas delayed compared to changes in soil fertility. Thetrend of reduced yield under no-tillage was maintainedfrom 2004 until the end of the trial (Duan et al. 2010).Our variables, measured at 9 y after the commencement

of a long-term tillage and crop residue experiment, verifythat soil fertility, crop yields and soil microbial activitieswere all enhanced by retaining residues, indicating that alink between nutrient cycling, grain yield and soil

microbial community function exists. The mechanism bywhich these factors interact requires further study.

CONCLUSIONS

This study focused on the long-term effects of tillage andresidue retention on the functional diversity of the soilmicrobial community and on the soil’s chemical andbiological properties. It clearly demonstrates that reten-tion of crop residues can significantly improve soilmicrobial functional diversity, soil fertility and cropyield. Residue retention could overcome the negativeeffect of conventional tillage on the soil microbial com-munity, which is the most beneficial soil management tocontribute to sustainable agriculture on the Loess Plateaucompared to the conventional tillage system.

ACKNOWLEDGMENTS

This research is supported by the Keygrant Projectof the Chinese Ministry of Education (No. 313028),the National Basic Research Programme of China(2007CB106804), the Australian Centre forInternational Agricultural Research project (LWR/2007/191) and the Fundamental Research Funds forthe Central Universities of China (lzujbky-2012-218).

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