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Dynamics of bacterial communities during solid-state fermentation using agro-industrial

Dynamics of bacterial communities during solid-state fermentation using agro-industrial
Dynamics of bacterial communities during solid-state fermentation using agro-industrial

BIOTECHNOLOGICAL PRODUCTS AND PROCESS ENGINEERING

Dynamics of bacterial communities during solid-state fermentation using agro-industrial wastes to produce poly-γ-glutamic acid,revealed by real-time PCR and denaturing gradient gel electrophoresis (DGGE)

Xiaoyu Yong &Yaqing Cui &Lihua Chen &Wei Ran &Qirong Shen &Xingming Yang

Received:28March 2011/Revised:6May 2011/Accepted:6May 2011/Published online:14June 2011#Springer-Verlag 2011

Abstract The dynamics of bacterial communities play an important role in solid-state fermentation (SSF).Poly-γ-glutamic acid (γ-PGA)was produced by Bacillus amyloli-quefaciens C1in SSF using dairy manure compost and monosodium glutamate production residuals as basic sub-strates.The production of γ-PGA reached a maximum of 0.6%after 20days fermentation.Real-time polymerase chain reaction showed the amount of total bacteria reached 3.95×10916S rDNA copies/g sample after 30days,which was in good accordance with the 4.80×109CFU/g obtained by plate counting.Denaturing gradient gel electrophoresis profile showed a reduction of microbial diversity during fermentation,while the inoculum,B.amyloliquefaciens C1,was detected as the dominant organism through the whole process.In the mesophilic phase of SSF,Proteobacteria was the dominant microbial,which was replaced by Firmicutes and Actinobacteria in the thermophilic phase.The molecular analysis of the bacterial diversity has significant potential for instructing the maturing process of SSF to produce γ-PGA at a large-scale level,which could be a benefit in the production of high quality and stable SSF products.

Keywords Poly-γ-glutamic acid (γ-PGA).Solid-state fermentation (SSF).Real-time PCR .Denaturing gradient gel electrophoresis (DGGE).Dynamics of bacterial communities

Introduction

A naturally occurring anionic biopolymer,poly-γ-glutamic acid (γ-PGA),which was first discovered as a component in the capsules of Bacillus anthracis (Ivánovics and Erdos 1937),is water-soluble,biodegradable,edible,and non-toxic to human and the environment,making it useful for various applications in food,cosmetics,medicine,agriculture,and the environment (Shih and Van 2001;Ashiuchi 2010).Solid-state fermentation (SSF)has been employed to produce γ-PGA by several groups using soybean curd,sweet potato residues,wheat bran,diary manure,and swine manure alone or in combination as substrate (Chen 2005;Xu et al.2005;Wang et al.2008b ).A large amount of heat is generated during a large-scale SSF,which is the most critical factor for controlling SSF process,since temperature directly affected the growth,spore formation and germination,the metabolic rate,and the population structure of microbials (Pandey 2003;Sasaki et al.2005).Studies have reported that microorganism diversity is different during SSF process because of the initial materials and the fermentation process (Yu et al.2009;Wang et al.2008a ;Zhu et al.2003;Giraffa 2004).Therefore,it is necessary to detect the temperature as well as the microbial diversity during SSF.

Traditional analysis of the microbial diversity in SSF is primarily based on the selective-plating method (Strom 1985a ,b ).However,this culture-dependent technique is known to only detect 0.1%to 1%of the bacterial composition of the total microbial community (Head et al.1998;Amann et al.1995;Daniel 2005).In recent years,culture-independent methods based on molecular biology techniques,such as real-time polymerase chain reaction

X.Yong :Y .Cui :L.Chen :W.Ran :Q.Shen :X.Yang (*)Jiangsu Provincial Key Lab for Organic Solid Waste Utilization,Nanjing Agricultural University,Nanjing 210095,China

e-mail:xingming@https://www.doczj.com/doc/c18568203.html,

Appl Microbiol Biotechnol (2011)92:717–725DOI 10.1007/s00253-011-3375-3

(PCR)and denaturing gradient gel electrophoresis(DGGE), have provide new methods for analyzing the structure and species composition of complex microbial communities in a wide range of samples from soil(Innerebner et al.2006), compost(Danon et al.2008),and SSF products(Yu et al. 2009;Giraffa2004;Haruta et al.2006).

Althoughγ-PGA produced by fermentation(submerged fermentation and SSF)has been previously studied,it has only been performed with pure cultures of isolated strains.In this study,a large-scale SSF was conducted to produceγ-PGA by Bacillus amyloliquefaciens C1 using agro-industrial residues,such as dairy manure compost(DMC)and monosodium glutamate production residuals(MGPR)as basic substrates.Real-time PCR and DGGE were employed to enumerate the total bacteria and detect the microbial communities,respectively,which could lead to a good identification of the different SSF phases and a better determination of the maturing process at the scale-up level.

Materials and methods

The strain used in SSF

The strain B.amyloliquefaciens C1(China General Micro-biological Culture Collection Center(CGMCC)No.3478), isolated by our laboratory with a highγ-PGA production of 18.3g/L in SMF and4.37%in SSF(20g sterile substrate in 250-mL flask),was used in the present study.C1was inoculated into50-mL Luria-Bertani(LB)medium and cultivated on a rotary shaker at170rpm at37°C for14h (mid-log phase of C1)until the cell concentration(OD600) reached2.0.Then,the liquid culture of C1was sub-inoculated to1,000mL LB at a level of2%(v/v)and incubated under the same condition,which was inoculated into a100-L stirred-tank fermentor thereafter.Finally,the liquid seed culture (109–1010CFU/mL)was acquired by submerged fermenta-tion and used as the inoculum adsorbed with rice bran.

Solid-state fermentation(SSF)

The SSF experiment was performed in a private composting facility located in Yixing,Jiangsu Province,China.Seven thousand kilograms DMC supplemented with500kg wheat bran,300kg soybean cake,350kg corn flour,1,350kg MGPR,100kg citric acid,25kg MgSO4,and15kg MnSO4 were used as the substrate(initial moisture was adjusted to approximately50%),which was inoculated with C1at a1% inoculum concentration.

The windrows of SSF were collected and stirred with a shovel car on a concrete floor in a pile2m in diameter, 1.5m in height,and10m in length at the start of the experiment.The temperature in the center zones,the middle zones,and the exterior zones of the piles was measured every day.To increase aeration,the windrows were turned when the temperatures of the exterior zones reached approximately60°C.Samples were collected on days1, 2,4,6,10,14,20,and30and stored at?20°C.

Extraction ofγ-PGA

Fifty milliliters of deionized water was added to20g of fermented matter,and the mixture was agitated at150rpm at room temperature(approximately25°C)for2h.Forty milliliters of the slurry was subjected to centrifugation at 2,000rpm for5min to remove the SSF substrate.The supernatant was subjected to centrifugation at12,000rpm for10min.The resulting supernatant was poured into four volumes of cold ethanol to precipitate theγ-PGA,which was collected by centrifugation at12,000rpm for20min.A 5-mL aliquot of deionized water was added to dissolve the precipitate,and the resulting solution was stored at4°C. Production analysis ofγ-PGA

A2-mL aliquot of the crudeγ-PGA sample solution and 10mL6M HCl were added to a hydrolysis flask and hydrolyzed at110°C for24h under vacuum.The hydrolyzate was evaporated to dryness using a rotary evaporator,followed by the addition of1mL deionized water to dissolve the dry sample.The liquid sample was then filtered through a0.45-μm membrane filter.The final solution was analyzed by a Biochrom30Amino Acid Analyzer(GE,USA).The corresponding unhydrolyzed sample was also analyzed,and the difference in the concentration of free glutamic acid between these two solutions was considered to be theγ-PGA production.γ-PGA production was expressed as a percentage (%,w/w),which indicated the ratio of the weight ofγ-PGA to the sample.

Enumeration of the bacterial populations by plate count

Serial dilutions(10?1to10?8)of the fermented samples at different times were prepared in sterilized water(w/v).A 0.1-mL aliquot of a diluted mixture of10?6to10?8was spread onto LB plates in triplicate.After incubation at37°C for24h,the numbers of colonies on the plates were counted to calculate the number of CFU per gram(CFU=colony-forming unit).

Extraction of the total genomic DNA of SSF samples

The total genomic DNA of the SSF samples were extracted by the method previously described with small modifications (LaMontagne et al.2002)and stored at?20°C.The DNA

extracts were electrophoresed in1%agarose gel and stained with ethidium bromide(EtBr).

Real-time PCR

A pair of primers,P338-358F(5′-AC TCC TAC GGG AGG CAG CAG-3′)and P534-518R(5′-ATT ACC GCG GCT GCT GG-3′),against the V2–V3region of the16S rRNA gene of bacterial groups were used to estimate the total number of16S rRNA gene copies in this study(Ahn et al. 2009).Real-time PCR amplifications were conducted on a 7500Fast Real-Time PCR System(Applied Biosystems) using the SYBR?Premix Ex Taq?(Perfect Real Time)kit (Takara).The standard curves were generated according to Mieszkin et al.(2009).

PCR-DGGE

PCR on the DNA extracts was performed on a S1000?Thermal Cycler(Bio-Rad Laboratories,Richmond,CA, USA)with primers against the V6–V8region of the16S rRNA gene of bacterial groups.The nucleotide sequences of the primers were as follows:U968-GC(5′-GC-Clamp [CGC CCG GGG CGC GCC CCG GGC GGG GCG GGG GCA CGG GGG G]-AAC GCG AAG AAC CTT AC-3′) and L1401(5′-GCG TGT GTA CAA GAC CC-3′)(Zhu et al. 2003;Konstantinov et al.2003).The PCR amplification mixture consisted of5μl10×PCR buffer(Mg2+free),4μl MgCl2(25mM),4μl dNTP mixture(2.5mM each),

0.2μM of each primer,1μL of template DNA,and

1.25units of rTaq polymerase(Takara,Shiga,Japan);the solution was filled up to a volume of50μL with sterile water.The PCR amplification was performed at94°C for 5min,followed by32cycles of94°C for1min,54°C for 1min,and72°C for1min,and final single extension at 72°C for10min.

The DGGE analysis was conducted according to Muyzer et al.(1993)using a DCode system(Bio-Rad Laboratories, Hercules,CA,USA).The PCR products were loaded onto 8%(w/v)polyacrylamide gel(acrylamide:bisacrylamide-mixture37.5:1)with denaturant gradients ranging from 40%to65%[100%denaturant was7M urea plus40%(w/v) formamide].The electrophoresis was initiated by a pre-running step for10min at a voltage of200V;subsequently, the sample was run at a fixed voltage of80V for16h at 60°C.After electrophoresis,the silver staining procedure was performed as described by Bassam et al.(1991).

Sequencing of the excised band from the DGGE gel

Each dominant DGGE band was excised,and the DNA was extracted in50-μl sterile water at4°C overnight.The supernatant(1μl)was used as the template in the re-amplification PCR reaction mixture with the primer set U968and L1401without a GC clamp.The nucleotide sequences sequenced by Genescript Company(Nanjing, China)were aligned in GeneBank(http://blast.ncbi.nlm.nih. gov/)using the BLAST program,and the most homologous sequences were downloaded for multiple-sequence alignments using ClustalX.A phylogenetic tree was constructed using the neighbor-joining method by MEGA software(Version4.1Beta),and1,000bootstraps were employed to assign confidence levels to the nodes in the tree(Asano et al.2010).

Nucleotide sequence accession numbers

The nucleotide sequences of the DGGE bands excised from the DGGE gel reported in this paper have been deposited in the GenBank databases under the following accession numbers:JF706289–JF706308.

Results

Solid-state fermentation

Changes in the temperature of the SSF process are shown in Fig.1,which was identified by an initial short mesophilic period(1–3days),followed by a long thermophilic period (4–29days)and a curing period with a decrease in temperature(30–33days).The temperature of the exterior zones was much higher than that of the middle and the center zones,and a large amount of heat is generated during

Day

T

e

m

p

e

r

a

t

u

r

e

Fig.1Changes in temperature during the solid-state fermentation processes.Temperature were obtained from the exterior zones(filled diamond),the middle zones(filled square),and the center zones(filled triangle),respectively,of the windrows

the SSF process.The highest temperature was recorded as 70.3°C in the exterior zones at 26days.The production of γ-PGA produced in SSF

There was a lag phase up to 4days of the growth of bacteria,after which,the exponential growth phase was observed with a rapid increase in the biomass.The number of viable cells reached a maximum of 4.8×109CFU/g at 30days (Table 1).The increase in γ-PGA production closely followed the growth pattern of the bacteria,which reached a maximum of 0.6%after 20days (Table 1)when the function microbial,strain C1,had established itself in the deeper layers of the substrates of the SSF.Real-time PCR

The standard curves used to quantify the 16S rRNA gene copies of the samples were generated by plotting threshold cycles against the logarithm of the initial number of DNA;these initial values were harbored by the target 16S rRNA gene using serial dilutions of a known concentration of the plasmid DNA as template in real-time PCR analysis beginning with 5.95×107copies/mL and continuing to 5.95×103copies/mL.Each reaction was performed in triplicate,and a high reproducibility between these three independent standard dilutions was obtained.The quantification showed a good linear rela-tionship (R 2=0.999)ranging from 5.95×107gene copies to 5.95×103gene copies of the target gene (Fig.2).In the range of the detection concentration,the real-time PCR efficiency was calculated as 1.06based on the equation Amplification Efficiency ?10à1=slope à1(Bustin et al.

2009).In the standard samples,a melting curve with a single melting peak was detected at 86.1°C,and no primer dimers or other unspecific PCR products were amplified,which indicated that the presence of a single amplicon in the real-time PCR analysis was accurate (date not shown).Table 1shows that 2.203×10916S rDNA gene copies/g sample was detected at the start of the SSF.Once the SSF was conducted,it increased steadily.At the end of the SSF,the 16S rDNA copies of total bacteria were 3.948×109copies/g sample,which was in good accordance with the results obtained by plate counting.PCR-DGGE

The dynamic change of the structure of the microbial community during the SSF process was detected by PCR-DGGE analysis (Fig.3),which showed a clear reduction of microbial diversity during fermentation and remained stable in the late phase of fermentation based on the DGGE banding patterns.Bands 2,8,10,13,and 19,which could be detected throughout the whole period of fermentation,seemed to be the main functional bacteria during the fermentation process.Some of the original bands (5,6,and 17)disappeared after 4to 6days,indicating either the substrates were not suitable as energy sources for these bacteria or their growth was inhibited by the SSF process,such as high temperature.Seven novel bands appeared in the DGGE profiles,and they were detected at different times and temperatures during the process of SSF.Bands 1,3,7,9,and 14emerged at the start of the SSF and throughout the whole process;the bands increased in intensity to become the major bands by day 6.Band 15appeared at day 10and band 16appeared at day 14,which remained weakly visible thereafter.Bands 4and 11were detected at day 2but disappeared at day 10,which indicated that these two bacteria could not survive at high temperatures.Bands 12and 20appeared in the raw substrate at a high denaturing gradient area,which could not be detected at the early stages of the SSF process,appeared again at the middle and late process.

Twenty dominant DGGE bands obtained with primer set U 968–L 1401were isolated and sequenced.Phylogenetic analyses showed that these 20sequences were grouped into 6phyla (Fig.4).Bands 2(JF706290),7(JF706295),and 19(JF706307)were classified as Firmicutes Bacillales .Bands 6(JF706294),10(JF706298),12(JF706300),and 13(JF706301)were detected as Firmicutes Lactobacillales .Bands 1(JF706289),5(JF706293),14(JF706302),15(JF706303),18(JF706306),and 20(JF706308)were relatives of Actinobacteria Actinobacteridae .Bands 16(JF706304)and 9(JF706297);bands 3(JF706291),

4

1518

21

24

27

30

Log10 Copies

C t V a l u e s

Fig.2The standard curve of the real-time PCR generated by plotting the logarithm amount of the initial target copies against the threshold ranging from 5.95×107to 5.95×103gene copies.The quantification showed a good linear relationship (R 2=0.999).The qPCR efficiency was calculates as 1.06based on the equation Amplification Efficiency ?10à1=slope à1,where the slope referred to the log-linear portion of the calibration curve

(JF706292),8(JF706296),and 11(JF706299);and band 17(JF706305)were identified into the Proteobacteria Alphaproteobacteria ,Proteobacteria Deltaproteobacteria ,and Proteobacteria Gammaproteobacteria ,respectively.Band 2(JF706290),which can be detected during the whole SSF process and finally identified as B.amyloliquefa-ciens ,was the dominant organism of the function bacteria C1incubated in the SSF system.

Discussion

Solid organic waste produced by livestock and agro-industries may cause environmental pollution if not properly treated.The utilization of these waste materials can not only assist in eco-friendly treatments but also reduce production cost of microbial product in SSF (Rai et al.2009).So,in the present study,DMC,MGPR,corn flour,and soybean cake were selected as the basic substrates to produce γ-PGA in SSF.The DMC used in the present study contained 33.24%carbon and 1.97%total nitrogen,whereas the free glutamic acid content in MGPR was 9.04%,which indicated that the substrate provided abundant nutrition for the growth and production of γ-PGA of the C1strain.However,in-depth study to enhance γ-PGA production is needed in the following research since only 0.6%γ-PGA was obtained after 20days fermentation in the mixed culture.

Traditional analysis of the microbial diversity in SSF relies on culture-based techniques that are time-consuming and can detect only cultivable cells.In this study,the bacterial populations were enumerated by real-time PCR,which provided one of the most promising uncultured-dependent techniques on research of microbial https://www.doczj.com/doc/c18568203.html,pared with the results obtained by plate counting (Table 1),the results obtained by real-time PCR (3.948×10916S rDNA copies/g sample;Table 1)showed a slightly lower bacterial population.This may be caused by the reduction of nuclear acid in the manipulation of DNA extraction.

PCR-DGGE was employed to give an overall view of the variation of the dominant microbial community during the SSF period.Sequences retrieved from the DGGE profile primarily belonged to the phyla of Firmicute ,Actinobacteria ,and Proteobacteria ,which indicated that these bacterial communities were dominant in the SSF process (Figs.3and 4).To the best of our knowledge,this is the first culture-independent research study that involved dynamic change of the structures of the microbial communities during the SSF process,which produced γ-PGA.The DGGE profile showed that band

2

Fig.3Profiles of PCR-DGGE analyses of the bacterial community structure established with the U968-GC/L1401primer set.A linear denaturant gradients ranging from 40%denaturant at the top of the gel to 65%denaturant at the bottom [100%denaturant was 7M urea plus 40%(w /v )formamide]were https://www.doczj.com/doc/c18568203.html,ne CK means the sample loaded on the DGGE gel was the PCR product using the genome DNA extracted from the pure culture of Bacillus amyloliquefaciens C1as template

Sample (days)

γ-PGA production (%)

Total number of bacteria,CFU/g sample Copy numbers (copies/g sample)

10.02±0.003 2.43E+09±2.75E+08 2.203E+09±3.325E+0820.06±0.007 2.55E+09±1.39E+08 2.526E+09±6.302E+0740.12±0.009 2.74E+09±2.25E+08 2.645E+09±8.854E+0760.25±0.013 2.84E+09±1.87E+08 2.827E+09±6.519E+07100.46±0.011 3.83E+09±7.33E+08 3.002E+09±3.367E+07140.57±0.017 4.33E+09±5.16E+08 3.414E+09±1.421E+08200.60±0.016 4.44E+09±4.68E+08 3.827E+09±1.140E+0830

0.57±0.010

4.80E+09±

5.89E+08

3.948E+09±

4.680E+07

Table 1The γ-PGA production (percent)produced by solid-state fermentation,the total number of bacteria of the SSF samples enumerated by plate counting,and the copy numbers of the V2–V3region of the 16S rDNA gene copies (copies per gram sample)in the SYBR green real-time PCR assay

(JF706290)could be detected during the whole SSF process,which matched the strains of B.amyloliquefa-ciens C1.Thus,the C1strain used as the inoculum became dominant in the community of the SSF,which indicated that C1could be used as a fast adaptation or intrinsic preference for the nutritional and environmental needs

of

Fig.4Unrooted neighbor-joining tree representing the phylogenetic relationship of the 20cloned V6–V8region of 16S rDNA PCR-DGGE bands to the most closely related identified sequences downloaded from NCBI by BLASTn searches.The numbers at the nodes of the tree are bootstrap values for each node with 100bootstrap resampling.The bar represents 0.1substitutions per site

the bacteria during the SSF process.In the present study, some original bands disappeared during the fermentation process(bands5(JF706293),6(JF706294),and17 (JF706305)),suggesting either that they were not suitable for this SSF medium or that their growth was inhibited by the inoculated bacterial strain.

During the SSF process using agro-industrial waste and livestock manure as substrates,a large amount of ammonia-nitrogen(N)generated by the degradation of organic-N was lost in the solution and subsequent NH3emission(Asano et al.2010).Therefore,during the middle and late SSF processes,the fermentation properties could be characterized by the rise of pH(Maeda et al.2010).Bands3(JF706291),11 (JF706299),and17(JF706305),which were characterized as the pseudomonas-like species,were characterized by their connection with the NH3emission(Maeda et al. 2010)and could be detected in stages in which NH3was actively emitted(date not shown).

It is reported that there were two periods in which the structure of the microbial community shifted significantly according to the different temperature-dependent phases (Danon et al.2008);therefore,two different groups of microorganisms were involved in the SSF process:meso-philic and thermophilic microorganisms.The first period occurred during the first12to24h,when the SSF process was initially characterized by a short mesophilic period. During this period,the development of the mesophilic microbial community was very important because it determined whether a smooth transition from mesophilic to thermophilic period was successfully achieved(Nakasaki et al.1985),whereas the activity of mesophilic bacteria may be greatly decreased under a thermophilic temperature. During this period,the Alphaproteobacteria(Band16 (JF706304))in the raw materials was the dominant microbial,which was effective for mass reduction in DMC because of the higher decomposition activity of the microbial community characterized by the predominance of the Proteobacteria(Bands3(JF706291),4(JF706292), 8(JF706296),9(JF706297),11(JF706299),and17 (JF706305))(Tang et al.2007).Another period occurred during the first60to72h,when a sharp increase in temperature was detected(Fig.1)with the active degradation of the organic waste and an increase in the metabolic activity of the thermophilic bacteria;the SSF then made a rapid transition to the thermophilic phase (Fig.1).During this period,the total microbial diversity decreased(Fig.3),while the diversity of thermophilic bacteria increased(Finstein and Morris1975).Most of the species that were identified belonged to the Firmicutes phylum(Bands2(JF706290),6(JF706294),7 (JF706295),10(JF706298),12(JF706300),13 (JF706301),and19(JF706307))and Actinobacteria phylum(Bands1(JF706289),5(JF706293),14(JF706302),15(JF706303),18(JF706306),and20 (JF706308)).Because Firmicute phyla and Actinobacteria phyla typically include spore-forming bacteria(Fracchia et al.2006),they possess a high thermo-tolerance that can be detected during the thermophilic stage in SSF,which showed that they were active or at least survived the high temperatures.Most Firmicutes detected from the DGGE profile in the present study were identified as belonging to the Bacillus group.These results are in accordance with several research studies(Schloss et al.2003;Zhang et al. 2002)that have indicated that the thermophilic aerobic bacilli are important in classical composting processes. The Actinobacteria detected during the latter stages of the 10-day thermophilic composting process became active during the maturing period.Band18(JF706306),which was closely related to members of the Cellulomonas group in this study,revealed that the decomposition of cellulose was performed by cellulolytic bacteria during the SSF process(Tang et al.2006).Bands12(JF706300)and13 (JF706301),which were identified as the Lactobacillus and Lactococcus,respectively,were found at the beginning of the SSF process,when the substrate was relatively wet, and were reported as the typical dominant microorganisms in degrading plant material under conditions with limited oxygen(Peters et al.2000).Thus,they might have been alive in the center zones of the windrows but not able to tolerate the high temperatures.

Some common bacterial pathogens,such as Escherichia or Salmonella species,were not detected in the SSF samples.However,that did not indicated that the SSF bio-solids were Escherichia-and Salmonella-free,but only that they were not the dominant species;the increase in pH could have been elevated enough to discourage the growth of these bacterial species(Filion et al.2009).The DGGE profile and gel-sequencing analysis revealed that there were several species related to uncultured bacterial, such as Actinobacteria Actinobacteridae(Band5 (JF706293))and Proteobacteria Deltaproteobacteria (Band9(JF706297));the role of their relatives in natural environments is unknown.

Real-time PCR and PCR-DGGE have several draw-backs,such as the low purity of the template DNA and primer mismatch,which can result in a biased banding pattern within the DGGE gel.The deployment of next-generation DNA-sequencing technologies such as454 high-throughput sequencing has greatly enhanced capa-bilities to deeply survey the diversity and composition of the bacterial communities within an environmental sample(Petrosino et al.2009).Such method is valuable in that it could provide our best assessments of overall bacterial diversity and community structure and the relative abundances of specific bacterial taxa within SSF substrates(Lauber et al.2009).Therefore,this method

should be employed to analyze the microbial community in future studies.

Acknowledgements The study was financially supported by Chinese Ministry of Science and Technology(2011CB100503)and by Jiangsu Bureau of Science and Technology(BE2010722and BA2008027). References

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