microbial community structure in a biogas digester utilizing the marine energy crop saccharina...

8
ORIGINAL ARTICLE Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima Phillip B. Pope Vivekanand Vivekanand Vincent G. H. Eijsink Svein J. Horn Received: 26 September 2012 / Accepted: 5 October 2012 / Published online: 25 October 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract Seaweed is a highly attractive marine crop for the production of biofuels, due to its rapid growth rate as well as high polysaccharide and low lignin content. One appealing exploitation route is the production of biogas by anaerobic digestion. Interestingly, despite the composi- tional differences between seaweed and lignocellulosic biomass, available data indicate that conditions and inocula traditionally used for the latter may work well for seaweed. To gain more insight into the underlying microbial pro- cesses, we have generated 16S rRNA gene amplicon py- rosequencing data to comparatively describe microbial communities in biogas digesters containing either the sea- weed Saccharina latissima or wheat straw. The seaweed digesters gave better biogas yield and a higher relative abundance of core group Methanosaeta-affiliated Archaea. Conversely, variation in biomass had only minor abun- dance effects towards dominant bacterial lineages and influenced only low-abundant bacterial OTUs. Affiliations between dominant archaeal and bacterial phylotypes described here and previously identified anaerobic diges- tion core groups indicate that trends are beginning to emerge within these newly explored microbial ecosystems, the understanding of which is currently impeded by limited published datasets. Keywords Biogas Á Anaerobic digestion Á Seaweed Á Macroalgae Á Methane Biogas production, particularly in the purified form of bi- omethane, is seen as a vital component of renewable energy technologies due to the wide variety of organic sources that can be used and the compatibility of methane with existing energy infrastructure. Efforts to augment the biogas processes have focused on utilizing waste materials as well as alternative biomass substrates that lessen the impact on arable land. To that end, seaweed species have been identified as high potential substrates for biomethane production, due to their rapid growth rate as well as high polysaccharide (*60 %) and low lignin content (Horn 2009). Compared to organic waste streams and terrestrial biomasses, relative little is known on the anaerobic digestion (AD) of marine substrates. Available data for seaweed are, however, quite promising, in particular for the brown seaweed Saccharina latissima (Nielsen and Heiske 2011; Vivekanand et al. 2012). Seaweed is less recalcitrant than lignocellulosic materials meaning that thermal pre- treatments that are often used to speed up biogas processes can be milder, thus reducing the risk of inhibitor formation that is common during the harsher pretreatments (Viveka- nand et al. 2012). In this study, we report compositional and comparative analysis of the microbial communities in anaerobic digesters. 16S rRNA gene amplification for both bacterial and archaeal domains was performed to ensure that rep- resentatives for all the key metabolic stages of AD were enveloped, that is, polymer hydrolysis, sugar fermentation, acetogenesis (all Bacteria) and methanogenesis (Archaea). Samples were collected from three 1.1 L batch digesters run in triplicate for 119 days at 37 °C (stable pH 7.3 over the course of the experiment). All three digesters were inoculated with 600 mL of pre-incubated waste water sludge containing 10.5 g L -1 of volatile solids (VS) (Vivekanand et al. 2012), and were defined according to P. B. Pope (&) Á V. Vivekanand Á V. G. H. Eijsink Á S. J. Horn Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Post Office Box 5003, 1432 A ˚ s, Norway e-mail: [email protected] 123 3 Biotech (2013) 3:407–414 DOI 10.1007/s13205-012-0097-x

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Page 1: Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

ORIGINAL ARTICLE

Microbial community structure in a biogas digester utilizingthe marine energy crop Saccharina latissima

Phillip B. Pope • Vivekanand Vivekanand •

Vincent G. H. Eijsink • Svein J. Horn

Received: 26 September 2012 / Accepted: 5 October 2012 / Published online: 25 October 2012

� The Author(s) 2012. This article is published with open access at Springerlink.com

Abstract Seaweed is a highly attractive marine crop for

the production of biofuels, due to its rapid growth rate as

well as high polysaccharide and low lignin content. One

appealing exploitation route is the production of biogas by

anaerobic digestion. Interestingly, despite the composi-

tional differences between seaweed and lignocellulosic

biomass, available data indicate that conditions and inocula

traditionally used for the latter may work well for seaweed.

To gain more insight into the underlying microbial pro-

cesses, we have generated 16S rRNA gene amplicon py-

rosequencing data to comparatively describe microbial

communities in biogas digesters containing either the sea-

weed Saccharina latissima or wheat straw. The seaweed

digesters gave better biogas yield and a higher relative

abundance of core group Methanosaeta-affiliated Archaea.

Conversely, variation in biomass had only minor abun-

dance effects towards dominant bacterial lineages and

influenced only low-abundant bacterial OTUs. Affiliations

between dominant archaeal and bacterial phylotypes

described here and previously identified anaerobic diges-

tion core groups indicate that trends are beginning to

emerge within these newly explored microbial ecosystems,

the understanding of which is currently impeded by limited

published datasets.

Keywords Biogas � Anaerobic digestion � Seaweed �Macroalgae � Methane

Biogas production, particularly in the purified form of bi-

omethane, is seen as a vital component of renewable

energy technologies due to the wide variety of organic

sources that can be used and the compatibility of methane

with existing energy infrastructure. Efforts to augment the

biogas processes have focused on utilizing waste materials

as well as alternative biomass substrates that lessen the

impact on arable land. To that end, seaweed species have

been identified as high potential substrates for biomethane

production, due to their rapid growth rate as well as high

polysaccharide (*60 %) and low lignin content (Horn

2009). Compared to organic waste streams and terrestrial

biomasses, relative little is known on the anaerobic

digestion (AD) of marine substrates. Available data for

seaweed are, however, quite promising, in particular for the

brown seaweed Saccharina latissima (Nielsen and Heiske

2011; Vivekanand et al. 2012). Seaweed is less recalcitrant

than lignocellulosic materials meaning that thermal pre-

treatments that are often used to speed up biogas processes

can be milder, thus reducing the risk of inhibitor formation

that is common during the harsher pretreatments (Viveka-

nand et al. 2012).

In this study, we report compositional and comparative

analysis of the microbial communities in anaerobic

digesters. 16S rRNA gene amplification for both bacterial

and archaeal domains was performed to ensure that rep-

resentatives for all the key metabolic stages of AD were

enveloped, that is, polymer hydrolysis, sugar fermentation,

acetogenesis (all Bacteria) and methanogenesis (Archaea).

Samples were collected from three 1.1 L batch digesters

run in triplicate for 119 days at 37 �C (stable pH 7.3 over

the course of the experiment). All three digesters were

inoculated with 600 mL of pre-incubated waste water

sludge containing 10.5 g L-1 of volatile solids (VS)

(Vivekanand et al. 2012), and were defined according to

P. B. Pope (&) � V. Vivekanand � V. G. H. Eijsink � S. J. Horn

Department of Chemistry, Biotechnology and Food Science,

Norwegian University of Life Sciences,

Post Office Box 5003, 1432 As, Norway

e-mail: [email protected]

123

3 Biotech (2013) 3:407–414

DOI 10.1007/s13205-012-0097-x

Page 2: Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

the new substrate added (1.05 g VS added at day 0 and 67,

2.1 g VS total): inoculum containing no additional organic

substrate (IC), inoculum with seaweed (S. latissima,

IC ? SW) and inoculum with steam exploded wheat straw

(Triticum aestivum, IC ? WS). The total liquid volume in

all digesters was then adjusted to 700 mL by adding dis-

tilled water. Total methane production in IC ? SW

(223 ± 61 mL g-1 VS) was approximately twice as high

as in IC ? WS (98 ± 44 mL g-1 VS); note that SW and

WS materials have different C/N ratios of 8.8 and 98.4,

respectively (Vivekanand et al. 2012). For each digester,

sub-samples from each triplicate (equal volume) were

pooled, and DNA extraction was performed as described

by Rosewarne et al. (2010). Rrs genes were amplified using

the broadly conserved primer sets 27F-515R [Bacteria:

(Pope et al. 2012)] and 340F-1000R [Archaea: (Gantner

et al. 2011)], both containing the 454 Life Sciences primer

A sequence and a unique 8-nt multiplex identifier (Hamady

et al. 2008). Rrs gene sequences were quality filtered using

the QIIME software package (Caporaso et al. 2010), whilst

error correction and chimera removal were performed

using OTUPIPE which incorporates UCHIME (Edgar et al.

2011). Operational taxonomic units (OTUs) were clustered

at 97 % sequence identity using UCLUST software (Edgar

2010) and taxonomy was assigned using the Ribosomal

Database Project classifier (Cole et al. 2003). After filtering

and normalization (datasets randomly ‘‘subsampled’’ to

remove sample heterogeneity), 1,992 bacterial and 651

archaeal 16S rRNA sequences (in total) clustered into 63

and 14 OTUs, respectively (Table 1; Acc. Numbers

JX279942–JX280018). Rarefaction analysis showed that

the three digester datasets afforded a similar degree of

adequate coverage of bacterial biodiversity within each

digester (Fig. 1; Table 1). Moreover, Fig. 1 illustrated that

the addition of seaweed appears to reduce archaeal species

diversity.

Comparisons of the archaeal communities revealed that

OTUs ARC_nor-1, ARC_nor-2 and ARC_nor-3, affiliated

to the Taxonomic Order-ranks Methanosarcinales, Met-

hanomicrobiales and Methanobacteriales, respectively,

were dominant in all three samples (Fig. 2a–b). However,

their composition varied considerably depending on the

digester substrate (Fig. 2b–c). The increased dominance of

ARC_nor-1 in the IC ? SW digester coincided with higher

methane production [Fig. 2; (Vivekanand et al. 2012)], as

well as a slightly higher methane content in the biogas

(57 % vs. 53 % in IC ? WS). Affiliation of ARC_nor-1 to

an acetoclastic methanogen (Methanosaeta concilii; 98 %

ID) was also in agreement with Methanosaeta dominance

in AD communities that utilize freshwater algae substrates

(Ellis et al. 2012). In contrast, hydrogenotrophic metha-

nogens, of which ARC_nor-2 is putatively categorized,

were most dominant in the inoculum digester (IC), and

their relative abundance decreased in digesters containing

either IC ? WS or IC ? SW (Fig. 2b). Interestingly, both

ARC_nor-1 and ARC_nor-3 were affiliated (99 % ID;

Table 1) to previously described and repeatedly detected

core group phylotypes (OTU-VI and OTU-V, respec-

tively), which dominate sludge AD communities (Riviere

et al. 2009).

Spirochaetes, Bacteroidetes and Chloroflexi were the

dominant bacterial phyla in all three samples (Fig. 3a).

Dominance of these phyla, with the exception of the Spi-

rochaetes, is commonly observed in biogas processes

(Nelson et al. 2011), whilst the low relative abundance of

Proteobacteria- and Firmicutes-affiliated OTUs is in con-

trast with previous studies that have demonstrated their

abundance in AD reactors (Kampmann et al. 2012; Nelson

et al. 2011). The majority of the bacterial OTUs were

distantly related to cultured relatives, whereas close simi-

larities were observed with previous biogas microbial

community studies describing uncultured phylotypes

(Table 1). In particular, both BAC_nor-3 and BAC_nor-4

exhibited 99 % sequence identity to dominant Chloroflexi-

affiliated OTUs that have been previously defined as highly

prevalent core phylotypes involved in AD of sludge [Core

group a-III and a-VI; (Riviere et al. 2009)]. The repeated

detection of Chloroflexi-affiliated phylotypes in high

abundance within biogas processes points towards a sig-

nificant role and reveals a need for future investigations.

Several OTUs of lower abundance demonstrated marked

shifts depending on which substrate was present (Fig. 3b–

c). BAC_nor-13, a Petrobacter-affiliated betaproteobacte-

ria decreased approximately seven-fold in IC ? SW

digesters, whereas, the Bacteroidales-affiliated BAC_nor-

12 and Victivallis-affiliated BAC_nor-26 experienced an

eight-fold and nine-fold increase, respectively. The phe-

notype of BAC_nor-26 may be potentially interesting, as

Victivallis sp. isolates have previously been described as

capable of fermenting a variety of sugars including glucose

and mannitol [found in brown seaweed; (Horn and Ostg-

aard 2001)] subsequently producing acetate, H2 and etha-

nol as end-products (Zoetendal et al. 2003).

The present study shows that the microbial consortia

involved in AD of seaweed comprise deeply branched

OTUs. However, there are indications that trends in AD

microbial profiles are beginning to emerge with the

detection of several previously identified core group ar-

chaeal and bacterial phylotypes (Table 1; Riviere et al.

2009). Compared to the IC ? WS digester, the IC ? SW

digester showed some conspicuous differences, the most

prominent being an increase in methane production and the

relative abundance of the Methanosaeta concilii-affiliated

(presumably acetoclastic) ARC_nor-1. Given that metha-

nogens are believed to rely on syntrophic relationships with

bacteria for key metabolites (i.e., acetate, H2/CO2),

408 3 Biotech (2013) 3:407–414

123

Page 3: Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

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3 Biotech (2013) 3:407–414 409

123

Page 4: Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

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44

39

84

)

97

BA

C-1

71

53

p_

Aci

do

ba

cter

ia;

o_

Aci

do

ba

cter

iale

sH

olo

ph

ag

afo

etid

a(X

77

21

5)

80

Ox

icri

cefi

eld

soil

(AY

36

06

04

)9

9

BA

C-1

81

62

p_

Sp

iro

cha

etes

;f_

Sp

iro

cha

eta

cea

eS

pir

och

aet

ast

eno

stre

pta

str.

JCM

16

53

4

(AB

54

19

84

)

97

MF

Cri

ce(G

Q4

58

08

5)

99

BA

C-1

92

44

p_

Ba

cter

oid

etes

;o

_B

act

ero

ida

les

Eu

ba

cter

ium

sp.

str.

F1

(EU

28

18

54

)8

2W

WS

(CU

91

80

36

)9

9

BA

C-2

07

11

p_

Sp

iro

cha

etes

Tre

po

nem

ap

rim

itia

str.

ZA

S-1

(AF

09

32

51

)8

3W

WS

(JQ

10

65

78

)9

8

BA

C-2

10

36

k_

Ba

cter

iaS

pir

och

aet

axy

lan

oly

ticu

s(A

Y7

35

09

7)

78

WW

S(J

Q1

18

64

2)

99

BA

C-2

24

53

k_

Ba

cter

iaC

itri

cocc

us

sp.

str.

30

56

(AM

11

10

07

)7

5W

WS

(JQ

13

62

58

)9

9

BA

C-2

30

50

k_

Ba

cter

iaS

trep

tom

yces

sp.

str.

21

-4(A

B2

22

07

2)

77

WW

S(J

Q0

96

16

5)

99

BA

C-2

41

44

p_

Ba

cter

oid

etes

;

f_P

orp

hyr

om

on

ad

ace

ae

Ba

cter

oid

essp

.st

r.S

A-7

(AY

69

58

38

)8

8W

WS

(CU

92

02

78

)9

9

BA

C-2

51

00

p_

Sp

iro

cha

etes

;f_

Sp

iro

cha

eta

cea

eS

pir

och

aet

axy

lan

oly

ticu

s(A

Y7

35

09

7)

85

WW

S(J

Q1

59

99

5)

98

BA

C-2

60

09

p_

Len

tisp

ha

era

e;f_

Vic

tiva

lla

cea

eV

icti

vall

isva

den

sis

str.

AT

CC

BA

A-5

48

(NR

_0

27

56

5)

94

MF

Cp

alm

oil

mil

lef

flu

ent

(JF

30

91

89

)

99

BA

C-2

72

12

p_

Sp

iro

cha

etes

Sp

iro

cha

eta

xyla

no

lyti

cus

(AY

73

50

97

)8

5W

WS

(JQ

15

89

80

)9

8

BA

C-2

81

34

p_

Fir

mic

ute

s;c_

Clo

stri

dia

Ca

lora

ma

tor

sp.

str.

8(E

U6

21

40

6)

84

Fo

od

-pro

cess

ing

was

tes

(GU

38

98

08

)9

8

BA

C-2

91

24

p_

Sp

iro

cha

etes

;f_

Sp

iro

cha

eta

cea

eS

pir

och

aet

azu

elze

rae

(M8

87

25

)9

2W

WS

(JQ

11

13

24

)9

9

BA

C-3

02

04

p_

OP

8G

eob

aci

llu

sth

erm

od

enit

rifi

can

sst

r.B

GS

C9

4A

1

(AY

60

89

60

)

79

WW

S(G

Q4

80

15

4)

99

BA

C-3

13

10

p_

WS

1S

trep

tom

yces

sca

bri

spo

rus

(EU

84

17

00

)7

8W

WS

(CU

91

77

40

)9

9

BA

C-3

23

13

k_

Ba

cter

iaM

oo

rell

ath

erm

oa

ceti

cast

r.D

SM

74

17

(FJ8

88

65

4)

82

WW

S(J

Q0

96

45

8)

98

BA

C-3

31

30

p_

Ch

loro

flex

i;f_

An

aer

oli

na

cea

eT

her

mo

des

ulf

ob

ium

na

rug

ens

(AB

07

78

17

)8

0W

WS

(CU

92

73

49

)9

9

BA

C-3

40

31

p_

Ba

cter

oid

etes

;o

_B

act

ero

ida

les

Per

sici

virg

asp

.st

r.P

HS

CD

-1(H

M8

54

01

7)

80

WW

S(J

Q1

27

39

6)

99

BA

C-3

53

11

p_

Sp

iro

cha

etes

;f_

Sp

iro

cha

eta

cea

eS

pir

och

aet

axy

lan

oly

ticu

s(A

Y7

35

09

7)

85

WW

S(J

Q0

91

69

7)

99

BA

C-3

61

23

p_

Syn

erg

iste

tes;

f_S

yner

gis

tace

ae

Syn

erg

iste

ssp

.st

r.R

MA

16

08

8(D

Q4

12

71

8)

89

BR

(EF

58

35

00

)9

9

BA

C-3

71

02

p_

Pro

teo

ba

cter

ia;

f_S

yntr

op

ha

cea

eS

mit

hel

lap

rop

ion

ica

str.

LY

P(A

F1

26

28

2)

89

WW

S(J

Q0

99

71

3)

99

BA

C-3

82

20

p_

Pro

teo

ba

cter

ia;

f_S

yntr

op

ho

rha

bd

ace

ae

Myx

oco

ccu

sfu

lvu

sst

r.0

19

8-1

(EU

26

30

01

)8

0P

etro

leu

mre

serv

oir

(JN

62

79

45

)9

9

BA

C-3

91

22

p_

WS

1S

trep

taci

dip

hil

us

sp.

str.

Aac

-20

(AB

18

07

66

)7

9W

WS

(JQ

14

12

19

)9

9

BA

C-4

03

40

p_

Fir

mic

ute

s;c_

Clo

stri

dia

Ca

lora

ma

tor

sp.

str.

8(E

U6

21

40

6)

86

WW

S(C

U9

21

65

7)

99

BA

C-4

10

42

p_

SA

R4

06

Des

ulf

uro

mo

na

sa

cete

xig

ens

(U2

31

40

)8

0W

WS

(CU

92

29

95

)9

9

BA

C-4

21

02

p_

Sp

iro

cha

etes

;f_

Sp

iro

cha

eta

cea

eS

pir

och

aet

axy

lan

oly

ticu

s(A

Y7

35

09

7)

85

WW

S(J

Q1

58

98

0)

99

BA

C-4

32

01

p_

Pro

teo

ba

cter

ia;

f_C

om

am

on

ad

ace

ae

Aci

do

vora

xst

r.R

-25

07

5(A

M0

84

10

9)

98

Fre

shw

ater

spri

ng

(AB

42

50

64

)9

9

BA

C-4

40

41

p_

Ch

loro

flex

i;f_

An

aer

oli

na

cea

eC

lost

rid

ium

pro

teo

lyti

cum

str.

DS

M3

09

0

(X7

34

48

)

75

WW

S(C

U9

21

61

4)

99

410 3 Biotech (2013) 3:407–414

123

Page 5: Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

Ta

ble

1co

nti

nu

ed

IDIC

IC?

WS

IC?

SW

Co

nse

nsu

sL

inea

gea

Cu

lt_

rep

(Acc

.n

um

ber

)ID

(%)

Clo

ne_

rep

_en

v(A

cc.

nu

mb

er)

ID(%

)

BA

C-4

52

12

p_

Ch

loro

flex

i;f_

An

aer

oli

na

cea

eC

lost

rid

ium

bo

tuli

nu

mst

r.A

TC

C1

93

97

(CP

00

07

26

)

77

An

aero

bic

swin

ela

go

on

(AY

95

32

35

)9

7

BA

C-4

60

41

p_

Ch

loro

flex

i;f_

An

aer

oli

na

cea

eC

lost

rid

ium

dif

fici

lest

r.6

30

(NC

_0

09

08

9)

74

WW

S(J

Q1

37

63

3)

99

BA

C-4

70

05

p_

Sp

iro

cha

etes

;f_

Sp

iro

cha

eta

cea

eS

pir

och

aet

ast

eno

stre

pta

str.

JCM

16

53

4

(AB

54

19

84

)

89

WW

S(J

Q3

46

77

3)

99

BA

C-4

81

20

p_

Sp

iro

cha

etes

;f_

Sp

iro

cha

eta

cea

eT

rep

on

ema

pri

mit

iast

r.Z

AS

-1(A

F0

93

25

1)

89

WW

S(J

Q3

46

77

3)

99

BA

C-4

90

04

p_

Pro

teo

ba

cter

ia;

f_D

esu

lfo

vib

rio

na

cea

e

Des

ulf

ovi

bri

ost

r.D

s3(E

U3

26

02

9)

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BR

-car

rot

was

te(J

F5

33

85

0)

99

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C-5

05

00

p_

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iro

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etes

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iro

cha

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axy

lan

oly

ticu

s(A

Y7

35

09

7)

85

WW

S(J

Q1

58

98

0)

99

BA

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14

00

k_

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cter

iaS

pir

och

aet

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lan

oly

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s(A

Y7

35

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-co

nt.

soil

(HQ

68

92

00

)9

5

BA

C-5

22

10

p_

Ba

cter

oid

etes

;o

_B

act

ero

ida

les

Ca

pn

ocy

top

ha

ga

can

imo

rsu

sst

r.C

IP1

03

93

6

(AY

64

30

75

)

88

BR

-ref

use

(GQ

45

36

34

)9

4

BA

C-5

30

21

k_

Ba

cter

iaB

aci

llu

ssp

.st

r.JS

4(A

Y3

72

92

4)

83

WW

S(J

Q1

44

54

6)

10

0

BA

C-5

40

41

p_

Ch

loro

flex

i;f_

An

aer

oli

na

cea

eT

her

mo

des

ulf

ob

ium

na

rug

ense

DS

M1

47

96

(NR

_0

24

78

9)

77

WW

S(C

U9

18

06

0)

99

BA

C-5

52

00

p_

Act

ino

ba

cter

ia;

o_

Co

rio

Ba

cter

iale

sS

trep

tom

yces

sp.

str.

Z6

1(E

F0

12

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1)

85

Nat

ura

lg

asen

rich

men

t(E

U0

37

97

1)

99

BA

C-5

60

12

p_

Arm

ati

mo

na

det

esS

ymb

iob

act

eriu

mth

erm

op

hil

um

str.

IAM

14

86

3

(NC

_0

06

17

7)

76

Mic

rob

ial

mat

(FJ2

07

11

2)

84

BA

C-5

71

00

p_

Pro

teo

ba

cter

ia;

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yntr

op

ho

ba

cter

ace

ae

Syn

tro

ph

ob

act

ersu

lfa

tere

du

cen

sst

r.T

B8

10

6

(AY

65

17

87

)

99

WW

S(C

U9

23

99

2)

99

BA

C-5

81

02

p_

WS

1T

her

mo

act

ino

myc

essa

cch

ari

str.

KC

TC

97

90

(AF

13

87

37

)

81

BR

-bre

wer

yw

aste

(EF

51

56

25

)9

9

BA

C-5

92

10

p_

Ba

cter

oid

etes

;o

_B

act

ero

ida

les

Per

sici

virg

asp

.st

r.P

HS

CD

-1(H

M8

54

01

7)

79

Was

tesi

lkre

fin

ing

syst

em

(HQ

45

33

34

)

98

BA

C-6

00

12

k_

Ba

cter

iaA

list

ipes

pu

tred

inis

str.

AT

CC

29

80

0

(NR

_0

25

90

9)

76

WW

S(J

Q0

93

37

7)

95

BA

C-6

12

01

p_

Pro

teo

ba

cter

ia;

c_B

etaP

rote

ob

act

eria

Azo

nex

us

sp.

str.

HM

E6

65

4(H

M5

90

82

8)

99

WW

S(J

Q4

13

51

5)

99

BA

C-6

22

00

p_

Pro

teo

ba

cter

ia;

f_R

ho

do

cycl

acea

eR

ho

do

cycl

us

sp.

str.

HO

D5

(AY

69

14

23

)9

6W

WS

(JQ

17

72

98

)9

8

BA

C-6

30

30

p_

Pro

teo

ba

cter

ia;

f_C

om

amo

nad

acea

eA

cid

ovo

rax

sp.

str.

GP

TS

A1

00

-27

(DQ

85

49

67

)9

4A

ctiv

ated

slu

dg

e(E

U1

04

26

7)

97

aH

iera

rch

ical

tax

on

om

icas

sig

nm

ent

for

each

OT

Uca

lcu

late

du

sin

gth

eR

DP

naı

ve

Bay

esia

nC

lass

ifier

(Co

leet

al.

20

03

).D

eep

est

lin

eag

eas

sig

nm

ents

(kk

ing

do

m,

pp

hy

lum

,c

clas

s,o

ord

er,

ffa

mil

y)

are

dis

pla

yed

on

lyw

her

eO

TU

sco

uld

be

assi

gn

edw

ith

an8

0%

bo

ots

trap

con

fid

ence

esti

mat

eb

Ind

icat

esaf

fili

atio

nto

hig

hly

pre

val

ent

core

ph

ylo

typ

esin

vo

lved

inA

Do

fsl

ud

ge

that

wer

ep

rev

iou

sly

des

crib

edin

(Riv

iere

etal

.2

00

9)

BR

bio

gas

reac

tor,

WW

Sw

aste

wat

ersl

ud

ge,

MF

Cm

icro

bia

lfu

elce

ll

3 Biotech (2013) 3:407–414 411

123

Page 6: Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

IC IC+WS: 98 ± 44mL g-1 VS* IC+SW: 223 ± 61mL g-1 VS*

Crenarchaeota; C2; GrfC26 Euryarchaeota; Methanobacteria; Methanobacteriales Euryarchaeota; Methanomicrobia; MethanomicrobialesEuryarchaeota; Methanomicrobia; Methanosarcinales

0.0

10.0

20.0

30.0

40.0

50.0

60.0

70.0

80.0

1 2 3 4 5 6 7 8 9 10 11 12 13 14

IC

IC+WS

IC+SW

-6

-4

-2

0

2

4

6

1 2 3 4 5 6 7 8 9 10 11 12 13 14

~98%: Methanosaeta conccilii GP6 Core-group OTU-VI (Methanosarcinales)

~96%: Methanosphaerula palustris str. E1-9c (Methanomicrobiales)

~85%: Methanobacterium alcaliphilum Core-group OTU-V (Methanobacteriales)

A

B C

Rel

ativ

e ab

unda

nce

(%)

97% OTUs 97% OTUs

OT

U a

bund

ance

shi

ft (f

old

x)

Fig. 2 Relative abundance and comparison profiles of archaeal 16S

rRNA OTUs identified in anaerobic digesters containing either waste

water sludge with no additional organic substrate (inoculum, IC), IC

plus wheat straw (IC ? WS), or IC plus seaweed (IC ? SW). a,

b The relative abundance of archaeal lineages at a phylum-level and

OTU-level, respectively. OTU abundance shifts between WS and SW

digesters c were measured as either fold-change increases (?) or

decreases (-) against IC measurements. Colour coding in b and c are

as follows: blue indicates IC, red indicates IC ? WS and green

indicates IC ? SW. Lineage information for selected OTUs and OTU

affiliation to previously described, highly prevalent core phylotypes

(Riviere et al. 2009) is provided. OTUs numbers in the x-axis

correspond to ARC_nor-terminology referred to in the text. Total

methane yields are included in a for IC ? WS and IC ? SW,

which are provided in the original publication on methane produc-

tion (Vivekanand et al. 2012) and normalized for production in IC.

VS* volatile solids

A B

Fig. 1 Rarefaction analyses using operational taxonomic unit (OTU)

frequency of archaeal (a) and bacterial (b) rrs gene datasets obtained

from the biogas digesters containing waste water sludge as inoculum

(IC blue), IC plus wheat straw (IC ? WS red) or IC plus seaweed

(IC ? SW green). A 97 % sequence identity threshold has been

employed for the OTU constructions used in these analyses

412 3 Biotech (2013) 3:407–414

123

Page 7: Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

ARC_nor-1 dominance is conceivably linked to bacterial

population shifts and/or changes in bacterial metabolism.

Surprisingly, dominant bacterial populations showed little

variation between the digesters with larger shifts only

observed for several low-abundant OTUs. Regardless, the

large phylogenetic variation between biogas-producing

communities and cultured representatives makes drawing

definitive functional or interactive conclusions, a signifi-

cant challenge. The functioning of biogas-producing

microbial communities on the whole is insufficiently

explored and requires further in depth structure–function

analysis involving a combination of cultivation directed

strategies and ‘‘meta-omic’’ approaches (i.e., metagenom-

ics, metatranscriptomics).

Acknowledgments This work was supported by The Research

Council of Norway’s RENERGI program (Grant numbers 190877)

and a Marie Curie International Incoming Fellowship from the

European Commission (awarded to PBP; PIIF-GA-2010-274303).

Conflict of interest The authors declare that they have no conflict

of interest.

Open Access This article is distributed under the terms of the

Creative Commons Attribution License which permits any use, dis-

tribution, and reproduction in any medium, provided the original

author(s) and the source are credited.

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IC IC+WS: 98 ± 44mL g-1 VS* IC+SW: 223 ± 61mL g-1 VS*

OtherSpirochaetesAcidobacteriaActinobacteriaArmatimonadetesBacteroidetesChloroflexi

FirmicutesLentisphaeraeOP8ProteobacteriaSAR406SynergistetesWS1

0.0

5.0

10.0

15.0

20.0

25.0

30.0

35.0

40.0

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63 -8

-6

-4

-2

0

2

4

6

8

10

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63

IC

IC+WS

IC+SW

~86%: Treponema primitia str. ZAS-1 (Spirochaetes)

~80%: aParabacteroides distasonis str. ATCC 8503 (Bacteroidetes)

~98%: bPetrobacter succinatimandens str. DSM 15512 (Betaproteobacteria)

~94%: cVictivallis vadensis str. ATCC BAA-548 (Lentisphaerae)

B C

A

~99%: Core-group α OTU-VI uncultured (Chloroflexi)

~99%: Core-group α OTU-III uncultured (Chloroflexi)

Rel

ativ

e ab

unda

nce

(%)

OT

U a

bund

ance

shi

ft (f

old

x)

97% OTUs97% OTUs

a

b

c

Fig. 3 Relative abundance and comparison profiles of bacterial 16S

rRNA OTUs identified in anaerobic digesters containing either waste

water sludge with no additional organic substrate (inoculum, IC), IC

plus wheat straw (IC ? WS), or IC plus seaweed (IC ? SW).

Relative abundance of bacterial lineages at a phylum-level (a) and

OTU-level (b) are shown. OTU abundance shifts between WS and

SW digesters (c) were measured as either fold-change increases (?)

or decreases (-) against IC measurements. Lineage information for

selected OTUs (a–c) and OTU affiliation to previously described,

highly prevalent core phylotypes (Riviere et al. 2009) is provided.

Colour coding in b and c are as follows: IC, red indicates IC ? WS

and green indicates IC ? SW. OTUs numbers in the x-axis

corresponds to BAC_nor-terminology referred to in the text. Total

methane yields are included in a for IC ? WS and IC ? SW,

which are provided in the original publication on methane produc-

tion (Vivekanand et al. 2012) and normalized for production in IC.

VS* volatile solids

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