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Applied and Environmental Microbiology, November 2004, p. 6580-6586, Vol. 70, No. 11
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.11.6580-6586.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis
Takuya Miyamoto,
Makoto Kawahara, and
Kiwamu Minamisawa*
Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Japan
Received 25 February 2004/
Accepted 18 July 2004

ABSTRACT
Anaerobic nitrogen-fixing consortia consisting of N
2-fixing
clostridia and diverse nondiazotrophic bacteria were previously
isolated from various gramineous plants (K. Minamisawa, K. Nishioka,
T. Miyaki, B. Ye, T. Miyamoto, M. You, A. Saito, M. Saito, W.
Barraquio, N. Teaumroong, T. Sein, and T. Tadashi, Appl. Environ.
Microbiol.
70:3096-3102, 2004). For this work, clostridial populations
and their phylogenetic structures in a stand of the grass
Miscanthus sinensis in Japan were assessed by a 16S rRNA gene-targeted
terminal restriction fragment length polymorphism (TRFLP) analysis
combined with most-probable-number (MPN) counts. PCR primers
and restriction enzymes were optimized for analyses of the plant
clostridia. Clostridia were detected in strongly surface-sterilized
leaves, stems, and roots of the plants at approximately 10
4 to 10
5 cells/g of fresh weight; they made up a large proportion
of N
2-fixing bacterial populations, as determined by MPN counts
associated with an acetylene reduction assay. Phylogenetic grouping
by MPN-TRFLP analysis revealed that the clostridial populations
belonged to group II of cluster XIVa and groups IV and V of
cluster I; this result was supported by a culture-independent
TRFLP analysis using direct DNA extraction from plants. When
phylogenetic populations from
M. sinensis and the soil around
the plants were compared, group II clostridia were found to
exist exclusively in
M. sinensis.

INTRODUCTION
Several diazotrophs have been isolated and characterized as
nitrogen-fixing endophytes from gramineous plants, including
Acetobacter (
20),
Herbaspirillum (
5,
8),
Klebsiella (
2), and
Serratia (
7). An
Azoarcus sp. from Kallar grass abundantly colonizes
and expresses
nif genes and nitrogenase protein inside its original
host as well as in rice roots (
11,
18). These diazotrophic endophytes
are all gram-negative aerobes and facultative anaerobes. Recently,
Minamisawa et al. (
16) discovered the existence of anaerobic
nitrogen-fixing consortia consisting of N
2-fixing clostridia
and diverse nondiazotrophic bacteria in nonleguminous plants
(
16). Clostridia are obligate anaerobic, gram-positive bacteria
(
1,
4,
9) which have not yet been recognized as bacterial endophytes.
A phylogenetic analysis (
16) indicated that the plant clostridia
fell exclusively into clusters XIVa and I, as defined by Collins
et al. (
4), and were further subdivided into five groups. In
particular, N
2 fixation by group II clostridia was induced by
metabolites of nondiazotrophs in culture, although N
2 fixation
in anaerobic nitrogen-fixing consortia is always supported by
the elimination of oxygen by the nondiazotrophs (
16).
The 16S rRNA gene has been used as a molecular marker that allows the phylogenetic assignment of target organisms in natural environments. Popular methods that rely on 16S rRNA gene analysis include terminal restriction fragment length polymorphism (TRFLP) analysis (14) and denaturing gradient gel electrophoresis (17). Recently, Sessitsch et al. (19) monitored endophytic populations in potato plants by TRFLP and found a wide range of organisms that fell into many distinct phylogenetic groups. Molecular population analyses targeting the 16S rRNA genes of clostridia in the environment have been reported for municipal landfill sites (22), human feces (6), and paddy fields (3, 23).
For this work, we investigated the population levels and phylogenetic structures of clostridia in the grass Miscanthus sinensis by TRFLP analysis targeting the 16S rRNA gene. M. sinensis is a rhizomatous, perennial grass that naturally dominates almost all of the tallgrass-type meadows and wastelands in Japan (13). The plant often grows as a pioneer plant in areas devastated by lahar from volcanic eruptions; in these areas the nitrogen content of the soil is very low. The objective of this work was to determine (i) how the population levels of endophytic clostridia compare with those of culturable diazotrophs and (ii) which are the dominant phylogenetic groups of plant clostridia.

MATERIALS AND METHODS
Bacterial strains, media, and cultivation.
Sixteen strains of a
Clostridium sp. that were previously isolated
mainly from
M. sinensis were used (
16). The strain names (and
accession numbers of the sequences) were Sukash-1 (
AB114226),
Kas203-2 (
AB114230), Kas401-4 (
AB114231), Kas107-2 (
AB114232),
Kas203-1 (
AB114238), Kas104-4 (
AB114239), Kas401-3 (
AB114240),
Kas107-1 (
AB114241), Kas301-1 (
AB114242), Kas404-1 (
AB114243),
Kas303 (
AB114244), Kas402-3 (
AB114249), Kas202-1 (
AB114252),
Kas201-1 (
AB114258), Kas106-4 (
AB114263), and B901-1b (
AB114264).
The type strains of
Clostridium aminovalericum,
Clostridium intestinali,
Clostridium acetobutylicum, and
Clostridium beijerinckii were purchased from culture collections of the Riken Institute
(Wako, Japan). Rice extract modified Rennie (RMR) semisolid
medium (
5) and nutrient agar (NA) (Difco, Detroit, Mich.) were
used for the enumeration of bacteria and diazotrophs from plants.
Viande-Levure (VL) agar and RMR agar plates were used for the
cultivation of clostridia. VL medium contained the following
components dissolved in 1 liter of water (pH 7.0): nutrient
broth (Difco), 8 g; yeast extract (Difco), 5 g; NaCl, 5 g; glucose,
2 g; cysteine-HCl, 0.3 g. Anaerobic cultivation was carried
out with the AnaeroPack system (Mitsubishi Gas Chemical, Tokyo,
Japan).
Sample collection and surface sterilization.
Plants were sampled from a stand of naturally vegetated M. sinensis in the town of Kashimadai, in the Miyagi prefecture, Japan, early in summer. Plant materials were carefully washed with tap water and separated into leaf, stem, and root parts. A sample of bulk soil was taken from around the grasses, air dried, and sieved through 2-mm mesh. To ensure the complete surface sterilization of the plant materials, we tested several sterilization conditions (with 1 to 2% NaOCl for 0.5 to 15 min). After surface sterilization, the plant materials were washed several times with sterile distilled water. NaOCl-treated 5-cm-long sections of leaves, stems, or roots or clostridial cell samples were rolled or plated on NA, VL, or RMR agar plates. VL and some RMR plates were anaerobically incubated at 30°C, and NA and other RMR plates were aerobically incubated at 30°C. A similar sterilization experiment was performed with spores of Clostridium sp. strain B901-1b.
Bacterial counts by the MPN method.
The surface-sterilized plant materials were mechanically macerated with 0.8% saline solution and quartz sand and then decimally diluted in 0.8% saline solution. The dilutions were used to seed RMR semisolid medium (five tubes per dilution) for determinations of the most probable numbers (MPN) of total bacteria and N2-fixing bacteria. MPN tubes were monitored for growth in the form of subsurface pellicles 5 days after inoculation. Growth-positive tubes were tested for acetylene reduction. After 24 h of incubation with 10% C2H2, the ethylene formed was measured in a gas chromatograph (GC-7A; Shimadzu, Kyoto, Japan) equipped with a flame ionization detector and a Porapack R column (0.3 mm [inner diameter] by 2 m) at 50°C. MPN counts were calculated at a level of 95% confidence according to the method of Hurley and Roscoe (12).
DNA extraction.
DNAs were isolated by two procedures from semisolid RMR cultures and directly from plant tissues and soil. For DNA isolation from semisolid cultures, a modification of the method of Hiraishi (10) was used as follows. Semisolid cultures (40 µl) from MPN tubes were frozen at 20°C and thawed at room temperature. Lysates were prepared by adding 10 µl of proteinase K (10 mg/ml) and 50 µl of BL buffer (pH 8; 40 mM Tris, 1% Tween 20, 0.5% Nonidet P-40, 1 mM EDTA, 1 N HCl) to the semisolid culture (40 µl), heated at 60°C for 20 min, and then heated at 95°C for 20 min, followed by centrifugation (17,000 x g for 10 min) to remove unbroken cells and large debris. The resultant lysates were used as DNA templates for PCR amplification of the 16S rRNA gene.
DNAs were prepared directly from plants and soil materials by use of a FastDNA kit and a FastDNA Spin kit for soil (BioSystems, Carlsbad, Calif.) according to the manufacturer's instructions. Surface-washed stems of M. sinensis were macerated in a mortar with liquid N2. The powdered tissues (0.1 g) were introduced to tubes containing cell lysis solution for vegetation (BioSystems) and homogenized with a bead beater (BioSpec, Bartlesville, Okla.) with two 1/4-in. cylindrical spheres and a garnet matrix (BioSystems). For DNA extraction from the soil, 0.5 g of air-dried soil was introduced into lysing matrix E (BioSystems) and homogenized as described above.
PCR amplification.
The primers used for amplification of the clostridial 16S rRNA gene are listed in Table 1. A seminested PCR assay was performed to eliminate amplified products from other bacteria. The clostridial 16S rRNA gene from 0.5 µl of a semisolid lysate was amplified in a reaction mixture containing 1.0 µl each of primers C142f and C1090r (20 µM [each]), 0.1 µl (1 U) of Ex Taq polymerase (Takara, Kyoto, Japan), 1.6 µl of 2.5 mM deoxynucleoside triphosphates, 2.0 µl of 10x Ex Taq buffer, and 13.8 µl of sterile distilled water. After a denaturation step of 5 min at 94°C, the amplification reactions were performed, with 30 cycles of denaturation (30 s, 94°C), primer annealing (30 s, 52°C), and primer extension (30 s, 72°C) and a final extension step of 7 min at 72°C. Aliquots (1 µl) of 16S rRNA gene products were used directly for a second PCR amplification of the 16S rRNA gene. The reaction mixture for the second PCR contained 1.5 µl each of primers Cy5-C142f and C796r (20 µM [each]), 0.1 µl (1 U) of Ex Taq polymerase, 4.0 µl of 2.5 mM deoxynucleoside triphosphates, 5.0 µl of 10x Ex Taq buffer, and 37 µl of sterile distilled water. After a denaturation step of 5 min at 94°C, the thermal cycles for the second PCR were identical to those for the first PCR. Aliquots (1 µl) were analyzed by electrophoresis in 1% (wt/vol) agarose gels, followed by staining with ethidium bromide. The bands were visualized by UV excitation. A polyethylene glycol solution (20% [wt/vol] polyethylene glycol, 1.6 M NaCl) was added to the second PCR product at a 0.6 volume and mixed by inversion, and then the mixture was kept at 4°C for 1 h. After centrifugation and discarding of the supernatant, the resulting pellet was resuspended in 150 µl of 70% ethanol and centrifuged at 17,000 x g at 4°C for 10 min. The supernatant was again discarded and the pellet was air dried before the DNA was dissolved in 10 µl of sterile distilled water.
TRFLP analysis.
For restriction enzyme digestion, the reagents were prepared
as a master mix before being added to the sample. One hundred
fifty nanograms of the purified PCR product was digested with
either 10 U of HaeIII (Toyobo, Osaka, Japan) or 15 U of MspI
(New England BioLabs, Beverly, Mass.) in a total volume of 15
µl at 37°C for 5 h. Next, 2.5 volumes of 99.5% ethanol
and 0.1 volume of 3 M sodium acetate were added to the samples
before centrifugation at 17,000
x g at 4°C for 15 min. After
the supernatant was discarded, the pellet was rinsed with 150
µl of 70% ethanol and centrifuged at 17,000
x g at 4°C
for 10 min. The supernatant was again discarded, and the air-dried
pellet was resuspended in 2 µl of sterile distilled water.
Fluorescently labeled fragments were mixed with 0.5 µl
of TE buffer (10 mM Tris-HCl [pH 7.6], 1 mM EDTA) containing
1 fmol each of ALFexpress Sizers 50 and 300 (Amersham Pharmacia
Biotech, Piscataway, N.J.) as internal standards and 1.5 µl
of loading dye. After gentle agitation, each sample was denatured
by heating at 95°C for 2 to 3 min and then was immediately
quenched on ice. After electrophoresis in an automated sequencer
(ALFexpress II DNA analyzer; Amersham Pharmacia Biotech) and
analysis with ALFwin Fragment Analyzer 1.00 software (Amersham
Pharmacia Biotech), the sizes (in base pairs) of the terminal
restriction fragments (TRFs) were estimated by reference to
the internal standard and to the external standard, ALFexpress
Sizers 50 to 500. TRFs of clostridial clusters I and XIVa were
determined by reference to the sizes of TRFs in mixtures of
clostridial groups I, II, IV, and V (Sukash-1, Kas107-2, Kas104-4,
and Kas106-4). TRFs with heights of <0.05% for the largest
TRF peak were excluded from analyses.
Clostridial counts.
All MPN tubes showing bacterial growth were subjected to TRFLP analysis. The MPNs of group I, II, IV, and V clostridia in the respective MPN tubes were determined by TRFLP analysis. The total number of clostridia was estimated from maximum values of the respective numbers of group I, II, IV, and V clostridia.
Microscopy.
Clostridial strains grown in RMR semisolid medium were vortexed and then serially diluted with saline solution. The cell numbers in the solutions were counted in a bacterial counting chamber (0.02 mm [depth] by 0.0025 mm2; Kayagaki Irika Kogyo, Tokyo, Japan) by phase-contrast microscopy (BX50; Olympus, Tokyo, Japan).

RESULTS AND DISCUSSION
Primers for TRFLP analysis of plant clostridia.
The objective of this work was to assess the densities and phylogenetic
populations of endophytic clostridia that had been previously
isolated from several gramineous plants (
16). Because they were
all cluster XIVa or I clostridia according to the system of
Collins et al. (
4), we aimed to develop a TRFLP detection system
specific for these clusters (Fig.
1). The clusters are subdivided
into five groups, groups I, II, III, IV, and V (Fig.
1) (
16).
Group III contains two clostridial isolates that were derived
from mature seeds of wild rice but not from fresh materials
such as plant shoots and roots (
16). Thus, this work focused
on group I, II, IV, and V clostridia.
The PCR primers used for this work are shown in Table
1. In
accordance with the 16S rRNA gene sequences of 40 strains of
plant clostridia (DDBJ accession numbers
AB114225 to -64), primers
C142f (Cy5-C142f) and C1090r were designed by the modification
of S-*-chis-0150-a-S-23 (
6) and S-*-Ccoc-1112-a-A-19 (
22), respectively.
Preliminary PCR assays suggested that the C142f and C1090r primers
produced a PCR product from presumptive enterobacteria other
than the plant clostridia from RMR semisolid cultures of
M. sinensis (data not shown). Thus, a seminested PCR strategy was
adopted with an additional reverse primer, C796r, based on the
16S rRNA gene sequences of the plant clostridia (Table
1; Fig.
2). The Probe Match program (
http://rdp.cme.msu.edu/html/) was
used to search the matching of the three primers (C142f, C796r,
and C1090r) to 16S rRNA gene sequences of bacteria according
to the method of Van Dyke et al. (
22). The three primers were
simultaneously in accord with 16S rRNA gene sequences of 11
clones of cluster XIVa clostridia and 41 clones of cluster I
clostridia, although 2 clones of cluster IV clostridia were
hit. Therefore, the combinations of these primers permitted
PCR amplification of the 16S rRNA genes of cluster XIVa and
I clostridia exclusively, including the previous clostridial
isolates.
Restriction enzymes for TRFLP analysis of plant clostridia.
To determine appropriate restriction enzymes for TRFLP analysis,
we calculated the lengths of TRFs derived from the 655-bp PCR
product of the 16S rRNA gene sequence (Fig.
2) by the use of
several restriction enzymes (Table
2). Two enzymes, HaeIII and
MspI, were selected to discriminate TRF sizes in a group-specific
manner (Table
2). HaeIII digestion generated the following expected
TRFs: 152 or 108 bp for group I, 109 bp for group II, 76 bp
for group IV, and 154 bp for group V. MspI digestion generated
the following expected TRFs: 58 bp for group I, 134 bp for group
II, and 375 bp for groups IV and V. Thus, the combination of
TRF sizes for products that were independently digested with
HaeIII and MspI could be used to specify the groups of clostridia.
From the strains for which we estimated TRF sizes, the 16 strains
of
M. sinensis-derived clostridia were examined (Table
2). Seminested
PCR assays were performed with their lysates, which were subsequently
subjected to a TRFLP analysis using HaeIII and MspI. The observed
sizes of the TRFs were almost identical to the predicted TRF
sizes, except for group I clostridia (Table
2). Two strains
(Kas203-2 and Kas401-4) in group I showed both a 152-kb and
a 108-bp TRF upon HaeIII digestion. Three strains in group I
showed both a 152-kb and a 58-bp TRF upon MspI digestion. These
differences were probably caused because different rRNA operons
within group I clostridia have slightly different sequences.
For group II, IV, and V clostridia, the observed TRF sizes were
identical to the predicted sizes.
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TABLE 2. Predicted and observed lengths of the 5' TRF 16S rRNA genes of plant clostridia and their neighbors digested with various restriction enzymesa
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Sensitivity and independence of TRFs.
To examine the sensitivity of TRFLP for semisolid RMR cultures,
we independently cultivated Sukash-1 (group I), Kas104-4 (group
IV), and Kas106-4 (group V) anaerobically in this medium. After
the cell densities had been measured by microscopy, cell lysates
were prepared from 40 µl of each culture. By using a dilution
series of lysates, we performed seminested PCR amplification
with the primers shown in Table
1. As a result, the detection
limit for these clostridia was <100 cells/ml of culture for
the second PCR (data not shown). When the templates (lysates)
of representative strains of groups I, II, IV, and V were mixed,
all peaks of TRFs derived from the different groups were equally
detected. This indicates that there was no PCR bias in the TRFLP
system (Fig.
3).
Surface sterilization.
To estimate the endophytic populations of clostridia by a combined
MPN-TRFLP system, we determined the optimum surface sterilization
conditions for the exclusion of epiphytic bacteria. One week
after the anaerobic or aerobic incubation of RMR, VL, and RMR
plates, no bacterial growth was observed under the following
sterilization conditions: 1% NaOCl for 0.5 to 15 min (leaves),
1 to 2% NaOCl for 10 to 15 min (stems), and 2% NaOCl for 15
min (roots). When spores of
Clostridium sp. strain B901-1b,
which is a close relative of
C. beijerinckii, were exposed to
a 1% NaOCl solution for 0.5 min, the spores completely lost
their viability on VL and RMR plates. Based on these results,
the surface sterilization conditions were fixed as follows:
1% NaOCl for 0.5 min for leaves of
M. sinensis and 2% NaOCl
for 15 min for stems and roots.
MPN counts of N2-fixing bacteria and clostridia.
MPN counts of N2-fixing bacteria and total numbers of bacteria were assessed by an acetylene reduction assay and bacterial growth in MPN tubes containing RMR semisolid medium. Diazotrophic bacteria were detected at levels from 104 to 105 cells/g of fresh weight in surface-sterilized leaves, stems, and roots of M. sinensis. Subsequently, we prepared cell lysates from the cultures in all MPN tubes showing cell growth in RMR semisolid medium and performed TRFLP analyses under conditions established as described above. For culture lysates from the respective MPN tubes, we observed clear peaks without noise; the peaks corresponded to those of group II, IV, and V clostridia, as was the case for the electrograms (Fig. 3) (data not shown). The populations of group II, IV, and V clostridia were separately estimated by the MPN method (Table 3). The populations of group II, IV, and V clostridia ranged from 1 x 103 to 4 x 104 cells/g of fresh weight for all tissues of M. sinensis, but group I clostridia were not detected at all. This indicates that clostridial cells of groups II, IV, and V resided in all parts of the plants, including the aerial parts. The total clostridial population was estimated from the maximum values of the respective groups (Table 3). When the population of clostridia was compared with that of diazotrophs, clostridial cells made up a large proportion of the diazotrophs in the leaves, stems, and roots of M. sinensis (C/D ratio in Table 3).
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TABLE 3. Cell densities of total bacteria, diazotrophs, clostridia, and phylogenetic populations of clostridia in M. sinensis by the MPN methoda
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The conditions used for the surface sterilization of leaves
and stems by NaOCl were effective enough to completely avoid
contamination by epiphytic bacteria. We may have underestimated
the population levels of endophytic clostridia by MPN-TRFLP
analysis because NaOCl is able to penetrate the plant tissues
and cause partial sterilization of endophytic clostridia. Thus,
the observed population levels were probably minimum values
for endophytic clostridia in
M. sinensis. Endophytic bacteria
are ubiquitous in most plant species. However, the known diazotrophic
endophytes (
2,
5,
7,
8,
11,
18,
20) and nondiazotrophic endophytes
(
15,
21) are all aerobes and facultative anaerobes. To our knowledge,
this is thus the first report that substantial populations of
obligate anaerobic clostridia actually reside in plants (Table
3).
TFRLP analysis of directly extracted DNA.
TRFLP is generally used for the detection and phylogenetic assignment of target organisms in natural environments without cultivation (3, 14, 19). When DNAs directly extracted from M. sinensis stems were used as a PCR template for the clostridium-specific TRFLP method, group I, II, IV, and V clostridia were detected (Fig. 4A). After a 102 dilution of the PCR template with water, signature peaks of groups II, IV, and V remained (Fig. 4A), although no signature peaks were detected at a 104 dilution for any group. This result agreed with the analysis of clostridial populations by MPN-TRFLP (Table 3) in that group II, IV, and V clostridia were dominant in M. sinensis stems. When a bulk sample of soil from around the M. sinensis stand was analyzed, peaks specific for group I, IV, and V clostridia were observed (Fig. 4B, asterisk), but no peaks for group II were detected (Fig. 4B, arrowhead).
Group II clostridia do not include currently known species of
the genus
Clostridium (Fig.
1). It was empirically difficult
to isolate them because they showed very weak growth on VL and
RMR agar media (
16). This is why only small numbers of group
II clostridia were isolated (Table
3) (
16). Moreover, they showed
community-dependent N
2 fixation. It is therefore surprising
that group II clostridia dominated the populations of diazotrophs
and clostridia (Table
3). Group II clostridia may function as
diazotrophic endophytes in
M. sinensis regardless of their poor
culturability.
The MPN approach to comparing relative population sizes of different clostridial groups requires that the groups have similar levels of culturability. Thus, culturing bias is one potential factor affecting the reliability of the population size estimates by MPN-TRFLP analysis. On the other hand, TRFLP analysis using directly extracted DNAs is a rapid and convenient method to survey clostridial populations in plants without a culturing bias.

ACKNOWLEDGMENTS
We are grateful for a grant from the Promotion of Basic Research
Activities for Innovative Biosciences (PROBRAIN) to support
this work.

FOOTNOTES
* Corresponding author. Mailing address: Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan. Phone: 81-22-217-5684. Fax: 81-22-263-9845. E-mail:
kiwamu{at}ige.tohoku.ac.jp.


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Applied and Environmental Microbiology, November 2004, p. 6580-6586, Vol. 70, No. 11
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.11.6580-6586.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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