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Applied and Environmental Microbiology, May 2004, p. 3096-3102, Vol. 70, No. 5
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.5.3096-3102.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577,1 Bio-Oriented Technology Research Advancement Institution (BRAIN), Nisshin-cyo, Omiya, Saitama 331-8537,2 National Institute of Livestock and Grassland Science, Nishi-nasuno, Tochigi 329-2793, Japan,3 Institute of Biology, University of the Philippines, Diliman, Quezon City 1101, Philippines,4 School of Biotechnology, Suranaree University of Technology, Nakhon-Ratchasima 30000, Thailand,5 Central Agriculture Research Institute, Gyogon, Insein, Yangon, Myanmar6
Received 18 November 2003/ Accepted 2 February 2004
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The availability of fixed nitrogen limits primary productivity in plant ecosystems. During their evolution, legumes have acquired a symbiotic relationship with rhizobia that fix atmospheric nitrogen. Among nonleguminous plants, several diazotrophs have been isolated and characterized as nitrogen-fixing endophytes, including Acetobacter (18), Azoarcus (11, 16), and Herbaspirillum (6, 8). Endophytes are microorganisms that spend most of their life cycles inside plant tissues without causing symptoms of plant damage (16). We still do not know whether these diazotrophic endophytes contribute substantially to the nitrogen economy of grasses (11, 12). It is possible that we have overlooked the real contributors to nitrogen fixation in nonleguminous plants. Indeed, nitrogenase transcript analysis has indicated that endophytes, such as Azoarcus sp. and others in an apparently unculturable state, fix nitrogen in plants (11).
Wild grasses can often grow in nitrogen-deficient soils, suggesting that functioning diazotrophic bacteria are associated with them. We therefore tried to isolate and characterize diazotrophic bacteria associated with wild rice species in situ and pioneer plants growing on a devastated lahar area with volcanic eruptions. For this work, we used mainly the aerial parts of plants as isolation materials to avoid bacterial contamination from soils. During efforts to isolate endophytic diazotrophs from these plants, we faced problems with unculturable diazotrophic bacteria and found an anaerobic nitrogen-fixing consortium (ANFICO) consisting of N2-fixing clostridia and diverse nondiazotrophic bacteria. The objective of this work was to clarify the members of ANFICOs and their interactions.
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Microscopy.
Cultures were stained with 5 µg of DAPI (4',6-diamidino-2-phenylindole) solution/ml for 10 min and then were observed by light microscopy (BX50 microscope; Olympus, Tokyo, Japan). Hucker's modified method was used to determine Gram staining characteristics, as described previously (7). Cell viability was visualized by use of a Live/Dead bac Light bacterial viability kit (L-7007; Molecular Probes, Eugene, Oreg.) and was observed by fluorescence microscopy (Axioplan 2 microscope; Carl Zeiss, Tokyo, Japan).
Phylogenetic analysis and substrate utilization.
A nearly-full-length 16S rRNA gene was amplified and sequenced as previously described (6). Multiple alignments and phylogenetic analyses were performed with the Clustal W program, as described previously (6). The utilization of substrates was examined by use of a bacterial identification kit (API20A; BioMerieux, Tokyo, Japan).
Oxygen tests.
Clostridium sp. strain B901-1b was inoculated into RMR broth and incubated, with shaking, for 21 h at 30°C with various oxygen concentrations (0.0 to 0.7% [vol/vol]) in 123-ml bottles, at a gas-to-liquid ratio of 39:1. Isolates B901-1b and B901-2 were inoculated into RMR broth in different arms of a Y-shaped test tube with a butyl-rubber stopper and were incubated at 30°C for 3 days. H2 and O2 concentrations in the headspace were determined with a gas chromatograph equipped with a thermal conductivity detector (GC-7A; Shimadzu, Kyoto, Japan). ARA was determined in the presence of 5% (vol/vol) acetylene as described previously (6).
N2 fixation of clostridia with nondiazotrophs and culture filtrate.
The clostridia and nondiazotrophs isolated in this work were coinoculated into test tubes containing semisolid RMR medium and were incubated for 3 to 4 days at 30°C in air. Culture filtrates of nondiazotrophs were prepared by centrifugation (8,000 x g for 15 min) and passaging through a sterile membrane filter (DISMIC-25; 0.20-µm pore size) (Advantec, Tokyo, Japan) after cultivation of the bacteria in RMR broth for 3 days. Subsequently, anaerobically grown cells of Clostridium sp. strain Kas107-2 were inoculated into RMR broth containing the culture filtrates and were incubated anaerobically for 72 h at 30°C. The N2-fixing activity was determined by an acetylene reduction assay performed for 24 h as described above (6).
Nucleotide sequence accession numbers.
The nucleotide sequences determined in this study appear in the DDBJ database under accession numbers AB114225 to AB114271.
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We isolated various bacteria aerobically or anaerobically from the original cultures exhibiting N2-fixing activity. After cocultivating random combinations of two different isolates in semisolid RMR medium, we found that N2-fixing activity appeared in a specific combination of an anaerobic isolate with an aerobic isolate in air. An example of this procedure with an Oryza officinalis stem is shown in Fig. 1A to D. The anaerobic isolate B901-1b (Fig. 1B) exhibited N2-fixing activity in semisolid RMR medium upon cocultivation under aerobic conditions (Fig. 1D, air) as well as upon single cultivation under anaerobic conditions (Fig. 1D, N2 gas). On the other hand, the aerobic isolate B901-2 (Fig. 1C) alone showed no N2-fixing activity in air or N2 gas (Fig. 1D). The anaerobic isolate of B901-1b alone did not grow in the oxygen-limited semisolid medium in air (Fig. 1D), suggesting that a strict anaerobic condition is required for the growth of this bacterium. This explains why we failed to isolate nitrogen-fixing bacteria from the original cultures. Because these bacteria differ morphologically (Fig. 1B and C), we observed them in cocultures. At the bottom of the test tube, the large rod-shaped cells of B901-1b and the small spherical cells of B901-2 formed a microconsortium in the culture (Fig. 1E).
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FIG. 1. N2-fixing activity (ARA) during isolation steps and fluorescence micrographs showing the structure and viability of consortia of the cells. (A) Test tube that is positive for ARA during isolation from a stem of O. officinalis. (B) Anaerobic isolate B901-1b after Gram staining. (C) Aerobic isolate B901-2 after Gram staining. (D) Growth and ARA of singly and cocultured B901-1b and B901-2 in air and N2 gas. ARA was detected exclusively in a single culture of B901-1b in N2 gas and in a mixed culture in air. Gas evolution and growth occurred in test tubes, except for the single culture of B901-1b in air, which sometimes caused an accumulation of agar in the uppermost layer of the medium. ARA+, test tubes that were positive for ARA (16 to 24 nmol of ethylene produced h1 tube1); , <0.1 nmol of ethylene produced h1 tube1. (E) Fluorescence micrograph showing a reconstructed consortium. (F and G) Living (green) and dead (red) cells of Clostridium sp. strain B901-1b (large rod) cultured in RMR broth under anaerobic conditions (F) and under aerobic conditions with the accompanying bacterium Enterobacter sp. strain B901-2 (small coccus) (G). Both preparations were exposed to air for 5 min before observation. Bar, 10 µm. According to their 16S rRNA gene sequences, B901-1b and B901-2 were identified as a Clostridium sp. and an Enterobacter sp., respectively (see Fig. 3).
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FIG. 2. Effect of O2 concentration on growth, N2-fixing activity (ARA), and hydrogen evolution by Clostridium sp. strain B901-1b (A) and synergetic effects of separate cultures of B901-1b and B901-2 on N2-fixing activity (B). C and E, inoculation of Clostridium sp. strain B901-1b and Enterobacter sp. strain B901-2, respectively. Gray shading shows bacterial growth after 4 days. ARA+, positive for ARA (106 nmol of ethylene produced h1 tube1); , no ARA (<0.1 nmol of ethylene produced h1 tube1).
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-Proteobacteria and the high-C+G-content and low-G+C-content gram-positive lineages (Fig. 3A). The 16S rRNA gene sequences of nondiazotrophic isolates B901-2 and Kas107-3 showed 99% homology to those of Enterobacter cloacae (Y17665) and Bacillus megaterium (AF142677) across a 1.45-kb region. Thus, B901-2 and Kas107-3 were identified as being an Enterobacter sp. and a Bacillus sp., respectively. Both bacteria were used as representatives of accompanying, nondiazotrophic bacteria for this work.
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FIG.3. Phylogenetic tree of anaerobic nitrogen-fixing bacteria (red) and accompanying bacteria (blue) from various origins and representative close relatives by 16S rRNA gene sequences. (A) Representative members of ANFICOs. Pairs of anaerobic N2-fixing bacteria and accompanying bacteria (source) are Kas107-2-Kas107-3 (Miscanthus sinensis stem), Sukashi-1-Sukashi-2 (M. sinensis stem), Kas203-1-Kas203-3 (M. sinensis root), P303-P312 (S. spontaneum stem), B913-1-B913-2 (Oryza rufipogon stem), and B901-1b-B901-2 (O. officinalis stem). (B) Tree of 40 isolates of anaerobic nitrogen-fixing bacteria from various pioneer plants and wild rice species, including M. sinensis, S. spontaneum (wild sugarcane), Polygonum sachalinense, Saccharum hybrid sp. (sugarcane), Oryza sativa (cultivated rice), and O. rufipogon, Oryza nivara, O. officinalis, and Oryza redleyi (wild rice species). In parentheses are details of the plant, tissue, and location of isolation. Clusters I and XIVa are phylogenetic clusters of the genus Clostridium (5). The trees are based on >1.2 kb of DNA sequences and were constructed by the neighbor-joining method. Bootstrap values (percentages from 1,000 replications) are indicated. The utilization of carbon sources was tested for 30 isolates, which are indicated with asterisks.
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The clostridial isolates were further subdivided into groups I and II in cluster XIVa and groups III, IV, and V in cluster I on the basis of a phylogenetic tree of their 16S rRNA gene sequences (Fig. 3B). Groups I, III, and V contained known species of Clostridium, such as C. saccharolyticum, C. pasteurianum, and C. acetobutylicum, respectively. In contrast, groups II and IV did not include known species of the genus Clostridium (Fig. 3B).
Four nutritional groups of clostridia have been distinguished, namely saccharolytic, proteolytic, saccharolytic and proteolytic, and specialist clostridia (9). When 30 isolates of clostridia (Fig. 3, asterisked isolates) were tested with an API20A bacterial identification kit, all isolates utilized various sugars, such as glucose, cellobiose, and mannose, but they did not utilize gelatin. These nutritional traits indicated that they are saccharolytic clostridia, which is seemingly suitable to their life in plants.
Ubiquitous distribution of clostridia in plants.
On the basis of our examination of the phylogenetic tree, the clostridial isolates were divided into two clusters (clusters XIVa and I) and five groups (groups I, II, III, IV, and V) (Fig. 3B). These clusters and groups were not clearly correlated with the plant species (Oryza sp., M. sinensis, S. spontaneum, or Polygonum sachalinense), plant tissue (stem, seed, leaf, or root), or location of isolation (Japan, Thailand, Myanmar, Philippines, or Cambodia). In contrast, the mosaic distribution of clostridial isolates from diverse origins on the phylogenetic tree excluded the possibility of spontaneous contamination. Clostridia were generally isolated from the most diluted tube showing N2 fixation in the MPN counting series under conditions of strong surface sterilization. For example, the clostridial population was estimated to be at least 104 cells/g of fresh weight in M. sinensis sampled in June 2001 at Kashimadai, Miyagi, Japan. These results strongly suggest that clostridia are naturally occurring bacteria in the shoots and roots of pioneer plants and wild rice species.
Table 1 summarizes the N2-fixing activities in semisolid RMR medium of cocultures of random combinations of two different isolates from various origins. Since we sought diazotrophic microbes and their consortia by using ARA, the mixed cultures of clostridial isolates and appropriate nondiazotrophs always exhibited the capability for N2 fixation. In contrast, single cultures of clostridia showed almost no N2- fixing activity in semisolid RMR medium in air. These results demonstrate the dependence of the N2-fixing activity of clostridia on nondiazotrophs in culture and their unculturability by conventional methodologies. Nevertheless, six clostridial isolates showed weak activities of N2 fixation in single cultures in semisolid RMR medium in air. Interestingly, they were confined to group IV (Table 1 and Fig. 3). It is possible that the clostridia in group IV are more tolerant to O2 to some extent than are the other clostridia.
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TABLE 1. N2-fixing activities of single cultures and cocultures of clostridial isolates with accompanying bacteria in semisolid RMR medium
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TABLE 2. N2-fixing activity of clostridial isolates cocultured with accompanying bacteria of different origins in semisolid RMR medium
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FIG. 4. N2-fixing activity of Clostridium sp. strain Kas107-2 culture with filtrates of accompanying bacterial isolates Kas107-3 and Kas107-4. Clostridium sp. strain Kas107-2 was anaerobically grown in RMR broth without rice extract at 30°C for 72 h with shaking in the presence of various concentrations (percentages [vol/vol]) of the culture filtrates of the accompanying bacteria Kas107-3 and Kas107-4. After the 72-h incubation, the cell densities of Kas107-2 in medium supplemented with the filtrates reached 3 x 107 to 5 x 107 CFU ml1. The ARAs of cultures of Clostridium sp. strain Kas107-2 were determined in triplicate. Error bars indicate standard deviations. Kas107-3 was identified as a Bacillus sp. by its 16S rRNA gene sequence (Fig. 3). The cell morphology of Kas107-4 was very similar to that of Kas107-3 in terms of its rod shape, gram-positive staining, and endospore formation (data not shown).
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To our knowledge, this is the first report on the ubiquitous distribution and phylogenetic characterization of clostridia from living plants, including their aerial parts. The existence of these organisms has not been suspected from prior works on plant endophytes, since most studies have not employed culturing techniques for the isolation of obligate anaerobes. We have clearly shown that the presence of ANFICOs explains the apparent unculturability of N2-fixing microbes by the conventional procedure of single-colony isolation. Indeed, a survey work on the purification of N2-fixing microbes from pasture grasses in Southeast Asia had failed due to the problem of the apparent unculturability of diazotrophs (M. Araragi, personal communication).
If clostridia and aerobic diazotrophs are mixed during aerobic isolation steps, the aerobic diazotrophs should be selectively purified because of no growth of strictly anaerobic clostridia under aerobic conditions. The discovery of ANFICOs is thus probably attributable to the fact that the in situ plant materials (mainly shoots) used in this work were not contaminated by conventional diazotrophic endophytes, such as Herbaspirillum sp. (6). Therefore, the results of this work do not contradict the existence of conventional diazotrophic endophytes but reveal the existence of ANFICOs that have been hidden by them.
This work indicates that clostridia are naturally occurring endophytes in gramineous plants and that N2 fixation by the clostridia arises in association with nondiazotrophic endophytes in culture. We still do not know whether ANFICOs really fix nitrogen in planta. However, the finding of ANFICOs in plants indicates that clostridia should be candidates as real diazotrophic endophytes in grass for future studies (12). This work also demonstrates a new principle in environmental microbiology, that consortia of bacteria, rather than monocultures, may stand for a particular activity in a complex environment.
K. Minamisawa, T. Miyaki, B. Ye, and M. Saito were supported by a grant from Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN).
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