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Previous Article | Next Article 
Applied and Environmental Microbiology, October 2001, p. 4726-4733, Vol. 67, No. 10
The Biological Laboratories, Harvard
University, Cambridge, Massachusetts 02138,1
and The Ecosystems Center, Marine Biological Laboratory,
Woods Hole, Massachusetts 025432
Received 9 April 2001/Accepted 17 July 2001
Methanotrophic bacteria play a major role in the global carbon
cycle, degrade xenobiotic pollutants, and have the potential for a
variety of biotechnological applications. To facilitate ecological
studies of these important organisms, we developed a suite of
oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes
target methanotrophs in the family Methylocystaceae
(type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family,
Methylocystis and Methylosinus, were
identified. Two other probes target, as a single group, a majority of
the known methanotrophs belonging to the family
Methylococcaceae (type I/X methanotrophs). The
remaining probes target members of individual genera of the
Methylococcaceae, including
Methylobacter, Methylomonas,
Methylomicrobium, Methylococcus, and
Methylocaldum. One of the family-level probes also
covers all methanotrophic endosymbionts of marine mollusks for
which 16S rRNA sequences have been published. The two known species of
the newly described genus Methylosarcina gen. nov. are
covered by a probe that otherwise targets only members of the
closely related genus Methylomicrobium. None of the
probes covers strains of the newly proposed genera
Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized
methanotrophic families. Empirically determined midpoint
dissociation temperatures were 49 to 57°C for all probes. In dot blot
screening against RNA from positive- and negative-control strains, the
probes were specific to their intended targets. The broad coverage and
high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.
Methanotrophic bacteria are
ecologically and technologically important because they comprise a
critical link in the global carbon cycle, act as
N2 fixers and ammonia oxidizers, degrade a wide
array of organic contaminants, and have biotechnological potential for
single-cell protein production and novel enzyme functions (34,
43). Methanotrophs are interesting biologically because they are
physiologically and phylogenetically unique. With the exception of two
recent isolates (8, 24), all known methanotrophs
belong to two monophyletic families: type I/X methanotrophs belong to the family Methylococcaceae within the
Although 16S rRNA-based phylogenies have been used
effectively to resolve long-standing confusion over
methanotroph taxonomy (13, 14), a comprehensive suite
of 16S rRNA-targeted oligonucleotide probes for the
methanotrophs has proven difficult to design (9, 34). Some probes have been useful in monitoring
CH4 enrichment cultures (9, 37) or
quantifying undifferentiated groups of diverse methylotrophs, including
nonmethanotrophs, in environmental samples (52).
However, the probes developed to date either are not specific to
methanotrophs (36, 56) or fail to cover a large
proportion of known methanotrophs (9, 34).
Moreover, due to substantial diversity among the
To facilitate ecological studies of methanotroph communities,
we designed a new suite of oligonucleotide probes and optimized them
for quantitative hybridization analysis of 16S rRNA from specific
groups of methanotrophic bacteria. Our aim was to design a
complementary suite of probes that would (i) target
methanotrophs to the exclusion of closely related
nonmethanotrophic bacteria, (ii) encompass a greater number and
wider diversity of known methanotrophic bacteria than achieved
previously, and (iii) allow specific detection of methanotrophs
at both the family and genus levels.
Bacterial cultures.
The reference cultures used in this
study were obtained from various sources, as indicated, and are
available from either the National Collection of Industrial and Marine
Bacteria (NCIMB, Aberdeen, United Kingdom) or the American Type Culture
Collection (ATCC, Manassas, Va.). Reference strains include
Methylosinus trichosporium OB3b (NCIMB 11131) and
Methylococcus capsulatus Bath (NCIMB 11132) (both provided
by J. C. Murrell), Methylobacter luteus (NCIMB 11914;
provided by R. Knowles), Methylobacter marinus A45
(nonextant culture; genomic DNA provided by A. A. DiSpirito), Methylomicrobium album BG8 (NCIMB 11123; provided by G. M. King), Methylomonas rubra (NCIMB 11913) and
Methylomonas methanica S1 (NCIMB 11130) (both provided by
J. D. Semrau), Methylocaldum gracile (NCIMB 11912;
purchased from NCIMB), Caulobacter crescentus CB15A (ATCC
19089; provided by J. S. Poindexter), and Escherichia
coli 01:K1(L1):H7 (ATCC 11775; from laboratory stock culture).
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.10.4726-4733.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Family- and Genus-Level 16S rRNA-Targeted Oligonucleotide Probes
for Ecological Studies of Methanotrophic Bacteria
ABSTRACT
Top
Abstract
Introduction
Materials and Methods
Results and Discussion
References
INTRODUCTION
Top
Abstract
Introduction
Materials and Methods
Results and Discussion
References
-Proteobacteria, and type II methanotrophs belong to
the family Methylocystaceae within the
-Proteobacteria (10, 11, 14). For
convenience and clarity, we will refer to the former as
-methanotrophs and to the latter as
-methanotrophs when identifying them phylogenetically. No
other phylogenetic clade is known to use CH4 as a
sole C and energy source (34). Hence,
methanotrophs provide a striking example of a direct
correspondence between physiology and phylogeny, making it possible to
link process measurements with molecular phylogenetic approaches in
situ (15, 17).
-methanotrophs that has been discovered in the past 4 years,
such as the genera Methylosphaera (12),
Methylocaldum (7), and
Methylosarcina (58), many of these organisms
have escaped detection by earlier probes.
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials and Methods
Results and Discussion
References
Sequencing of 16S rRNA genes. Because ambiguous and missing bases in several of the sequences available from GenBank hindered sequence comparisons, we resequenced the 16S rRNA genes of Methylomonas rubra NCIMB 11913, Methylobacter luteus NCIMB 11914, Methylomonas methanica S1 NCIMB 11130, and Methylobacter marinus strain A45. Nearly complete (1,450-bp) sequences were obtained for both the sense and antisense strands of the 16S rRNA gene using 5% Long Ranger gel and an ABI PRISM DNA sequencer (41).
Selection of reference sequences. Probes were designed based on reference 16S rRNA sequences available from GenBank (6) and the Ribosomal Database Project (RDP-II) (42), as well as resequencing of key laboratory strains (see Table 1 and Fig. 3). BLAST (GenBank) and Probe Match (RDP-II) database searches were used to assess the potential breadth and specificity of the probe sequences. The reference sequences were aligned with the probe sequences to determine the apparent range of coverage of the candidate probes relative to the abundance and diversity of known methanotrophs. The 16S rRNA sequences specified by accession numbers in Fig. 2 and 3 represent all those available in the databases for confirmed methanotrophic isolates at the time of analysis. With the exception of the methanotrophic endosymbionts of marine mollusks (see below), we did not include sequences obtained from cultures that had not been characterized phenotypically or that were obtained by PCR amplification of environmental DNA.
Only cultured isolates with published, genus-level phylogenetic data were assigned genus designations in Fig. 2 and 3. Three general groups of confirmed methanotrophs were placed under "other-methanotrophs" (Fig. 2) or "other
-methanotrophs" (Fig. 3): (i) strains clearly belonging to
the - or -methanotrophs, but lacking or having dubious
generic affiliations because of insufficient phylogenetic and taxonomic
information (for example, "Methylomonas methanica " strain 81Z is clearly a -methanotroph [57]
but has not been characterized at the genus level); (ii) isolates validly assigned to the genera Methylocella,
Methylosphaera, and Methylosarcina, for which we
did not design genus-level probes because there were only one or two
known representatives of each genus; and (iii) the
methanotrophic endosymbionts of marine mollusks, which lack
generic descriptions. Although uncultured, the mollusk endosymbionts
were included because they are of active interest to microbial
ecologists and evolutionary biologists and because there is strong
phenotypic and phylogenetic evidence that they are
-methanotrophs (19, 20, 25, 28).
All available methanotroph 16S rRNA sequences that met the
criteria given above were included in our analysis, regardless of
sequence quality. However, a number of sequences appeared to be
affected by common sequencing errors, including transposition of bases
and duplicated or omitted bases. Some errors could be confirmed because
they violated the integrity of the secondary structure of the 16S rRNA
molecule, but others could not because they occurred in unpaired loop
positions. Because sequence errors make designing group-level probes
very difficult, we developed specific criteria for disregarding
unexpected mismatches between a probe and a target sequence. We deemed
destabilization of secondary structure sufficient grounds for
disregarding mismatches. Additionally, we considered any two of the
following criteria sufficient: (i) the mismatch occurs in a low-quality
sequence as indicated by ambiguous bases in >0.5% of the positions in
the entire sequence; (ii) the mismatch results from an ambiguous or
missing base in the probe target region; (iii) multiple sequences for
the same strain disagree in the mismatch position, and the
higher-quality sequence, as indicated by percent ambiguity, matches the
probe; (iv) a multiple alignment of all available sequences
representing the target group shows that the mismatch is not
representative of the target group; (v) the mismatch occurs in a highly
conserved position of the 16S rRNA molecule; (vi) the mismatch is
consistent with a common sequencing error, such as the transposition of
two bases or the repetition of the same base, that disagrees with several other related sequences.
Oligonucleotide probe design.
The oligonucleotide probes
developed and/or optimized in this study are described in Table
1. The numbering used in probe designation represents the forward position of the homologous base in the E. coli 16S rRNA gene. By use of the SEQLAB
sequence editor in the Wisconsin Package (Genetics Computer Group,
Madison, Wis.), 16S rRNA sequences (>1,300 bp) were aligned initially
using the PILEUP function within the editor and then adjusted manually with secondary-structure considerations as described previously (2). With the help of computer-generated consensus
sequences, the alignments were scanned visually for signature sequences
of 18 to 30 nucleotides that distinguished methanotrophs at the
family or genus level. Candidate oligonucleotide sequences were then examined for specificity using the basic BLAST search and Probe Match
functions of GenBank and the RDP-II, respectively (5, 42).
Except as described below, only sequences exhibiting high specificity
for methanotrophs and retrieving a majority of the sequences in
their target groups were pursued further.
|
Td determination and specificity testing. Oligodeoxynucleotides were synthesized commercially (DNAgency, Malvern, Pa.). Each probe was characterized by empirical determination of its midpoint dissociation temperature (Td) using a serial washing procedure with progressively higher temperatures in a PCR thermal cycler as described by Gulledge and Cavanaugh (32). All Td curves were determined using triplicate blots for both positive and negative controls (see Fig. 1).
The ability of each probe to distinguish between positive and negative controls was screened in Northern dot blot hybridization assays, as described below, using total RNA from reference cultures representing target strains as positive controls and total RNA from reference cultures representing nontarget strains with 1- or 2-base mismatches as negative controls. In all but two cases, a strain with a single-base mismatch with the probe was used as a negative control (Table 1). Because no nontarget organisms that had fewer than two mismatches with probe Am445 were identified, an organism with two mismatches was used as a negative control. Also, because no potential control organisms with fewer than four mismatches to probe Mcd77 were identified, we designed a probe with a single mismatch at position 15 to serve as a negative control (Table 1).RNA extraction from bacterial cultures.
Pure cultures were
grown to late-log phase in 40 ml of liquid growth medium and
centrifuged at 5,000 × g for 10 min at 4°C. Total
RNA was extracted selectively from cell pellets using the FastPrep bead
beater system with the FastRNA Blue kit according to the
manufacturer's protocol (Bio 101, La Jolla, Calif.). Cells were beaten
in the FP120 bead beater for 25 to 40 s at a speed of 6 m/s. After extraction and centrifugation, the RNA pellets were
air dried, resuspended in diethyl pyrocarbonate-treated
H2O, and stored at 
80°C.
RNA dot blotting and hybridization. Northern dot blots were prepared from RNA extracts as described previously (48) using a Minifold I Microsample Filtration Manifold (Schleicher & Schuell, Keene, N.H.). Blots were prepared with 100 ng of 16S rRNA per dot to be blotted, assuming that 16S rRNA represented 27% of total RNA (47), as described previously (49).
Oligonucleotide probes were labeled enzymatically with 32P (49), and hybridization assays were carried out as described previously (48). Labeled oligonucleotides were hybridized to the dot blots overnight at 30°C, finishing with two 30-min rinses at the appropriate Td for each probe (Table 1). Oligonucleotide labeling of the dot blots was analyzed by radiodensitometry using a BAS-MS 2025 imaging plate and a Fujix 2000 PhosphorImager, with MacBAS, version 2.5, image analysis software (Fuji Medical Systems, Stamford, Conn.).Nucleotide sequence accession numbers. The new sequences of the 16S rRNA genes of Methylomonas rubra NCIMB 11913, Methylobacter luteus NCIMB 11914, Methylomonas methanica S1 NCIMB 11130, and Methylobacter marinus strain A45 have been deposited in GenBank (accession numbers AF304194 to AF304197).
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RESULTS AND DISCUSSION |
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Top
Abstract
Introduction
Materials and Methods
Results and Discussion
References
|
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Overview. In recent years, interest in the physiology, ecology, and evolution of methanotrophs has intensified, and there is high demand for tools to facilitate quantitative studies of in situ methanotroph community structure (21, 34, 46, 50). Our objectives were to develop phylogenetic oligonucleotide probes for analysis of methanotrophs at the family and genus levels and to optimize the probes for use in quantitative hybridization through empirical determination of their Tds under standard hybridization conditions.
Visual comparison of aligned 16S rRNA reference sequences initially revealed 36 potential probe sequences for further analysis. Additionally, we assessed the efficacy of a PCR primer (Mmb1007 in Table 1) designed by others (44) for use as a probe. We rejected many of the potential probe sequences identified initially because of inadequate coverage of the intended target group or because they exhibited identity with nonmethanotroph 16S rRNA sequences, as revealed by BLAST and Probe Match searches. Most of the remaining oligonucleotides hybridized successfully with target rRNA and not with nontarget rRNA in low-stringency hybridization screening assays. When tested under high-stringency conditions, 14 probes clearly discriminated (e.g., Fig. 1) against their respective negative controls (Table 1). Twelve of these probes proved viable based on the multiple criteria of broad coverage, specificity for the target group, and stringent discrimination of sequences in hybridization assays. We retained two additional probes that were less specific than desired but offered exceptional coverage and potential utility for certain experimental strategies, such as monitoring CH4 enrichment cultures. The probes are described in Table 1.
|
Probe coverage for -methanotrophs.
Two
family-level probes, Am445 and Am976, perfectly match the 16S
rRNA sequences of nearly all known -methanotrophs (Fig. 2), including some novel strains recently
isolated from landfill soils (59) and lake sediments
(22). Methylocella palustris strain
KT, a novel acidophilic methanotroph
isolated recently from a northern peat bog and the only cultured
representative of its genus (24), was the only
-methanotroph whose 16S rRNA sequence was not covered by
either probe. Because these probes do not distinguish between the
Methylosinus and Methylocystis genera, they can
detect -methanotrophs only as a group. No oligonucleotide
signatures that distinguish between these two genera were identified.
|
Probe coverage for -methanotrophs.
For
-methanotrophs we identified both family- and genus-level
probes. Together, two family-level probes (Gm633 and Gm705) covered
82% of the available -methanotroph 16S rRNA sequences (Fig.
3). Gm705 had the broadest coverage,
including representatives of six -methanotroph genera and
the methanotrophic endosymbionts of marine mollusks. Gm633 was
more limited, but it provided better coverage of
Methylobacter and Methylomicrobium spp. The
genera Methylocaldum and Methylosarcina
eluded these two probes. However, almost complete coverage of the
family can be achieved by combining these family-level probes with two
or more of the genus-level probes described below.
|
-methanotroph genera Methylobacter,
Methylomicrobium, and Methylomonas (Fig. 3).
Together, probes Mlb482 and Mlb662 covered all representatives of the
genus Methylobacter. An indicated 6-base mismatch
between Mlb482 and the 16S rRNA sequence for
Methylobacter sp. strain T20 (AF131868) stems from
seemingly errant insertions at positions 497 and 505 (E. coli numbering), as judged by the level of within-genus sequence
conservation in the probe region and the fact that the indicated base
change would violate the secondary structure of the 16S rRNA molecule.
If the two apparent insertions are disregarded, the sequence matches
Mlb482 perfectly. Probes Mmb482 and Mmb1007 each matched all available
Methylomicrobium sequences. Mmb1007 also covered both
strains of the newly described genus Methylosarcina, which
are closely related to Methylomicrobium spp.
(58). Three other probes covered all of the recognized Methylomonas isolates. Representatives of this
genus fell into two groups that differ by an A versus a C at position
746 (E. coli numbering). We designed two probes
(Mlm732a and Mlm732b) to distinguish between the two subgenus groups.
Mlm482 provided the broadest coverage of Methylomonas spp.,
but all representatives of the genus were covered only when the
three Mlm probes were combined.
Three probes covered all representatives of the two recognized
thermophilic genera, Methylococcus and
Methylocaldum. Mlc123 and Mlc1436 each matched all
Methylococcus sequences available. PCR primers
corresponding to these two probes might be ideal for specific
amplification of nearly complete (~1,300-bp) 16S rRNA genes from
Methylococcus strains in environmental samples. Probe Mcd77
covered the three recognized strains of the recently described genus
Methylocaldum. The target region was unique, and a Probe Match analysis retrieved no sequences with fewer than four mismatches from non-Methylocaldum species.
The complete suite of -methanotroph probes covered 97% of
the strains listed in Fig. 3; only two sequences were not covered. One
is that of Methylomonas methanica strain 81Z, cultures of which are no longer extant and whose affiliation with the genus Methylomonas was never verified (J. P. Bowman and
P. N. Green, personal communication). Because this sequence is of
low overall quality (3.3% ambiguity), one or more of the indicated
mismatches could be incorrect. The other organism not covered by
the probes is a novel thermophilic methanotroph,
"Methylothermus " sp. strain HB. Because it is the only
known -methanotroph that is polyphyletic with respect to the
family Methylococcaceae (8), this result was expected.
Probe specificity and optimization for quantitative hybridization. The probes described here are intended to quantify 16S rRNA from specific microbial populations against a background of many unknown populations in environmental samples. The probes must discriminate against unknown, nontarget 16S rRNA that may have a difference of only 1 base from the intended target. The primary factor for achieving stringent specificity and quantitative hybridization of 16S rRNA from environmental samples is accurate determination of the melting characteristics of the probe-target duplex. Hence, empirical determination of the Td is essential (32, 54). We have optimized the probes presented here for stringent discrimination against nontarget RNA and also for quantitative hybridization by empirically determining the Td for each probe.
The Tds of the probes ranged from 49 to 57°C (Table 1). When Northern blots were hybridized overnight and then washed at the appropriate Td, target and nontarget rRNAs were visually distinguishable on blots and yielded quantitatively distinct results when analyzed using a scintillation counter (Fig. 1) or a phosphorimager (data not shown). These results verify that the use of known concentrations of reference rRNA as standards will permit quantitative analysis of environmental rRNA possessing the target sequence, as demonstrated previously (49, 54). Probes Am445, Mmb1007, Mlm482, Mlm732b, Mlc123, and Mcd77 each exhibited at least two base mismatches against any nonmethanotroph sequence, whereas probes Gm633, Gm705, Mlb482, Mmb482, Mlm732a, and Mlc1436 each exhibited at least one base mismatch with any nonmethanotroph sequence. Probes Mlb662, Mmb482, and Mmb1007 matched sequences from one to four-methanotrophs outside their respective target genera (Fig.
3). Although we consider this problem to be minor, these probes could
yield ambiguous results for fine-scale descriptions of
-methanotroph communities. All other genus-level probes were
specific to their intended target genera. The - and -methanotroph probes had no cross-family hybridization potential.
Two probes, Am976 and Mlb662, present the more serious problem
of complementing 16S rRNA sequences of some
nonmethanotrophic bacteria. They have been retained despite
this weakness for two reasons. First, they are needed to ensure
complete coverage of their target groups, in combination with other
probes, when broad-spectrum probing is desired. Second, they were
deemed particularly useful for certain experimental approaches, such as
monitoring of CH4 enrichment cultures, use as PCR
primers in cases where amplified products are to be sequenced for
identification, or analysis of community composition in environmental
samples where the nontarget organisms with which the probes hybridize
should be minor components of the community. For instance,
because marine Cycloclasticus spp. were the only
nonmethanotrophs that matched Mlb662 (Fig. 3), this probe
might be appropriate for probing nonmarine samples.
Probing the database. The GenBank database contains thousands of bacterial 16S rRNA gene sequences from cultures and environmental clones (6). Hence, "probing" this database should provide a powerful assessment of a probe's ability to select specifically for methanotroph sequences against a background of myriad nonmethanotroph sequences. We subjected each probe sequence to a basic BLAST search (5) and examined sequences retrieved with an identical match. Only sequences identified as 16S rRNA genes were considered. The organism identifications were based solely on information provided in the accession records or in publications cited therein.
Eleven of 14 probes retrieved only sequences that were identified as methanotrophs (Table 2). Probes Am976, Mlb662, and Mlc1436 retrieved a number of sequences representing a narrow range of nonmethanotrophic taxa. The first two of these probes matched environmentally restricted taxa, such as obligate pathogens (Afipia spp.) and obligate marine bacteria (Cycloclasticus spp.). If used strategically, therefore, these probes are likely to be useful for studying methanotroph communities. From the data in Table 2, it would be premature to conclude that Mlc1436 is nonspecific. All but one of the nonmethanotroph sequences retrieved by this probe were nearly identical clones of putative
-Proteobacteria from
an activated sludge reactor. However, no cultured organisms belonging
to the -Proteobacteria were retrieved, and no published data were cited in the accession records to confirm the phylogenetic position of these environmental clones. Overall, the data in Table 2
suggest that at least 11 and possibly 12 of the probes presented here
are highly specific to methanotrophic bacteria and that the two
clearly nonspecific probes should hybridize to a phylogenetically limited range of nonmethanotrophs with restricted
environmental distributions.
|
Summary and conclusions. The breadth and specificity of the probes reported here are unprecedented, providing 97% coverage of the 87 methanotroph 16S rRNA sequences examined (Fig. 2 and 3). Several new methanotroph genera that have been proposed recently following the isolation of novel strains are covered. Of the three strains apparently not covered by the probes, one is no longer extant and the available 16S rRNA sequence is of low overall quality, bringing into question whether the indicated probe mismatches are correct. The other two strains (Methylocella palustris sp. strain K and Methylothermus sp. strain HB) that did not match any probe are polyphyletic with respect to the Methylocystaceae and Methylococcaceae, thus reflecting the high specificity of the probes to the phylogenetic clades they were designed to target. Initial results from studies with several soils indicate that the probes are effective for studying methanotroph communities in soil (unpublished data), perhaps the most difficult substrate on which to perform quantitative hybridization assays (4). Hence, all of the methanotroph taxa that have become well known through years of laboratory studies, as well as several recently described taxa, can now be studied at both the family and genus levels in environmental samples by using the probes reported here.
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ACKNOWLEDGMENTS |
|---|
J. Gulledge and A. Ahmad contributed equally to this work.
We gratefully acknowledge the following individuals: M. Polz for training and helpful discussions on designing oligonucleotide probes; A. J. Auman, A. M. Costello, and M. E. Lidstrom for updated 16S rRNA sequences and a protocol for extracting nucleic acids from methanotrophs; G. M. King, R. Knowles, J. C. Murrell, J. S. Poindexter, and J. D. Semrau for providing reference cultures; and A. A. DiSpirito for reference genomic DNA.
This work was supported by the U.S. National Science Foundation (award DEB9708092) and was initiated while J. Gulledge was a DOE-Energy Biosciences Research Fellow of the Life Sciences Research Foundation.
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FOOTNOTES |
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* Corresponding author. Mailing address: Harvard University, The Biological Laboratories, 16 Divinity Ave., Cambridge, MA 02138. Phone: (617) 496-2177. Fax: (617) 496-6933. E-mail: cavanaug{at}fas.harvard.edu.
Present address: Department of Ecology and Evolutionary Biology,
Tulane University, New Orleans, LA 70118.
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Abstract
Introduction
Materials and Methods
Results and Discussion
References
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