Molecular Ecology (2006) 15, 3131– 3138 doi: 10.1111/j.1365-294X.2006.03008.x Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis Blackwell Publishing Ltd H . H . D E F I N E L I C H T , J . J . B O O M S M A and D . K . A A N E N * Department of Population Biology, Institute of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark, *Laboratory of Genetics, Wageningen University and Research Center, the Netherlands Abstract All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would be compatible with clonal vertical transmission, as is known to occur in Macrotermes bellicosus. We investigated this hypothesis by analysing DNA sequence polymorphisms as codominant SNP markers of four single-copy gene fragments of Termitomyces isolates from 31 colonies of M. natalensis. A signature of free recombination was found, indicative of frequent sexual horizontal transmission. First, all 31 strains had unique multilocus genotypes. Second, SNP markers (n = 55) were largely in Hardy–Weinberg equilibrium (90.9%) and almost all possible pairs of SNPs between genetically unlinked loci were in linkage equilibrium (96.7%). Finally, extensive intragenic α fragment. Substantial genetic variation recombination was found, especially in the EF1α and a freely recombining population structure can only be explained by frequent horizontal and sexual transmission of Termitomyces. The apparent variation in symbiont transmission mode among Macrotermes species implies that vertical symbiont transmission can evolve rapidly. The unexpected finding of horizontal transmission makes the apparent absence of Termitomyces mushrooms on M. natalensis mounds puzzling. To our knowledge, this is the first detailed study of the genetic population structure of a single lineage of Termitomyces. Keywords: mutualism, population structure, recombination, symbiont transmission, symbiosis, Termitomyces Received 18 December 2005; revision received 12 April 2006; accepted 2 May 2006 Introduction Fungus-growing termites (Macrotermitinae: Termitidae: Isoptera) live in an obligate symbiosis with fungi of the genus Termitomyces (Basidiomycota). The fungus is cultured on special structures inside the termite nest (fungus combs) and depends on the termites for substrate provisioning and protection. The comb is constructed from finely fragmented plant material, which is inoculated with asexual spores of the fungal symbiont (Leuthold et al. 1989). After a few weeks, the inoculated fungus comb produces nitrogen-rich basidiocarp primordia (nodules) which contain conidia with asexual spores. The mycelium Correspondence: Henrik H. De Fine Licht, Fax: 45 35321250, E-mail: hhdefinelicht@bi.ku.dk. © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd at the surface, the nodules with asexual spores, and (later) the entire comb are eaten by the termites (Rouland-Lefevre 2000; Rouland-Lefevre & Bignell 2002; Hyodo et al. 2003). The few available studies of intranest genetic diversity of symbionts of the genus Termitomyces have shown that the fungus is kept as a single-strain monoculture within a single colony (Aanen et al. 2002; Katoh et al. 2002; Shinzato et al. 2005). This may be due to vertical uniparental transmission, which implies that either the female or the male reproductive brings fungal mycelium and asexual conidiospores from the natal colony when dispersing, and that this inoculum is used to establish a new fungus garden after pair formation. Such vertical transmission would thus be associated with clonal reproduction of the Termitomyces fungus (Korb & Aanen 2003). However, the alternative, horizontal symbiont transmission, is much 3132 H . H . D E F I N E L I C H T , J . J . B O O M S M A and D . K . A A N E N more widespread in the fungus-growing termites (Korb & Aanen 2003), and is almost certainly the ancestral transmission mode (Aanen et al. 2002). Horizontal transmission depends on fruiting bodies (mushrooms) growing out of the exterior of the termite mound to release spores. Uniparental vertical transmission has only been observed in species of the termite genus Microtermes (always via the female in the five species studied) and (via the male) in the species Macrotermes bellicosus (Johnson et al. 1981). However, other Macrotermes species [M. subhyalinus ( Johnson et al. 1981) and M. michaelseni (Sieber 1983)] have been shown to acquire their fungal symbiont horizontally and the same is true for a few studied species of Ancistrotermes, Pseudoacanthotermes and Odontotermes (Korb & Aanen 2003). Fungal transmission modes have not been studied directly for M. natalensis. However, it has recently been shown that the Termitomyces symbiont associated with this species grows as a heterokaryon in the fungus comb and has a heterothallic mating system (De Fine Licht et al. 2005). This implies that horizontal transmission of the fungus necessarily has to be associated with sexual reproduction, resulting in recombination and ample population-wide genetic variation (Orr-Weaver & Szostak 1985; Stumpf & McVean 2003; Halkett et al. 2005). Frequent recombination would mean that alleles at single loci are in Hardy– Weinberg equilibrium (HWE) and that genetically unlinked loci are in linkage equilibrium. In contrast, vertical transmission and clonal reproduction of the fungus would result in deviations from HWE and in significant linkage disequilibrium (LD) across loci (Tibayrenc 1997; Vilgalys et al. 1997; Brown 1999; Maynard Smith 1999; Taylor et al. 1999; Awadalla 2003). Basidiocarps (mushrooms) have not been observed on Macrotermes natalensis mounds, although it has been shown that functional basidiocarps, producing sexual spores, can be formed on comb fragments in the laboratory (De Fine Licht et al. 2005). Furthermore, a recent study of symbiont genetic variation showed that M. natalensis cultures only a single lineage of Termitomyces symbionts, in contrast to most other fungus-growing termite species (Aanen et al., in preparation). These observations would be suggestive of vertical symbiont transmission, but the decisive tests of HWE and linkage equilibrium at marker loci have not been carried out. Our present study is the first to address these fundamental characteristics of the genetic population structure in a single lineage of Termitomyces. We show that the symbiont breeding system is consistent with horizontal transmission. This unexpected result brings up the question why mushrooms on M. natalensis mounds have so far not been observed. Materials and methods Sampling Termite mounds of Macrotermes natalensis (n = 31) were excavated in South Africa during January 2003 and January–March 2004 (Fig. 1). Macrotermes natalensis has the most southern range within the genus Macrotermes and is the most widespread species of southern Africa (Ruelle et al. 1975). The termites feed predominantly on dead plant Fig. 1 Map of the seven sampling localities of Macrotermes natalensis in South Africa. Numbers refer to the number of sampled colonies at each site. All samples were collected in January–February 2004, except for the three northernmost colonies and seven of the colonies from Pretoria (point 13), which were collected in January 2003. The dashed line represents the approximate southwestern distribution limit of the genus Macrotermes (Uys 2002). © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd S Y M B I O N T T R A N S M I S S I O N I N M . N A T A L E N S I S 3133 material such as wood and leaf litter and are a serious pest of wood in buildings (Uys 2002). The sampled mounds were 0.3–2 m high and primarily present in grassland habitats, but some were located at the edge of woodland vegetation. The mounds were opened and fragments of Termitomyces fungus comb collected and transported to the laboratory in plastic bags. The fungus was isolated by aseptically placing nodules on malt-yeast agar in Petri dishes under a dissecting microscope (MYA; 20 g/L malt extract, 2 g/L yeast extract and 15 g/L agar). When a mycelium developed without contaminants, the fungus was further subcultured on a new agar Petri dish. Liquid cultures were prepared with nodules and mycelium from these secondarily cultivated plates (20 g/L malt extract and 2 g/L yeast extract). All isolates were incubated at 25 °C in complete darkness. Sequence analysis DNA was extracted from the 31 liquid cultures after 4 weeks of growth. Approximately 1.5 mL of fungal mycelium was transferred to 2-mL Eppendorf tubes and freeze-dried on a SpeedVac connected to a Lyovac GT 2 (Savant, Leybold-Heraus). We used a DNeasy Plant Mini Kit (cat. no. 69104, QIAGEN GmbH) and measured the DNA concentration of each sample with a NanoDrop ND1000 Spectrophotometer (NanoDrop Technologies). Four gene fragments were amplified using standard polymerase chain reactions (PCRs): the internal transcribed spacer (ITS) region between the 18 S and the 25 S nuclear RNA genes, partial sequences of the two largest nuclear RNA Polymerase II subunits, RPB1 and RPB2, and partial sequences of the nuclear Elongation Factor 1 alpha (EF1α). The following primer combinations were used: ITS1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS4 (5′-TCCTCCGCTTATTGATATGC-3′) (White et al. 1990), RPB1-AF (5′-GARTGYCCDGGDCAYTTYGG-3′) and Frpb1-CR (5′-CCNGCDATNTCRTTRTCCATRTA-3′) (Matheny et al. 2002), bRPB2 – 6F (5′-TGGGGYATGGTNTGYCCYGC-3′) and bRPB2-7.1R (5′-CCCATRGCYTGYTTMCCCATDGC-3′) (Matheny 2005), and EF595F (5′-CGTGACTTCATCAAGAACATG-3′) and EF1160R (5′CCGATCTTGTAGACGTCCTG-3′) (Kauserud & Schumacher 2001). To improve amplification of isolates, which were difficult to amplify with standard primers for EF1α, we developed specific primers for this gene for the Termitomyces associated with M. natalensis: EF634F-Mnat (5′-AGGCTGACTGCGCTATCCTTAT-3′) and EF1127R-Mnat (5′GGTTCGATGGCATCGATGGCAT-3′). PCRs were run on a Hybaid PCR Express Thermal Cycler or on a Hybaid Omn-E Thermal Cycler (Thermo Molecular Biology). PCR was performed in 20-µL reactions containing 2 µL MgCl2, 2 µL PCR buffer (Applied Biosystems), 2 µL of each primer, 8 µL GATC mix, 0.1 µL © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd AmpliTaq Gold polymerase (Applied Biosystems) and 3.6 µL ddH2O. PCR programmes consisted of an initial denaturing step of 10 min at 95 °C followed by 35 cycles (30 s at 95°, 30 s at 57° and 30 s at 72°) finished by a final elongation step of 5 min at 72 °C, except for the RPB1 primers. Here, an initial step of 5 min at 95 °C was followed by 35 cycles (30 s at 95°, 30 s at 55°, 1° increase per 5 s until 72° and then 30 s at 72°), finished by a final elongation step of 10 min at 72 °C. The PCR products were checked on a 2.0% agarose gel with EtBr before purification with a QIAquick PCR purification kit (cat. no. 28106, QIAGEN). Sequencing was performed by MWG Biotech. For all four gene fragments, PCR products were directly sequenced. DNA sequences of different strains were aligned and analysed with sequencher version 3.1.1 for Macintosh (Gene Codes Corporation). Double peaks with similar height were present in the sequence chromatogram at multiple positions indicating intrastrain variation and allowing us to obtain codominant unphased data for all single nucleotide polymorphisms (SNPs) for ITS, RPB1 and RPB2. In addition, for the EF1α gene, separate DNA sequences of the two alleles were determined. The purified PCR products were cloned with a TOPO TA cloning kit (Invitrogen A/S). Procedures were according to the manual, except that all reaction amounts were three times less than stated. One cloned EF1α fragment from each strain was purified using the QIAquick PCR purification kit (cat. no. 28106, QIAGEN) and sequenced. By comparing the cloned sequences with the direct sequences of the PCR products, the two alleles of the EF1α locus of each isolate were obtained. Sequences have been deposited in GenBank with accession nos DQ436938–DQ437074. Population-genetic and phylogenetic analysis SNPs were tested for deviations from HWE using the exact probability test (Guo & Thompson 1992) implemented in arlequin version 2.0 (Slatkin & Excoffier 1996), with 1000 steps in Markov chain and 1000 dememorization steps. Observed and expected heterozygosity and F-statistics (FIS) were estimated using popgene version 1.32 (Yeh & Boyle 1997). The presence of LD between all pair-wise comparisons of these SNPs in the four unlinked genes was analysed with a likelihood-ratio test in arlequin version 2.0 with 20 000 permutation steps. The SNPs within the EF1α gene were analysed for LD with an exact test based on a Markov chain in arlequin version 2.0 with 1000 steps in Markov chain and 1000 dememorization steps. For the most variable locus, EF1α, for which we had obtained the two allele sequences for each strain, intragenic recombination was checked with a parsimony analysis of the sequences using paup* 4.0b10 (Swofford 2001). In the absence of intragenic recombination and recurrent mutation, the ancestry of the alleles can be represented as 3134 H . H . D E F I N E L I C H T , J . J . B O O M S M A and D . K . A A N E N Table 1 The characteristics of the four gene sequences obtained for each isolate: the number of isolates for which it was possible to amplify the four sequences is given with the base-pair length of each fragment, the number of single nucleotide polymorphisms (SNPs), and the percentage of these that did not depart significantly from Hardy–Weinberg proportions (exact probability test implemented in arlequin version 2.1) Gene Sequenced isolates Length SNPs Hardy–Weinberg equilibrium ITS EF1α (in phase) RPB1 RPB2 29 31 21 31 17 (100%) 16 (89%) 9 (75%) 8 (100%) 586 bp 444 bp 716 bp 552 bp 17 18 12 8 Table 2 Observed and expected heterozygosity and Wright’s fixation index (FIS) of single nucleotide polymorphisms (SNPs) from the four gene sequences of Termitomyces sp. associated with Macrotermes natalensis Locus ITS (n = 29) EF1α (n = 31) RPB1 (n = 21) RPB2 (n = 31) HO HE FIS 0.087 0.083 −0.047 0.208 0.241 0.073 0.202 0.271 0.180 0.129 0.126 −0.030 a tree with a length that is equal to the number of SNPs and with a consistency index of 1 (e.g. Burt et al. 1996). In contrast, if intragenic recombination is frequent, the tree will be poorly resolved and rife with homoplasy (see, e.g. Burt et al. 1996). In paup*, a heuristic search was performed [settings: 10 random addition sequences; mulpars on; treebisection–reconnection (TBR) branch swapping]. To test whether recombination is completely free, the length of the shortest trees was compared to the length of 1000 randomized data sets [using the permutation tail probability (PTP) test in paup*]. Results SNPs in the four sequenced genes concerned either single base-pair substitutions (76.4%) or indels (23.6%) in introns of the gene fragments. Adjacent double and triple SNPs made up 9.1% of the total variation (Table 1). At all SNP sites only two of the possible five character states (the four nucleotides plus gap) were observed, except one with three states. This indicates that mutations at those sites are rare so that any changes in combinations of character states are likely to be due to recombination rather than to recurrent mutations. All SNPs of ITS, RPB1, RPB2 and EF1α were treated as single loci and checked for deviation from Hardy–Weinberg proportions with an exact probability test (Guo & Thompson 1992). The genotypic distribution of the large majority (90.9%) of these SNPs was Table 3 Percentages of Termitomyces single nucleotide polymorphisms (SNPs) that were in linkage equilibrium in pairwise comparisons within and across loci. The presence of LD was analysed with a likelihood-ratio test with 20 000 permutation steps, except for comparisons within the EF1α gene where an exact test based on 1000 steps in Markov chain and 1000 dememorization steps was used % SNPs ITS EF1α RPB1 RPB2 ITS EF1α RPB1 RPB2 89.7 94.2 100 96.4 72.5 96.5 96.9 87.3 99.0 92.9 not significantly different from HW proportions (Table 1). Observed and expected heterozygosity and Fis values are shown in Table 2. A small heterozygote deficit was observed for ITS and RPB2, whereas a small heterozygote excess was observed for EF1α and RPB1 (Table 2). Almost all possible pairs of SNPs between the four genetically unlinked loci were in linkage equilibrium (96.7%; Table 3). Also most of the pairs of SNPs within the gene regions (89.7% for ITS, 87.3% for RPB1, 92.9% for RPB2 and, 72.5% for EF1α) were in linkage equilibrium (Table 3), showing that frequent intragene recombination has occurred. The distribution of SNPs in ITS, RPB1, RPB2 and EF1α is presented in Table S1 (Supplementary material). Phylogenetic analysis for EF1α For the EF1α fragment, sequences of both alleles for each strain were determined so that this fragment could be studied in more detail. Forty-two different haplotypes were found among the 62 sequenced alleles and all 31 isolates had distinct genotypes (see also Table S1). To check for intragenic recombination within the EF1α fragment, we performed a parsimony analysis of the 42 different EF1α alleles. Parsimony analysis of the 18 SNPs resulted in > 30 000 trees (length 48: consistency index 0.31: Fig. 2a), the strict consensus tree of which is completely unresolved (Fig. 2b). This shows that extensive intragenic recombination has occurred in the EF1α gene. As expected, recombination is not completely free as the length of the shortest trees is still shorter than the length of trees fitted to randomized data (Fig. 3). The frequency of sexual reproduction Our analyses show that Termitomyces sp. associated with Macrotermes natalensis has a recombining population structure. However, a low frequency of sex in a population can be sufficient to create a recombining population structure in a sample of that population (Bengtsson 2003; Stumpf © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd S Y M B I O N T T R A N S M I S S I O N I N M . N A T A L E N S I S 3135 Fig. 2 Phylogenetic analysis of the 42 different EF1α alleles. (a) One of the > 30 000 most parsimonious trees of length 48 (c.i. 0.31). (b) The completely unresolved strict consensus tree of the > 30 000 most parsimonious trees, which indicates frequent intragenic recombination. Fig. 3 Frequency distribution of tree lengths for randomized data of the 42 different EF1α alleles. The observed length (48) falls well below the distribution of lengths of the randomized data, indicating that recombination is not completely free. © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd 3136 H . H . D E F I N E L I C H T , J . J . B O O M S M A and D . K . A A N E N Fig. 4 The expected number of clones (genotypes) in a population with a low frequency of sex based on a sample of 31. The expected number of clones was estimated from the absolute number of sexual events, using the formula y = [(2σN/2σN) + (2σN/2σN + 1) + ··· + (2σN/2σN + r − 1)], where y is the expected number of clones in a sample of size r, N is the population size and σ is the rate of sexuality (see text for details). A few sexual events rapidly increase the expected number of clones, even in a population with a low frequency of sex. & McVean 2003; Halkett et al. 2005). With a low frequency of sex, the expected number of different genotypes in a sample can be calculated as a function of the absolute number of sexual events per generation (Ewens 1979; as described in Bengtsson 2003). In Fig. 4, we plotted the expected number of different genotypes in a sample of 31 as a function of the absolute number of sexual events per generation (i.e. the product of the fraction of sexually reproducing individuals and the total population size). As all 31 samples represent different genotypes, this figure indicates that the minimum number of sexually reproducing individuals per generation is > 100. Discussion The samples analysed in this study indicate that the Termitomyces strains associated with Macrotermes natalensis have a sexual population structure with frequent recombination, which is consistent with horizontal transmission (see also Korb & Aanen 2003; De Fine Licht et al. 2005). All genes used as markers in this study are present in the genome as single-copy genes, except for the ITS, which is part of the ribosomal RNA repeat unit, and occurs in multiple copies per genome. Theoretically therefore the intrastrain variation in the ITS sequences that we found could also represent variation between copies within the repeat (Selosse et al. 2002; Okabe & Matsumoto 2003). However, previous studies of basidiomycete fungi have shown that multiple ITS types only occur in heterokaryons and never in homokaryons and that the different ITS variants from a heterokaryon always segregate in the homokaryotic offspring (Aanen et al. 2001; Kauserud & Schumacher 2003). This has also been shown for Termitomyces (De Fine Licht et al. 2005). This implies that the ITS gene in heterothallic basidiomycetes effectively behaves as a single locus with Mendelian segregation. The distinct genotypes of all the isolates clearly suggest that Termitomyces recombines and creates novel genotypes each generation. Because nearly all SNPs were in HWE and LD between loci was rare, the accumulation of mutations is unlikely as an alternative explanation for the observed population structure. Earlier studies of termite symbiont transmission modes have used direct experimental tests with incipient colonies and/or dissection of alates (Lüscher 1951; Sands 1960; Johnson 1981; Johnson et al. 1981; Sieber 1983; Leuthold et al. 1989). Compared to these studies, our genetic evidence for horizontal transmission remains indirect. In particular, the frequency by which horizontal transmission occurs in the field is unknown and this is important because even a low frequency of recombination can result in an apparently fully recombining population structure in a random sample from the population (Bengtsson 2003; Stumpf & McVean 2003; Halkett et al. 2005). As all 31 samples represented different genotypes, the recombination frequency analysis indicated that the minimum number of sexually reproducing individuals per generation was > 100 (Fig. 4). The alternative clonal dispersal mode of Termitomyces would rely on vertical dispersal via the winged termites, which is known to be much less effective than windborne spore dispersal (Nutting 1969; Korb & Linsenmair 2001). Therefore, clonally related fungal genotypes would be expected to be clustered in space. Several of the collected samples were from neighbouring termite mounds (from four sites we sampled: 13, 9, 3 and 3 mounds, respectively, see also Fig. 1). We did not find any clonally related (i.e. identical) genotypes within a single locality, which corroborates our conclusion that transmission is horizontal and sexual. Furthermore, a low frequency of sex would also be at odds with the extensive intragenic recombination that we found in this study. Two interesting new questions arise from our results. First, it now seems beyond reasonable doubt that symbiont transmission within the genus Macrotermes is variable. This suggests that transmission modes can evolve rapidly quickly, which implies that generalizations for entire genera may not hold even when based on several case studies. For example, the five species of Microtermes that have now been shown to rely on vertical symbiont transmission via the female sex (Johnson 1981; Johnson et al. 1981) do not preclude that there may be Microtermes species that have either retained or have reverted to horizontal transmission. Second, although our Fig. 4 shows that sex and recombination do not need to occur every generation, it remains puzzling that field observations have so far failed to find symbiont mushrooms on M. natalensis mounds. One © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd S Y M B I O N T T R A N S M I S S I O N I N M . N A T A L E N S I S 3137 explanation could be that fruiting only happens in some years and that basidiospores are relatively long lived after dispersal. However, it is also possible that M. natalensis workers actively suppress fruiting of their symbiont, which is a waste of resources for the termites (Aanen, 2006). Reproductive conflicts of this kind have been extensively treated elsewhere (Korb & Aanen, 2003; Aanen, 2006; Aanen & Boomsma, 2006). Worker suppression of fruiting bodies can persist as an evolutionary stable strategy if M. natalensis in reality ‘parasitizes’ on other sympatric Macrotermes species where the symbiont is known to produce fruiting bodies (Aanen & Boomsma, 2006), such as M. subhyalinus (Johnson et al. 1981) and M. michaelseni (B. Slippers & W. de Beer, personal observation). This hypothesis remains to be tested by comparing Termitomyces genotypes of all three species. Because the fungal transmission mode is variable across species, the genus Macrotermes may therefore be the most suitable genus to look for the expression of these conflicts, and M. natalensis would be a promising species to start. Acknowledgements We thank Sylvia Mathiasen, Pia Friis and Tina Brand for assistance in the laboratory, Jannette Mitchell and Wilhelm de Beer for help during fieldwork and Fons Debets for comments on an earlier version of this manuscript. Supplementary material The supplementary material is available from http:// www.blackwellpublishing.com/products/journals/suppmat/ MEC/MEC3008/MEC3008sm.htm Table S1 Distribution of single nucleotide polymorphisms (SNPs) of the internal transcribed nuclear rDNA spacer sequence (ITS), and partial EF1á, RPB1 and RPB2 sequences of Termitomyces sp. associated with Macrotermes natalensis. Variable positions in the sequences are indicated (vertical numbers). 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