Research Article |
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Corresponding author: Susana Valencia-Díaz ( susana.valencia@uaem.mx ) Academic editor: Luiza Teixeira-Costa
© 2026 Magaly Valeria Silvestre-Moreno, Kenya León-Carvajal, Susana Valencia-Díaz, Jonas Morales-Linares, Víctor Hugo Toledo-Hernández, Beatriz Olivia Cortes-Anzures, Alejandro Flores-Palacios.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Silvestre-Moreno MV, León-Carvajal K, Valencia-Díaz S, Morales-Linares J, Toledo-Hernández VH, Cortes-Anzures BO, Flores-Palacios A (2026) Regeneration niche and terrestrial orchid rarity: a case study with Malaxis. Plant Ecology and Evolution 159(2): 431-443. https://doi.org/10.5091/plecevo.188226
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Background and aims – It has been suggested that the rarity of orchids is caused by pollination limitation and a restricted regeneration niche, including their germination dependence on specific microhabitat conditions. We hypothesize that terrestrial orchids descended from epiphyte ancestors (i.e. re-terrestrialized orchids) are rare because their germination depends on coarse woody debris (CWD), which is scarce in forests.
Material and methods – In a mixed oak forest in central Mexico, we documented the association of Malaxis orchids with CWD and experimentally tested whether the germination of Malaxis brachyrrhynchos (terrestrial) and the sympatric Stelis retusa (true epiphyte) depends on CWD, forest soil, Quercus rugosa bark, or mixtures of these substrates.
Key results – We found that CWD are scarce in the forest (< 1% of the forest floor), and the abundance of Malaxis spp. individuals is associated with large CWD. The germination of M. brachyrrhynchos is higher in CWD than in the soil or tree bark, while S. retusa shows better germination in bark than in the soil or CWD.
Conclusion – Our data suggest that the re-terrestrialization of Malaxis orchids may be facilitated by their affinity to germinate in decayed wood, which is also present in the canopy. This dependency restricts their regeneration niche and may make these orchids rare. Our results suggest that keeping CWD on the forest floor will help orchid management and conservation.
epiphytes, re-terrestrialization, oak forest, orchid evolution, orchid germination
Species rarity (i.e. those with low spatial frequency or individual abundance) has received theoretical and empirical attention because species are assumed to become rare as part of an extinction process (
More than 60% of orchids are epiphytes, so they must germinate on canopy substrates (e.g. canopy soils = histosols, decayed wood, bark) (
The re-terrestrialization of epiphytes shows that epiphytism is not an evolutionary endpoint, but re-terrestrialization is controversial. It has been suggested that one selective force impelling plants to colonize the canopy is the escape from terrestrial enemies (i.e. epiphyte enemy escape hypothesis;
Orchid re-terrestrialization may occur because the seeds of some orchid species germinate in decayed wood in the canopy. However, the decayed wood would eventually fall to the forest floor as coarse woody debris (CWD) (
We tested the hypothesis whether Malaxis species depend on CWD that has fallen to the forest floor for their germination. To do so, we: 1) measured the abundance of CWD in a mixed oak forest; 2) tested the affinity of Malaxis spp. with different decaying CWD stages; and 3) experimentally tested the CWD dependence for seed germination of a terrestrial (Malaxis brachyrrhynchos (Rchb.f.) Ames) and a true epiphytic orchid (as a control; Stelis retusa (Lex.) Pridgeon & M.W.Chase). Malaxis brachyrrhynchos and Stelis retusa belong to different Epidendroidae tribes (
The study was done in a mixed oak forest located between San Juan Tlacotenco (Tepoztlán) and Coajomulco (Huitzilac), Morelos, Mexico in the Tepozteco national park (99°02’00”–99°12’55”N, 18°53’20”–19°05’30”W) (
In August–September 2013 (rainy season), we randomly selected ten sampling points within the mixed oak forest (Suppl. material
In each transect, we searched for CWD (diameter ≥ 10 cm) lying on the forest floor (i.e. fallen branches, trunks, and stumps). We measured the larger diameter at one of its extremes for each CWD, its length, plant coverage (mosses, fungi, and each vascular plant species), and the number of orchid individuals. To estimate coverages, we measured the length of each fungus/plant species on the CWD and divided it by the CWD length. Except for orchids (identified in the field with a field guide;
We experimentally tested seed germination in forest soil, bark, and decayed CWD. In this experiment, we used seeds of two of the most common orchids in the study area: Malaxis brachyrrhynchos and, in the absence of true epiphytic Malaxidinae, Stelis retusa (
In May 2020, we split the sample of seeds into 105 sets of 0.003 mg (containing ca 1798 seeds of M. brachyrrhynchos and ca 1916 seeds of S. retusa). Each seed set was put inside a 4 × 3 cm mesh envelope (Nitex screen, NTX50, 50 μm opening). With this method, it is possible to study the germination of dust seeds, allowing them to interact with microorganisms without seed losses (
Three CWD in decay class 4 (Suppl. materials
Because of the closure of activities caused by the COVID-19 pandemic, we could not conduct the experiment under field conditions or in a greenhouse at the Universidad Autonoma del Estado de Morelos. Therefore, we performed the seed germination experiment ex situ in the garden of the first author (M.V. S.-M.). Ex situ experiments have several strengths because they allow more accurate control of secondary factors (e.g. site variability) while manipulating the factors (e.g. substrate type) (
Data analyses were done in R v.4.2.1 (
To test whether the abundance of Malaxis was related to CWD diameter, decay class, species richness (S), and fungal cover (%), we compared the performance of 16 candidate models, including all combinations of these variables. All predictor variables were standardized before analysis and were not strongly correlated with one another (Suppl. material
Seed germination of each orchid species was analysed with a generalized linear model for a binomial response variable (
In the ten transects, we counted 89 pieces of CWD (eight stumps and 81 fallen branches and trunks) on the forest floor. The mean length of CWD was 393 cm (± 349 cm, minimum = 12 cm, maximum = 1356 cm) with a mean diameter of 24.8 cm (± 11.8 cm, minimum = 10 cm, maximum = 57 cm) (Suppl. material
The average number of CWD per 0.1 ha transect was 8.9 (± 4.6 CWD/0.1 ha, minimum = 3, maximum = 19). The availability of CWD in the forest is low. The average area of the forest floor covered by CWD is 9.1 ± 5.8 m2/0.1 ha (minimum = 1.5 m2/0.1 ha, maximum = 19.0 m2/0.1 ha), meaning that the average percentage of forest floor covered by CWD is 0.009 ± 0.006% (minimum = 0.002%, maximum = 0.02%).
Most CWD were in decay class 2 (36.0%) (Table
Decay class distribution of coarse woody debris (CWD) on the forest floor of ten 10 × 100 m transects in a mixed oak forest in central Mexico.
| Diameter of CWD | Decay classes of CWD | |||
| 1 | 2 | 3 | 4 | |
| 10 ≤ 15 | 7 | 11 | 8 | 1 |
| ≤ 20 | 0 | 7 | 3 | 6 |
| ≤ 25 | 1 | 4 | 4 | 0 |
| ≤ 30 | 0 | 9 | 5 | 4 |
| ≤ 35 | 0 | 0 | 1 | 3 |
| ≤ 40 | 0 | 0 | 1 | 5 |
| ≤ 45 | 0 | 0 | 0 | 1 |
| ≤ 50 | 0 | 0 | 1 | 1 |
| ≤ 55 | 0 | 1 | 1 | 1 |
| ≤ 60 | 0 | 0 | 1 | 0 |
| ≤ 65 | 0 | 0 | 1 | 1 |
| Total | 8 | 32 | 26 | 23 |
In the CWD, we found 83 Malaxis individuals and one Sarcoglottis schaffneri (Rchb.f.). Ames. Because most individuals were immature, had developing inflorescences, or were bearing fruit during sampling, we were unable to identify the Malaxis species. Orchids appeared on CWD from decay class 2 (14 Malaxis and one S. schaffneri individuals) to 4 (63 Malaxis individuals).
Among the 16 candidate models, the model including all variables (CWD diameter, CWD decay stage, species richness, and fungus coverage) was the best at explaining Malaxis abundance in CWD (Table
The performance of 16 candidate models explaining the abundance of Malaxis species on 89 coarse woody debris (CWD) sampled on the forest floor of a mixed oak forest in central Mexico. The independent variables for each CWD are its decay class (Decay), diameter (Diameter), coverage of fungus, and richness of vascular plants (S). K = number of parameters in the model, QAICc = Quasi AIC value, ΔQAICc = change in the QAICc value between the model and the model with the lowest QAICc.
| Candidate model | K | QAICc | ΔQAICc | QAICc weight |
| Diameter + Decay + S + Fungus | 6 | 60.61 | 0 | 0.73 |
| Diameter + S + Fungus | 5 | 62.85 | 2.24 | 0.24 |
| Diameter + Decay + S | 5 | 68.94 | 8.33 | 0.01 |
| Decay + S + Fungus | 5 | 69.87 | 9.25 | 0.01 |
| Diameter + S | 4 | 70.16 | 9.54 | 0.01 |
| Decay + S | 4 | 76.31 | 15.69 | 0 |
| S + Fungus | 4 | 78.63 | 18.01 | 0 |
| S | 3 | 83.01 | 22.39 | 0 |
| Diameter + Decay +Fungus | 5 | 107.32 | 46.7 | 0 |
| Diameter + Decay | 4 | 108.25 | 47.64 | 0 |
| Decay + Fungus | 4 | 114.23 | 53.62 | 0 |
| Decay | 3 | 114.68 | 54.07 | 0 |
| Diameter + Fungus | 4 | 116.81 | 56.2 | 0 |
| Diameter | 3 | 116.87 | 56.25 | 0 |
| Intercept only | 2 | 133.17 | 72.55 | 0 |
| Fungus | 3 | 133.38 | 72.77 | 0 |
Seed germination occurred after six weeks. By the seventh week, germination was observed in 70% of the pots with Malaxis brachyrrhynchos seeds and 75% of the pots with Stelis retusa seeds. The overall mean germination rate was 64% for M. brachyrrhynchos and 63% for S. retusa.
For M. brachyrrhynchos, seed germination was affected by each substrate type and by all interactions among substrates (Table
Seed germination percentage of Malaxis brachyrrhynchos (A, C, E) and Stelis retusa (B, D, F) in the presence (with, +) or absence (without, -) of three substrates: forest soil (E, F; soil), Quercus rugosa bark (A, B; bark), and coarse woody debris (C, D; CWD). Different letters in each substrate indicate significant differences (contrast test, p < 0.05). Dispersion lines are the 95% confidence intervals for a binomial variable.
Outcomes of the generalized linear regression models testing the effect of three substrates and their mixtures in the seed germination of the orchids Stelis retusa and Malaxis brachyrrhynchos.
| Source of variation | d.f. | Stelis retusa | Malaxis brachyrrhynchos | ||
| χ2 | p | χ2 | p | ||
| Soil | 1 | 266.8 | < 0.001 | 3185.2 | < 0.001 |
| CWD | 1 | 8.1 | < 0.01 | 3811.2 | < 0.001 |
| Bark | 1 | 105.7 | < 0.001 | 36.5 | < 0.001 |
| Soil - Bark | 1 | 60.7 | < 0.001 | 2109.4 | < 0.001 |
| CWD - Bark | 1 | 349.7 | < 0.001 | 6096.7 | < 0.001 |
| Soil - CWD | 1 | 2.4 | 0.120 | 2845.3 | < 0.001 |
| Soil - Bark - CWDs | 1 | 283.4 | < 0.001 | 85.7 | < 0.001 |
Seed germination in the two-factor interactions (bark-CWD, soil-CWD, and soil-bark interactions) resembles the behaviour of the main factors (Fig.
Seed germination percentage of Malaxis brachyrrhynchos (A, C, D) and Stelis retusa (B, D, F) in the paired presence (with, +) or absence (without, -) of three substrates: forest soil (soil), Quercus rugosa bark (bark), and decayed coarse woody debris (CWD). Different letters indicate significant differences in the germination inside each panel (p < 0.05). Dispersion lines are the 95% confidence intervals for a binomial variable. Names on the y-axis indicate the substrates forming each interaction pair.
The seed germination of S. retusa was similar in all four treatments involving soil-CWD interaction (Fig.
In the soil-bark interaction (Fig.
Finally, seed germination in the interaction between the three substrates (Fig.
Seed germination percentage of Malaxis brachyrrhynchos (A) and Stelis retusa (B) in the simultaneous presence/absence of the substrates: forest soil (soil), Quercus rugosa bark (bark), and decayed coarse woody debris (CWD). Different letters indicate significant differences in the germination inside each panel (p < 0.05). Dispersion lines are the 95% confidence intervals for a binomial variable.
The causes of species rarity remain controversial, as becoming rare may represent a step toward extinction. Understanding the strategies that allow small populations to persist warrants further study (
In our study area, the accumulated basal area of dead standing trees (snags) is associated with Malaxis abundance and orchid richness, suggesting that forest patches with coarse, decaying wood favour the presence of orchids (
The best-predicting model shows that Malaxis abundance on CWD depends on plant species richness, CWD size, fungal coverage, and the CWD’s decaying state. Among these variables, fungus coverage is another indicator of CWD decay. Large CWD are infrequent; therefore, this critical resource is scarce. However, we recorded large Malaxis plants on the CWD. We did not observe dormant adults or protocorms, as has been done in other studies (
We did not count the number of Malaxis plants on the forest floor because the substrate for germination of these individuals could not be inferred from their presence in the soil; they may germinate and establish on CWD, and when the CWD decomposes completely (i.e. becoming soil), the Malaxis plants remain as terrestrial plants. However, our germination experiment shows that decayed CWD is a key factor in the germination of Malaxis brachyrrhynchos.
The association between the abundance of Malaxis species on large CWD and CWD scarcity aligns with the first part of our hypothesis. We can conclude that one of the most critical factors limiting Malaxis abundance is the size of the CWD, and that decayed wood is a scarce substrate on the forest floor. Consequently, forest management practices that help maintain CWD on the forest floor will aid in orchid conservation (as opposed to CWD extraction for firewood or timber).
The general mean germination of Malaxis brachyrrhynchos and Stelis retusa was in the range reported in other orchid studies. For example, it was 89.1% in Corallorhiza odontorhiza (Willd.) Nutt., 77.8% in Dendrobium friedericksianum Rchb.f., 10.2% in Galearis spectabilis (L.) Raf., and 50.0% in Goodyera pubescens (Willd.) R.Br. (
Our ex situ experiment exposed random seed groups to the forest’s natural substrates, helping to discern the effects of these substrates on orchid germination (
Our results support the idea that the regeneration niche may explain orchid rarity (
Is the germination preference of M. brachyrrhynchos a phylogenetic signal from epiphytic ancestors? All the species in Malaxidinae descend from an epiphytic ancestor (
What does the germination behavior of terrestrial Malaxidinae orchids growing on coarse decayed wood suggest about orchid re-terrestrialization? Epiphytic orchid seeds may be selected for germinating on bark with the assistance of the mycorrhizal fungi associated with this substrate (
The high herbivory (
In a mixed oak forest in the centre of Mexico, we found that Malaxis species are associated with large CWD, but this material is scarce on the forest floor. We experimentally found that the germination of Malaxis brachyrrhynchos is higher on coarse woody debris. These outcomes suggest that a restricted regeneration niche may be one of the factors contributing to the rarity of some orchids. An open question is whether the dependence on coarse woody debris for germination is a phylogenetically inherited behaviour from epiphytic ancestors that occurs in other Malaxidinae species. We provide evidence for Malaxis species in our study area, but further research may document the association of other Malaxidinae species with CWD. We suggest that some epiphytic orchid lineages may have re-terrestrialized through a gradual shift from living on canopy bark, to decayed wood in the canopy, and eventually to decayed wood on the forest floor. But more research is needed to cover more Malaxis species and other orchid lineages.
Fernando Martínez Ocampo helped during the fieldwork. Gabriel Flores Franco helped with species identification. Comments and criticism from A. Flores Morales helped improve the manuscript. KL-C and MVS-M presented early partial versions as their bachelor’s theses at the Facultad de Biología, Universidad Autonoma del Estado de Morelos. This work was supported with a grant from the Programa para el Mejoramiento del Profesorado (project: “Sistemática y Ecología de Comunidades Forestales y Cultivos”, PROMEP 2009–2011) assigned to the Cuerpo Académico de Biología del Dosel (UAEMOR-CA-115).
Study area (A) in Morelos (C), the centre of Mexico (D). In A, the triangles are the transects used to study the relationship between Malaxis orchids and coarse woody debris. In B, the climate chart bars show the average monthly precipitation, and the line shows the average monthly temperature (data from the Automatic Meteorological Station: 1703, San Juan Tlacotenco; solid circle).
Examples of the decay classes 1 (A), 2 (B), 3 (C), and 4 (D) of coarse woody debris (CWD) in a mixed oak forest in central Mexico. In D, we show a Malaxis sp. rooted in a CWD.
Decay classes of coarse woody debris (
Method to randomize without replacement 105 seed sets into seven treatments (R script).
Pearson product-moment correlation coefficients between the standardized variables: decay class (Decay), diameter (Diameter), coverage of fungus, and richness of vascular plants (S) measured in a sample of 89 coarse woody debris (CWD) in a mixed oak forest in central Mexico.
Descriptive statistics of the size variables (diameter, length, area), species richness, and the abundance of moss, fungus, and vascular plant species found in 89 coarse woody debris (CWD) sampled on the forest floor of a mixed oak forest in central Mexico. We also show each species’ growth habit and frequency in the CWD.
Plant species richness and decay class cross-frequencies of 89 coarse woody debris sampled on the forest floor of a mixed oak forest in central Mexico.
Mean proportion of germinated seeds of the orchids Malaxis brachyrrhynchos and Stelis retusa after sowing in a full three-factor factorial design. The substrates used were Quercus rugosa bark (bark), coarse woody debris (CWD), and soil from a mixed oak forest in central Mexico.