Ecology

African swine fever has breached the island of Borneo, where it is wiping out populations of the wild bearded pig Sus barbatus. First confirmed in early February, the outbreak has driven a precipitous decline in this species in less than two months. Field sites in the east of the Sabah region are reporting a complete absence of live pigs in forests. Local extinctions across swathes of Borneo are a realistic prospect.Bearded pigs are listed as vulnerable by the International Union for Conservation of Nature. They are seen as ‘ecosystem engineers’ in the Bornean rainforest, where they are one of the most abundant species of mammal. Bearded pigs can be legally hunted under permit, and are an important source of animal protein for many communities.The African swine fever virus is already island-hopping across southeast Asia, threatening 11 species of endemic pig, including the Sulawesi warty pig (Sus celebensis). Opportunities to control the disease in wild-pig populations are limited. Vaccines for domestic pigs are still in development, so the best hope for stemming loss of the wild animals could be to protect isolated populations in geographically defensible locations. More

Morphological changes of the leavesThe influence of NO2 stress on the plants was first reflected by the morphological changes of the leaves (Fig. 1)20,22. Slight NO2 injury was manifested by slight green deficiency and light color. Moderate NO2 injury was manifested by irregular watery spots between leaf veins, which gradually developed into yellow necrotic spots followed by lesions at the leaf stalk and margins. When the exposure time extended to 72 h, the leaves turned yellow, and irreversible injury occurred, which led to leaf death. The damaged areas of the leaves of the two species at different time points of NO2 exposure are summarized in Table 1.Figure 1Leaf injury symptoms of Carpinus betulus (A) and Carpinus putoensis (B) under different NO2 exposure time and after recovery.Full size imageTable 1 The damaged areas (percentage) of the leaves of Carpinus betulus and Carpinus putoensis at different time points of NO2 stress.Full size tableChanges in MDA contentThe changes in the MDA content of C. betulus and C. putoensis at different time points of NO2 stress are shown in Fig. 2. With the prolongation of NO2 stress, the MDA content of C. betulus showed an increasing tendency with the variation range from 0.016 to 0.029 µmol g−1 fw. However, no significant differences were observed at different time points of NO2 exposure.Figure 2Changes in the MDA content of C. betulus and C. putoensis at different time points of NO2 stress and after self recovery. Letters or letter combinations containing the same letter indicate no significant difference between the corresponding NO2 exposure time points in the same plant species according to ANOVA or nonparametric Kruskal–Wallis ANOVA followed by Bonferroni tests. Capital letters for C. putoensis and lower letters for C. betulus.Full size imageAs NO2 fumigation time extended, the MDA content of C. putoensis also showed an increasing tendency, with the variation range from 0.015 to 0.034 µmol g−1 fw. Compared with the control group, a significant difference was observed in the MDA content from 24 h, which peaked at 72 h. In C. putoensis, although the recover group and the control group did not show a significant difference, the MDA content of the former lay between 0.015 (6 h) and 0.019 µmol g−1 fw (12 h), which suggests that the plant did not recovered completely from the stress damage.Compared with C. putoensis, C. betulus exhibited a smaller variation amplitude in the MDA content under NO2 stress. The MDA content of C. betulus did not show noticeable changes at 1, 6, and 12 h, and it was till 24 h when a rapid increase occurred. These findings indicate a delayed injury response of C. betulus. In contrast, with the prolongation of NO2 stress, the MDA content of C. putoensis noticeably increased, which indicates an increase in the membrane lipid peroxidation activity of C. putoensis under NO2 stress.Changes in POD activityThe changes in POD activity of C. betulus and C. putoensis at different time points of NO2 stress are shown in Fig. 3. With the prolongation of NO2 stress, the POD activity of C. betulus showed an increasing tendency, with a variation range from 323 to 663 U (g * min)−1 fw. After 30-d self recovery, the POD activity returned to 409 U (g * min)−1 fw, which was comparable to that of the control.Figure 3Changes in POD activity of C. betulus and C. putoensis at different time points of NO2 stress and after self recovery. Letters or letter combinations containing the same letter indicate no significant difference between the corresponding NO2 exposure time points in the same plant species according to ANOVA or nonparametric Kruskal–Wallis ANOVA followed by Bonferroni tests. Capital letters for C. putoensis and lower letters for C. betulus.Full size imageAs NO2 fumigation time extended, the POD value of C. putoensis also showed an increasing tendency, with a variation range from 385 to 596 U (g * min)−1 fw. The recovery group did not show a significant difference compared with the control group.In C. betulus, the POD activity value rapidly increased at 72 h of NO2 stress, which showed a significant difference compared with any other group (adjusted p  0.05).Figure 4Changes in the soluble protein content of C. betulus and C. putoensis under NO2 stress at different time points and after self recovery. Letters or letter combinations containing the same letter indicate no significant difference between the corresponding NO2 exposure time points in the same plant species according to ANOVA or nonparametric Kruskal–Wallis ANOVA followed by Bonferroni tests. Capital letters for C. putoensis and lower letters for C. betulus.Full size imageIn C. putoensis, the soluble protein content also showed an increasing trend as the fumigation time prolonged. The variations ranged from 2.61 to 3.27 mg g−1 fw. Compared with the control group, the recovery group exhibited a lower soluble protein content, although no significant difference was observed between them.As shown in Fig. 4, the maximum difference in the soluble protein content of C. betulus was 2.33 mg g−1 fw, which was greatly larger than that of C. putoensis (0.66 mg g−1 fw). Particularly, C. betulus exhibited a rapid increase in the soluble protein content from 12 h of fumigation, which indicates that C. betulus increased protein synthesis when encountered with NO2 stress, whereas C. putoensis showed only weak resistance against the stress.Changes in NRAt 0 h of NO2 treatment, the NR activity of C. betulus was 1.43 ± 0.14 µmol NO2−·g−1fw·h−1. With the prolongation of NO2 exposure, the NR activity of C. betulus exhibited a gradual increase followed by a gradual decrease, and a significant difference (adjusted p  0.05). In C. putoensis, the NR activity of the control group was 0.58 ± 0.06 µmol NO2−·g−1fw·h−1. As the NO2 exposure time prolonged, NR activity exhibited a rapid increase (adjusted p  0.05). The results were shown in Fig. 5.Figure 5Changes in the NR activity of C. betulus and C. putoensis under NO2 stress at different time points and after self recovery. Letters or letter combinations containing the same letter indicate no significant difference between the corresponding NO2 exposure time points in the same plant species according to ANOVA or nonparametric Kruskal–Wallis ANOVA followed by Bonferroni tests. Capital letters for C. putoensis and lower letters for C. betulus.Full size imageChanges in NO3
−NAs the NO2 treatment time extended, the NO3−N content of C. betulus exhibited an increase followed by a gradual decrease, and a significant difference (adjusted p  0.05). In C. putoensis, the NO3−N content also exhibited an increase followed by a decrease after NO2 exposure. However, a significant difference was observed from 12 h. After 30-d recovery, the index returned to a normal level (adjusted p  > 0.05). The results were shown in Fig. 6.Figure 6Changes in the NO3−N content of C. betulus and C. putoensis under NO2 stress at different time points and after self recovery. Letters or letter combinations containing the same letter indicate no significant difference between the corresponding NO2 exposure time points in the same plant species according to ANOVA or nonparametric Kruskal–Wallis ANOVA followed by Bonferroni tests. Capital letters for C. putoensis and lower letters for C. betulus.Full size imageChanges in mineral elementsThe changes in the mineral elements of C. betulus and C. putoensi under NO2 stress and after self recovery are summarized in Table 2.Table 2 Changes in the mineral element contents of C. betulus and C. putoensis under NO2 stress and after self recovery.Full size tableMacroelements(1) N. At 1 h of NO2 stress, the total nitrogen content of C. betulus increased slightly to 1.68 ± 0.17 g/kg; this value was higher than that of control (1.4 ± 0.13 g/kg), but no significant difference was observed (adjusted p  > 0.05). With the prolongation of the stress, the content decreased, with the variations ranging from 0.84 to 1.68 g/kg and the maximum difference of 0.84 g/kg. The recovery group did not show a significant difference compared with the control group (1.53 ± 0.15 vs. 1.4 ± 0.13; adjusted p = 1.00).Overall, the changes in the total nitrogen content of C. putoensis showed a similar trend with those of C. betulus. At 1 h of NO2 stress, the total nitrogen content of C. putoensis significantly increased compared with that of the control (1.68 ± 0.15 g/kg vs. 1.12 ± 0.11 g/kg; adjusted p  0.05).(4) Ca. With the prolongation of NO2 exposure, the Ca content of C. betulus exhibited an increase followed by a gradual decrease, and the variations ranged from 84 to 243 µg L−1 dw. A significant difference was observed at 72 h of NO2 exposure. In C. putoensis, significant differences in the Ca content were observed during NO2 exposure, except at 12 h. In both species, the Ca content of the recovery group did not show a significant difference compared with the control group. The variation amplitude of the Ca content of C. betulus (159 µg L−1 dw) was noticeably greater than that of C. putoensis (68 µg L−1 dw).(5) Mg. As the NO2 stress prolonged, the Mg content of C. betulus did not show a significant drop, except at 48 h. The variations ranged from 21.4 to 31.3 µg L−1 dw. In C. putoensis, the variations ranged from 12.2 to 32.2 µg L−1 dw. In both species, the Ca content of the recovery group did not show a significant difference compared with the control group. The variation amplitude of the Ca content of C. betulus (9.9 µg L−1 dw) was remarkably smaller than that of C. putoensis (20 µg L−1 dw).Microelements(1) Zn. With the prolongation of NO2 exposure, the Zn content of C. betulus exhibited an increase followed by a gradual decrease. Compared with the control, significant differences were observed at 1, 6, and 12 h. The variations anged from 7.1 to 10.6 µg L−1 dw. In C. putoensis, significant differences in the Zn content were observed at 6 h and 48 h, and the variations ranged from 5.7 to 11.2 µg L−1 dw. The variation amplitude of the Zn content of C. betulus (3.5 µg L−1 dw) was smaller than that of C. putoensis (5.5 µg L−1 dw). In each species, the Zn content of the recovery group showed a significant difference compared with the control group.(2) Mn. At 1 h of NO2 fumigation, a sharp drop was observed, compared with the control. Afterwards, the Mn content of C. betulus exhibited a general increase followed by a gradual decrease. However, at any time point during NO2 exposure, a significant lower Mn content was observed when compared to the control. The variations of the Mn content ranged from 11.2 to 78.1 µg L−1 dw. In C. putoensis, the Mn content during NO2 exposure significantly decreased compared with control, and the variations ranged from 9.4 to 85.5 µg L−1 dw. The variation amplitude of the Mn content of C. betulus (66.9 µg L−1 dw) was slightly smaller than that of C. putoensis (76.1 µg L−1 dw). In each species, the Mn content of the recovery group did not show a significant difference compared with the control group.Correlation analysisThe correlations between the investigated indices and NO2 exposure time were analyzed using the Pearson’s method (Table 3). POD and soluble protein had a strong positive correlation with NO2 exposure time (correlation coefficient: 0.891 and 0.799, respectively), and NR, NO3−N, N, K, and Ca had a strong negative correlation with NO2 exposure time (correlation coefficient: -0.691, -0.805, -0.744, -0.606 and -0.696, respectively). MDA and the Zn content were not correlated with the exposure time.Table 3 Correlations of the investigated indices with NO2 exposure time.Full size table More

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Mist wafts through the trees at the Monteverde Cloud Forest Biological Preserve in Costa Rica. Cloud forests around the world are threatened by development, wood collection and climate change. Credit: Stefano Paterna/Alamy

Conservation biology
04 May 2021
Forests that float in the clouds are drifting away

Tropical cloud forests are safe havens for a vast range of creatures and plants, but they are under siege around the globe.

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Remote habitats called tropical cloud forests, which cling to misty mountains and tap humid air for water, are in decline. So says a global analysis also reporting that cloud forests, despite occupying just 0.4% of Earth’s land, harbour around 15% of the global biodiversity of birds, mammals, amphibians and tree ferns.Dirk Karger at the Swiss Federal Institute for Forest, Snow and Landscape Research in Birmensdorf, Walter Jetz at Yale University in New Haven, Connecticut, and their colleagues created habitat-prediction models that incorporate remote-sensing data on cloud cover and other conditions to predict the coverage of tropical cloud forests worldwide. They then studied satellite imagery of land cover from 2001 to 2018 to determine the rate of cloud-forest loss and analysed how this loss would affect 3,700 species living in this ecosystem.The team estimates that more than 15,000 square kilometres of tropical cloud forest — 2.4% of the global total — were lost during the 18-year period. Africa and the Americas had the greatest losses. The authors note that the establishment of protected areas did little to halt the loss of habitat and its biodiversity, highlighting the urgent need for other safeguards.

Nature Ecol. Evol. (2021)

Conservation biology More

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Although Malar et al. “do not exclude the possibility that the genes identified by Mateus et al. are involved in mating,” they qualify the homology inference between genes differentially expressed in the co-inoculation treatment and genes involved in mating in other fungal species as “spurious evolutionary relationships” or “not the best ortholog”. Those statements imply that they attach no importance to the demonstrated sequence homology relationships identified in Mateus et al. Orthology does not necessarily imply conservation of gene function and genes with equivalent functions are not necessarily orthologs [3]. Therefore, it is misleading to assume that two genes have the same function when interpreting the role of a “best candidate ortholog” identified in silico. Moreover, relying only on an in silico search for exploring orthologs can lead to serious problems for inferring function as none of the search algorithms are free from bias if subfunctionalization or neofunctionalization events occurred among the homologs.Malar et al. have not considered, or have misunderstood, the experimental evidence on gene expression in interpreting their homology search. It is not surprising that their “best homologs” were not upregulated, because we already saw that those genes were not upregulated in the original dataset. Our approach comprised performing an experiment to identify genes that were specifically upregulated when two isolates coexisted in planta. We then identified their putative function by homology. We did not look at whether the genes were the closest orthologs. However, we discussed the limitations of an homology approach to identify gene function [2]. To our surprise, a consistent set of 20 genes was upregulated in the co-inoculation treatment in different host plants, and 9 of these 20 (upregulated in more than one host plant) shared the common feature of homology to genes involved in different steps of mating in other fungal species (Figs. 3 and 4 of Mateus et al.).Malar et al. claim the identification of hundreds of hits of the 18 genes differentially expressed in Mateus et al. “against the high-quality protein databases from the JGI Mycocosm Rhiir2” (referring to the protein database “Rhiir2” of R. irregularis). In fact, Malar et al. compared the 18 genes against “all protein gene catalogs of fungal species from the JGI fungal genomic resource” comprising 1318 taxa. The interpretation of the number of hits on a such large dataset is misleading because if a gene is highly conserved across the fungal kingdom, we would expect hundreds of hits in this database. In contrast, if an R. irregularis gene is highly specific to the Glomeromycotina taxa, we would expect very few hits (because there are less Glomeromycotina genomes in the database). Consequently, the number of hits in Table 1 from Malar et al. reflect the size of the database used and how conserved a given gene is, rather than whether a gene is from a large gene family. Malar et al. identified the so-called “closest ortholog” in R. irregularis of fungal mating genes from other fungal species by showing the “best hit” using OrthoMCL. However, differentiating paralogs from orthologs is a complicated task, in very distant species, especially if the organisms are highly paralogous. A more cautious analysis for each gene, including a confirmation that they are located in similar genomic locations, would lend more certitude that a given gene could be an ortholog. Consequently, the evaluation of RNA expression of their “best hit” remains incomplete in terms of the effort to find the best orthologs. More