Extinction at the end-Cretaceous and the origin of modern Neotropical rainforests.

The end-Cretaceous event was catastrophic for terrestrial communities worldwide, yet its long-lasting effect on tropical forests remains largely unknown. We quantified plant extinction and ecological change in tropical forests resulting from the end-Cretaceous event using fossil pollen (>50,000 occurrences) and leaves (>6000 specimens) from localities in Colombia. Late Cretaceous (Maastrichtian) rainforests were characterized by an open canopy and diverse plant-insect interactions. Plant diversity declined by 45% at the Cretaceous-Paleogene boundary and did not recover for ~6 million years. Paleocene forests resembled modern Neotropical rainforests, with a closed canopy and multistratal structure dominated by angiosperms. The end-Cretaceous event triggered a long interval of low plant diversity in the Neotropics and the evolutionary assembly of today's most diverse terrestrial ecosystem.

Seasonal upwelling reduces herbivore control of tropical rocky intertidal algal communities.

Communities are shaped by a variety of ecological and environmental processes, each acting at different spatial scales. Seminal research on rocky shores highlighted the effects of consumers as local determinants of primary productivity and community assembly. However, it is now clear that the species interactions shaping communities at local scales are themselves regulated by large-scale oceanographic processes that generate regional variation in resource availability. Upwelling events deliver nutrient-rich water to coastal ecosystems, influencing primary productivity and algae-herbivore interactions. Despite the potential for upwelling to alter top-down control by herbivores, we know relatively little about the coupling between oceanographic processes and herbivory on tropical rocky shores, where herbivore effects on producers are considered to be strong and nutrient levels are considered to be limiting. By replicating seasonal molluscan herbivore exclusion experiments across three regions exposed to varying intensity of seasonal upwelling, separated by hundreds of kilometers along Panama's Pacific coast, we examine large-scale environmental determinants of consumer effects and community structure on tropical rocky shores. At sites experiencing seasonal upwelling, grazers strongly limited macroalgal cover when upwelling was absent, leading to dominance by crustose algae. As nutrients increased and surface water cooled during upwelling events, increases in primary productivity temporarily weakened herbivory, allowing foliose, turf and filamentous algae to replace crusts. Meanwhile, grazer effects were persistently strong at sites without seasonal upwelling. Our results confirm that herbivores are key determinants of tropical algal cover, and that the mollusk grazing guild can control initial stages of macroalgal succession. However, our focus on regional oceanographic conditions revealed that bottom-up processes regulate top-down control on tropical shorelines. This study expands on the extensive body of work highlighting the influence of upwelling on local ecological processes by demonstrating that nutrient subsidies delivered by upwelling events can weaken herbivory in tropical rocky shores.

Soil carbon loss by experimental warming in a tropical forest.

Tropical soils contain one-third of the carbon stored in soils globally1, so destabilization of soil organic matter caused by the warming predicted for tropical regions this century2 could accelerate climate change by releasing additional carbon dioxide (CO2) to the atmosphere3-6. Theory predicts that warming should cause only modest carbon loss from tropical soils relative to those at higher latitudes5,7, but there have been no warming experiments in tropical forests to test this8. Here we show that in situ experimental warming of a lowland tropical forest soil on Barro Colorado Island, Panama, caused an unexpectedly large increase in soil CO2 emissions. Two years of warming of the whole soil profile by four degrees Celsius increased CO2 emissions by 55 per cent compared to soils at ambient temperature. The additional CO2 originated from heterotrophic rather than autotrophic sources, and equated to a loss of 8.2 ± 4.2 (one standard error) tonnes of carbon per hectare per year from the breakdown of soil organic matter. During this time, we detected no acclimation of respiration rates, no thermal compensation or change in the temperature sensitivity of enzyme activities, and no change in microbial carbon-use efficiency. These results demonstrate that soil carbon in tropical forests is highly sensitive to warming, creating a potentially substantial positive feedback to climate change.

Greater root phosphatase activity of tropical trees at low phosphorus despite strong variation among species.

Soil phosphorus (P) availability in lowland tropical rainforests influences the distribution and growth of tropical tree species. Determining the P-acquisition strategies of tropical tree species could therefore yield insight into patterns of tree ß-diversity across edaphic gradients. In particular, the synthesis of root phosphatases is likely to be of significance given that organic P represents a large pool of potentially available P in tropical forest soils. It has also been suggested that a high root phosphatase activity in putative nitrogen (N) -fixing legumes might explain their high abundance in lowland neotropical forests under low P supply. Here, we measured phosphomonoesterase (PME) activity on the first three root orders of co-occurring tropical tree species differing in their N-fixation capacity, growing on soils of contrasting P availability in Panama. Our results show that root PME activity was higher on average in P-poor than in P-rich soils, but that local variation in PME activity among co-occurring species within a site was larger than that explained by differences in soil P across sites. Legumes expressed higher PME activity than nonlegumes, but nodulated legumes (i.e., actively fixing nitrogen) did not differ from legumes without nodules, indicating that PME activity is unrelated to N fixation. Finally, PME activity declined with increasing root order, but the magnitude of the decline varied markedly among species, highlighting the importance of classifying fine roots into functional groups prior to measuring root traits. Our results support the hypothesis that low-P promotes a high root PME activity, although the high local variation in this trait among co-occurring species points toward a high functional diversity in P-acquisition strategies within an individual community.

Why are tropical conifers disadvantaged in fertile soils? Comparison of Podocarpus guatemalensis with an angiosperm pioneer, Ficus insipida.

Conifers are, for the most part, competitively excluded from tropical rainforests by angiosperms. Where they do occur, conifers often occupy sites that are relatively infertile. To gain insight into the physiological mechanisms by which angiosperms outcompete conifers in more productive sites, we grew seedlings of a tropical conifer (Podocarpus guatemalensis Standley) and an angiosperm pioneer (Ficus insipida Willd.) with and without added nutrients, supplied in the form of a slow-release fertilizer. At the conclusion of the experiment, the dry mass of P. guatemalensis seedlings in fertilized soil was approximately twofold larger than that of seedlings in unfertilized soil; on the other hand, the dry mass of F. insipida seedlings in fertilized soil was ~20-fold larger than seedlings in unfertilized soil. The higher relative growth rate of F. insipida was associated with a larger leaf area ratio and a higher photosynthetic rate per unit leaf area. Higher overall photosynthetic rates in F. insipida were associated with an approximately fivefold larger stomatal conductance than in P. guatemalensis. We surmise that a higher whole-plant hydraulic conductance in the vessel bearing angiosperm F. insipida enabled higher leaf area ratio and higher stomatal conductance per unit leaf area than in the tracheid bearing P. guatemalensis, which enabled F. insipida to capitalize on increased photosynthetic capacity driven by higher nitrogen availability in fertilized soil.

Methane emissions from tree stems in neotropical peatlands.

Neotropical peatlands emit large amounts of methane (CH4 ) from the soil surface, but fluxes from tree stems in these ecosystems are unknown. In this study we investigated CH4 emissions from five tree species in two forest types common to neotropical lowland peatlands in Panama. Methane from tree stems accounted for up to 30% of net ecosystem CH4 emissions. Peak CH4 fluxes were greater during the wet season when the water table was high and temperatures were lower. Emissions were greatest from the hardwood tree Campnosperma panamensis, but most species acted as emitters, with emissions declining exponentially with height along the stem for all species. Overall, species identity, stem diameter, water level, soil temperature and soil CH4 fluxes explained 54% of the variance in stem CH4 emissions from individual trees. On the landscape level, On the landscape level, the high emissions from C. panamensis forests resulted in that they emitted at 340 kg CH4  d-1 during flooded periods despite their substantially lower areal cover. We conclude that emission from tree stems is an important emission pathway for CH4 flux from Neotropical peatlands, and that these emissions vary strongly with season and forest type.

Co-occurring Fungal Functional Groups Respond Differently to Tree Neighborhoods and Soil Properties Across Three Tropical Rainforests in Panama.

Abiotic and biotic drivers of co-occurring fungal functional guilds across regional-scale environmental gradients remain poorly understood. We characterized fungal communities using Illumina sequencing from soil cores collected across three Neotropical rainforests in Panama that vary in soil properties and plant community composition. We classified each fungal OTU into different functional guilds, namely plant pathogens, saprotrophs, arbuscular mycorrhizal (AM), or ectomycorrhizal (ECM). We measured soil properties and nutrients within each core and determined the tree community composition and richness around each sampling core. Canonical correspondence analyses showed that soil pH and moisture were shared potential drivers of fungal communities for all guilds. However, partial the Mantel tests showed different strength of responses of fungal guilds to composition of trees and soils. Plant pathogens and saprotrophs were more strongly correlated with soil properties than with tree composition; ECM fungi showed a stronger correlation with tree composition than with soil properties; and AM fungi were correlated with soil properties, but not with trees. In conclusion, we show that co-occurring fungal guilds respond differently to abiotic and biotic environmental factors, depending on their ecological function. This highlights the joint role that abiotic and biotic factors play in determining composition of fungal communities, including those associated with plant hosts.

Isolation of Inositol Hexakisphosphate from Soils by Alkaline Extraction and Hypobromite Oxidation.

Inositol hexakisphosphates are extracted from soil in strong alkali and isolated from other organic phosphates by hypobromite oxidation. The procedure yields the four stereoisomeric forms of inositol hexakisphosphate in a form suitable for spectroscopic or chromatographic identification.

The Response of Litter-Associated Myxomycetes to Long-Term Nutrient Addition in a Lowland Tropical Forest.

Myxomycetes (plasmodial slime molds) are abundant protist predators that feed on bacteria and other microorganisms, thereby playing important roles in terrestrial nutrient cycling. Despite their significance, little is known about myxomycete communities and the extent to which they are affected by nutrient availability. We studied the influence of long-term addition of N, P, and K on the myxomycete community in a lowland forest in the Republic of Panama. In a previous study, microbial biomass increased with P but not N or K addition at this site. We hypothesized that myxomycetes would increase in abundance in response to P but that they would not respond to the sole addition of N or K. Moist chamber cultures of leaf litter and small woody debris were used to quantify myxomycete abundance. We generated the largest myxomycete dataset (3,381 records) for any single locality in the tropics comprised by 91 morphospecies. In line with our hypothesis, myxomycete abundance increased in response to P addition but did not respond to N or K. Community composition was unaffected by nutrient treatments. This work represents one of very few large-scale and long-term field studies to include a heterotrophic protist highlighting the feasibility and value in doing so.

Soil drivers of local-scale tree growth in a lowland tropical forest.

Soil nutrients influence the distribution of tree species in lowland tropical forests, but their effect on productivity, especially at local scales, remains unclear. We used tree census, canopy occupancy, and soil data from the Barro Colorado Island (BCI; Panama) 50-ha forest dynamics plot to investigate the influence of soil nutrients and potential toxins on aboveground tree productivity. Growth was calculated as the increase in diameter of 150,000 individual stems ≥1 cm diameter at breast height, representing 207 species. The effects of soil variables and other strong predictors of growth (e.g., light) were estimated using hierarchical, linear, mixed-effects models. Growth was weakly positively associated with phosphorus (P), particularly for understory tree species that are typically considered to be limited by light. In contrast, growth was strongly negatively related to manganese (Mn) and aluminum (Al), although the latter effect was confounded by strong correlations between Al and other soil variables. The negative response to increasing Mn (and Al) suggests a toxicity effect due to solubilization and uptake of amorphous pools of metal oxides in the soil. These results show that P limits tropical tree growth at local scale on BCI, but that toxic metals represent an even greater constraint on productivity.

Responses of arbuscular mycorrhizal fungi to long-term inorganic and organic nutrient addition in a lowland tropical forest.

Improved understanding of the nutritional ecology of arbuscular mycorrhizal (AM) fungi is important in understanding how tropical forests maintain high productivity on low-fertility soils. Relatively little is known about how AM fungi will respond to changes in nutrient inputs in tropical forests, which hampers our ability to assess how forest productivity will be influenced by anthropogenic change. Here we assessed the influence of long-term inorganic and organic nutrient additions and nutrient depletion on AM fungi, using two adjacent experiments in a lowland tropical forest in Panama. We characterised AM fungal communities in soil and roots using 454-pyrosequencing, and quantified AM fungal abundance using microscopy and a lipid biomarker. Phosphorus and nitrogen addition reduced the abundance of AM fungi to a similar extent, but affected community composition in different ways. Nutrient depletion (removal of leaf litter) had a pronounced effect on AM fungal community composition, affecting nearly as many OTUs as phosphorus addition. The addition of nutrients in organic form (leaf litter) had little effect on any AM fungal parameter. Soil AM fungal communities responded more strongly to changes in nutrient availability than communities in roots. This suggests that the 'dual niches' of AM fungi in soil versus roots are structured to different degrees by abiotic environmental filters, and biotic filters imposed by the plant host. Our findings indicate that AM fungal communities are fine-tuned to nutrient regimes, and support future studies aiming to link AM fungal community dynamics with ecosystem function.

Publisher Correction: Pervasive phosphorus limitation of tree species but not communities in tropical forests.

In this Letter, the y axis of the right-hand panel of Fig. 2a was mislabelled 'Phosphomonoesterase' instead of 'Phosphodiesterase'. This error has been corrected online.

Pervasive phosphorus limitation of tree species but not communities in tropical forests.

Phosphorus availability is widely assumed to limit primary productivity in tropical forests, but support for this paradigm is equivocal. Although biogeochemical theory predicts that phosphorus limitation should be prevalent on old, strongly weathered soils, experimental manipulations have failed to detect a consistent response to phosphorus addition in species-rich lowland tropical forests. Here we show, by quantifying the growth of 541 tropical tree species across a steep natural phosphorus gradient in Panama, that phosphorus limitation is widespread at the level of individual species and strengthens markedly below a threshold of two parts per million exchangeable soil phosphate. However, this pervasive species-specific phosphorus limitation does not translate into a community-wide response, because some species grow rapidly on infertile soils despite extremely low phosphorus availability. These results redefine our understanding of nutrient limitation in diverse plant communities and have important implications for attempts to predict the response of tropical forests to environmental change.

Plant responses to fertilization experiments in lowland, species-rich, tropical forests.

We present a meta-analysis of plant responses to fertilization experiments conducted in lowland, species-rich, tropical forests. We also update a key result and present the first species-level analyses of tree growth rates for a 15-yr factorial nitrogen (N), phosphorus (P), and potassium (K) experiment conducted in central Panama. The update concerns community-level tree growth rates, which responded significantly to the addition of N and K together after 10 yr of fertilization but not after 15 yr. Our experimental soils are infertile for the region, and species whose regional distributions are strongly associated with low soil P availability dominate the local tree flora. Under these circumstances, we expect muted responses to fertilization, and we predicted species associated with low-P soils would respond most slowly. The data did not support this prediction, species-level tree growth responses to P addition were unrelated to species-level soil P associations. The meta-analysis demonstrated that nutrient limitation is widespread in lowland tropical forests and evaluated two directional hypotheses concerning plant responses to N addition and to P addition. The meta-analysis supported the hypothesis that tree (or biomass) growth rate responses to fertilization are weaker in old growth forests and stronger in secondary forests, where rapid biomass accumulation provides a nutrient sink. The meta-analysis found no support for the long-standing hypothesis that plant responses are stronger for P addition and weaker for N addition. We do not advocate discarding the latter hypothesis. There are only 14 fertilization experiments from lowland, species-rich, tropical forests, 13 of the 14 experiments added nutrients for five or fewer years, and responses vary widely among experiments. Potential fertilization responses should be muted when the species present are well adapted to nutrient-poor soils, as is the case in our experiment, and when pest pressure increases with fertilization, as it does in our experiment. The statistical power and especially the duration of fertilization experiments conducted in old growth, tropical forests might be insufficient to detect the slow, modest growth responses that are to be expected.

Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil.

Phosphorus is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting phosphorus deficiency at the gene and protein levels remains unknown. Here, we report a metagenomic and metaproteomic comparison of microbial communities in phosphorus-deficient and phosphorus-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A greater than fourfold increase in the gene abundance of 3-phytase was the strongest response of soil communities to phosphorus deficiency. Phytase catalyses the release of phosphate from phytate, the most recalcitrant phosphorus-containing compound in soil organic matter. Genes and proteins for the degradation of phosphorus-containing nucleic acids and phospholipids, as well as the decomposition of labile carbon and nitrogen, were also enhanced in the phosphorus-deficient soils. In contrast, microbial communities in the phosphorus-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, transformation of nitrogenous compounds and assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints.

Biogeochemistry drives diversity in the prokaryotes, fungi, and invertebrates of a Panama forest.

Humans are both fertilizing the world and depleting its soils, decreasing the diversity of aquatic ecosystems and terrestrial plants in the process. We know less about how nutrients shape the abundance and diversity of the prokaryotes, fungi, and invertebrates of Earth's soils. Here we explore this question in the soils of a Panama forest subject to a 13-yr fertilization with factorial combinations of nitrogen (N), phosphorus (P), and potassium (K) and a separate micronutrient cocktail. We contrast three hypotheses linking biogeochemistry to abundance and diversity. Consistent with the Stress Hypothesis, adding N suppressed the abundance of invertebrates and the richness of all three groups of organisms by ca. 1 SD or more below controls. Nitrogen addition plots were 0.8 pH units more acidic with 18% more exchangeable aluminum, which is toxic to both prokaryotes and eukaryotes. These stress effects were frequently reversed, however, when N was added with P (for prokaryotes and invertebrates) and with added K (for fungi). Consistent with the Abundance Hypothesis, adding P generally increased prokaryote and invertebrate diversity, and adding K enhanced invertebrate diversity. Also consistent with the Abundance Hypothesis, increases in invertebrate abundance generated increases in richness. We found little evidence for the Competition Hypothesis: that single nutrients suppressed diversity by favoring a subset of high nutrient specialists, and that nutrient combinations suppressed diversity even more. Instead, combinations of nutrients, and especially the cation/micronutrient treatment, yielded the largest increases in richness in the two eukaryote groups. In sum, changes in soil biogeochemistry revealed a diversity of responses among the three dominant soil groups, positive synergies among nutrients, and-in contrast with terrestrial plants-the frequent enhancement of soil biodiversity.

Plasticity in nitrogen uptake among plant species with contrasting nutrient acquisition strategies in a tropical forest.

Nitrogen (N) availability influences the productivity and distribution of plants in tropical montane forests. Strategies to acquire soil N, such as direct uptake of organic compounds or associations with root symbionts to enhance N acquisition in exchange for carbon (C), may facilitate plant species coexistence and ecosystem N retention. Alternatively, rapid microbial turnover of soil N forms in tropical soils might promote flexible plant N-uptake strategies and mediate species coexistence. We tested whether sympatric plant species with different root symbiont associations, and therefore potentially different nutrient acquisition strategies, partition chemical forms of N or show plasticity in N uptake in a tropical pre-montane forest in Panama. We traced the movement of three 15 N forms into soil pools, microbes, and seedlings of eleven species differing in root traits. Seedlings were grown in a split-plot field transplant experiment, with plots receiving equimolar mixtures of ammonium, nitrate, and glycine, with one form isotopically labeled in each block. After 48 h, more 15 N was recovered in microbes than in plants, while all pools (extractable organic and inorganic N, microbial biomass, and leaves) contained greater amounts of 15 N from nitrate than from ammonium or glycine. Furthermore, 13 C from dual-labeled glycine was not recovered in the leaves of any seedling, suggesting the studied species do not directly take up organic N or transform organic N prior to translocation to leaves. Nitrogen uptake differed by root symbiont group only for nitrate, with greater 15 N recovery in plants with arbuscular mycorrhizal (AM) associations or proteoid roots compared to orchids. Some root trait groups differed in 15 N recovery among N forms, with greater nitrate uptake than ammonium or glycine by AM-associated and N2 -fixing plants. However, only five of eleven species showed differences in uptake among N forms. These results indicate flexibility in uptake of N forms in tropical plants across root trait groups, with only a few species displaying weak preferences for a specific N form.

A phosphorus threshold for mycoheterotrophic plants in tropical forests.

The majority of terrestrial plants associate with arbuscular mycorrhizal (AM) fungi, which typically facilitate the uptake of limiting mineral nutrients by plants in exchange for plant carbon. However, hundreds of non-photosynthetic plant species-mycoheterotrophs-depend entirely on AM fungi for carbon as well as mineral nutrition. Mycoheterotrophs can provide insight into the operation and regulation of AM fungal relationships, but little is known about the factors, fungal or otherwise, that affect mycoheterotroph abundance and distribution. In a lowland tropical forest in Panama, we conducted the first systematic investigation into the influence of abiotic factors on the abundance and distribution of mycoheterotrophs, to ask whether the availability of nitrogen and phosphorus altered the occurrence of mycoheterotrophs and their AM fungal partners. Across a natural fertility gradient spanning the isthmus of Panama, and also in a long-term nutrient-addition experiment, mycoheterotrophs were entirely absent when soil exchangeable phosphate concentrations exceeded 2 mg P kg-1 Experimental phosphorus addition reduced the abundance of AM fungi, and also reduced the abundance of the specific AM fungal taxa required by the mycoheterotrophs, suggesting that the phosphorus sensitivity of mycoheterotrophs is underpinned by the phosphorus sensitivity of their AM fungal hosts. The soil phosphorus concentration of 2 mg P kg-1 also corresponds to a marked shift in tree community composition and soil phosphatase activity across the fertility gradient, suggesting that our findings have broad ecological significance.

Liana effects on biomass dynamics strengthen during secondary forest succession.

Secondary forests are important carbon sinks, but their biomass dynamics vary markedly within and across landscapes. The biotic and abiotic drivers of this variation are still not well understood. We tested the effects of soil resource availability and competition by lianas on the biomass dynamics of young secondary tropical forests in Panama and assessed the extent to which liana effects were mediated by soil resource availability. Over a five-year period, growth, mortality, and recruitment of woody plants of ≥1 cm diameter were monitored in 84 plots in 3-30-year-old secondary forests across the Agua Salud site in central Panama. Biomass dynamics and the effects of lianas and soil resources were examined using (generalized) linear mixed-effect models and a model averaging approach. There was strong spatial and temporal variation in liana biomass within and across the plots. The relative biomass of lianas had a strong negative effect on overall tree growth, growth of understory trees decreased with soil fertility and dry season soil water content, and the effect of lianas on tree mortality varied with soil fertility. Tree recruitment was not associated with any of the predictor variables. Our model indicates that tree biomass growth across our landscape was reduced with 22% due to competition with lianas, and that the effect of lianas increased during succession, from 19% after five years to 32% after 30 years. The projected liana-induced growth reduction after 60 years was 47%, which was consistent with data from a nearby site. Our study shows that the observed liana proliferation across tropical forests may reduce the sequestration and storage of carbon in young secondary forests, with important implications for the carbon balance of tropical forest landscapes and consequently for global climate change. Our study highlights the need to incorporate lianas and soil variables in research on the biomass dynamics of secondary forest across tropical landscapes, and the need for well-replicated longitudinal studies to cover landscape-level variability in the relevant abiotic and biotic components.