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AbstractExplaining diversity in tropical forests remains a challenge in community ecology. Theory tells us that species differences can stabilize communities by reducing competition, while species similarities can promote diversity by reducing fitness differences and thus prolonging the time to competitive exclusion. Combined, these processes may lead to clustering of species such that species are niche differentiated across clusters and share a niche within each cluster. Here, we characterize this partial niche differentiation in a tropical forest in Panama by measuring spatial clustering of woody plants and relating these clusters to local soil conditions. We find that species were spatially clustered and the clusters were associated with specific concentrations of soil nutrients, reflecting the existence of nutrient niches. Species were almost twice as likely to recruit in their own nutrient niche. A decision tree algorithm showed that local soil conditions correctly predicted the niche of the trees with up to 85% accuracy. Iron, zinc, phosphorus, manganese, and soil pH were among the best predictors of species clusters.

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The role of facilitation in shaping natural communities has primarily been studied in the context of plant assemblages, while its relevance for mobile animals remains less understood. Our study investigates whether reciprocal interspecific facilitation may exist between fire ants (Solenopsis richteri) and cavies (Cavia aperea), two mobile animals, in the SW Atlantic coast brackish marshes. Field samples showed a spatial association between ant mounds and cavies, and that ants prefer to use cavy runways for movement within the marsh. Through experiments involving transplanting the dominant plant, cordgrass (Spartina densiflora), and manipulating cavy presence in areas with and without ant mounds, we observed that cavies forage extensively (and defecate more) near ant mounds. The ants actively remove cavy droppings in their mound vicinity. These ant activities and interactions with cavy droppings led to reduced moisture and organic content while increasing nitrate and phosphate levels in marsh sediment. Consequently, this enhanced plant growth, indirectly facilitating the cavies, which preferred consuming vegetation near ant mounds. These cascading indirect effects persisted over time; even four months after cavies left the marshes, transplanted plants near ant mounds remained larger and exhibited more leaf senescence when exposed to cavy herbivory. Therefore, the networks of positive interactions appear to generate simultaneous selection among species (populations), promoting coexistence within the community. Although complex, these reciprocal facilitative effects among mobile animals may be more common than currently believed and should be further studied to gain a better understanding of the underlying mechanisms driving species coexistence in natural communities.

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Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.

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Fine flavor cocoa is a unique category of cocoa that produces almonds with high aromatic potential and several sensory benefits that make it different from the basic or ordinary cocoas. Ecuador is the world's leader in the production and export of fine flavor cocoa, responsible for 63% of the world's total production due to the commercialization of the Arriba Nacional variety, known to possess an intense aroma that is unique in the cocoa world market. Besides its organoleptic specificity, this variety represents a source of important bioactive compounds associated with both sensory and health properties. This study evaluates the influence of an abiotic factor, nutritional soil status, on the phytochemical composition (methylxantines and phenolic compounds), and antioxidant and sensory properties of Arriba variety cocoa beans originating from three different geographical regions of Ecuador. We used the Diagnosis and Recommendation Integrated System (DRIS), Folin-Ciocalteau, high-performance liquid chromatography (HPLC), ABTS free-radical-scavenging activity, the α, α-diphenyl-ß-picrylhydrazyl free-radical-scavenging method (DPPH), and Ferric reducing antioxidant power (FRAP) analysis to reveal a significant correlation between Mn ions and total phenolic content, a positive implication of N in methylxanthine composition and antioxidant properties, and the importance of Ca, Mg, and K ions in increasing the flavonoid and anthocyanin content of raw cocoa beans. We showed that these nutritional elements can interfere with the nutraceutical and sensory properties of cocoa beans, as Cu, Mg, and K are correlated with anthocyaninic content, while Fe, Ca, P and Zn influenced the flavonoid content. We underline that the Arriba variety is suitable not only for the production of high-quality chocolate, but also for the increasing worldwide nutraceutical market, generating qualitative and competitive products.

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The process of forest degradation, along with deforestation, is the second greatest producer of global greenhouse gas emissions. A key challenge that remains unresolved is how to quantify the critical threshold that distinguishes a degraded from a non-degraded forest. We determined the critical threshold of forest degradation in mature stands belonging to the temperate evergreen rain forest of southern Chile by quantifying key forest stand factors characterizing the forest degradation status. Forest degradation in this area is mainly caused by high grading, harvesting of fuelwood, and sub-canopy grazing by livestock. We established 160 500-m2 plots in forest stands that represented varied degrees of alteration (from pristine conditions to obvious forest degradation), and measured several variables related to the structure and composition of the forest stands, including exotic and native species richness, soil nutrient levels, and other landscape-scale variables. In order to identify classes of forest degradation, we applied multivariate and machine-learning analyses. We found that richness of exotic species (including invasive species) with a diameter at breast height (DBH) < 10 cm and tree density (N, DBH > 10 cm) were the two composition and structural variables that best explained the forest degradation status, e.g., forest stands with five or more exotic species were consistently found more associated with degraded forest and stands with N < 200 trees/ha represented degraded forests, while N > 1,000 trees/ha represent pristine forests. We introduced an analytical methodology, mainly based on machine learning, that successfully identified the forest degradation status that can be replicated in other scenarios. In conclusion, here by providing an extensive data set quantifying forest and site attributes, the results of this study are undoubtedly useful for managers and decision makers in classifying and mapping forests suffering various degrees of degradation.

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Land degradation is a global problem caused by improper agricultural practices. In tropical China, the rubber (Hevea brasiliensis) plantations are predominantly practiced on forest-cleared lands, considering their sustainable land management potential compared to annual cropping. However, all rubber plantations may not have similar land management capacity. Soil quality index (SQI) can reveal the overall soil status with a single score, which is an efficient tool to evaluate the soil quality of each category of rubber plantations. We investigated 23 soil physical and chemical parameters of three categories of rubber plantations and a primary rainforest, and derived SQI based on these parameters. Soil samples were collected from a rubber monoculture (RM), a rubber-Camellia sinensis agroforestry (RT), a rubber-Dracaena cochinchinensis agroforestry (RD), and a primary rainforest (RF). The results showed that the SQI value of the RM decreased by 15.50% compared to the RF, with a significant degree of soil nutrient loss (18.90%). This indicates that monocultural rubber cultivation is causing land degradation to some extent. However, the SQI was significantly enhanced by rubber-based agroforestry practices (25.30% by RT and 33.10% by RD) compared to the RM, suggesting that polyculture practices are suitable to recover the soil quality in degraded agricultural lands. Moreover, the chemical parameters contributed more to the SQI than did the physical parameters, indicating that nutrient management is important in soil quality recovery. Overall, our results suggest that agroforestry should be preferred over monoculture in the rubber plantations for sustainable land management in tropical China.

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At local scales, it has been suggested that high levels of resources lead to increased tree growth via trait optimization (highly peaked trait distribution). However, this contrasts with (1) theories that suggest that trait optimization and high growth occur in the most common resource level and (2) empirical evidence showing that high trait optimization can be also found at low resource levels. This raises the question of how are traits and growth optimized in highly diverse plant communities. Here, we propose a series of hypotheses about how traits and growth are expected to be maximized under different resource levels (low, the most common, and high) in tree seedling communities from a subtropical forest in Puerto Rico, USA. We studied the variation in the distribution of biomass allocation and leaf traits and seedlings growth rate along four resource gradients: light availability (canopy openness) and soil K, Mg, and N content. Our analyses consisted of comparing trait kurtosis (a measurement of trait optimization), community trait means, and relative growth rates at three resource levels (low, common, and high). Trait optimization varied across the three resource levels depending on the type of resource and trait, with leaf traits being optimized under high N and in the most common K and Mg conditions, but not at any of the light levels. Also, seedling growth increased at high-light conditions and high N and K but was not related to trait kurtosis. Our results indicate that local-scale variability of soil fertility and understory light conditions result in shifts in species ecological strategies that increase growth despite a weak trait optimization, suggesting the existence of alternative phenotypes that achieve similar high performance. Uncovering the links between abiotic factors, functional trait diversity and performance is necessary to better predict tree responses to future changes in abiotic conditions.

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Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.

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Little is known about the soil factors influencing root-associated fungal communities in Orchidaceae. Limited evidence suggests that soil nutrients may modulate the association with orchid mycorrhizal fungi (OMF), but their influence on non-mycorrhizal fungi remains unexplored. To study how nutrient availability affects mycorrhizal and non-mycorrhizal fungi associated with the orchid Bipinnula fimbriata, we conducted a metagenomic investigation within a large population with variable soil conditions. Additionally, we tested the effect of phosphorus (P) addition on fungal communities and mycorrhizal colonization. Soil P negatively correlated with the abundance of OMF, but not with the abundance of non-mycorrhizal fungi. After fertilization, increments in soil P negatively affected mycorrhizal colonization; however, they had no effect on OMF richness or composition. The abundance and richness of pathotrophs were negatively related to mycorrhizal colonization and then, after fertilization, the decrease in mycorrhizal colonization correlated with an increase in pathogen richness. Our results suggest that OMF are affected by soil conditions differently from non-mycorrhizal fungi. Bipinnula fimbriata responds to fertilization by altering mycorrhizal colonization rather than by switching OMF partners in the short term, and the influence of nutrients on OMF is coupled with indirect effects on the whole fungal community and potentially on plant's health.

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Along the Patagonian coast, there are processing factories of marine products in land that produce fish-processing effluents. The aim of the present study was to assess the physicochemical properties and the prokaryotic community composition of soils receiving fish-processing effluent discharges (effluent site-ES), and to compare them with those of unaltered soils (control site-CS) in the arid Patagonian steppe. We analyzed soil prokaryotic communities (using amplicon-based sequencing of 16S rRNA genes), soil physicochemical properties and fish-processing effluent characteristics. Soil moisture, electrical conductivity (EC), total and inorganic C were significantly higher in ES than in CS (p < .05). Effluent discharges induced a decrease in the total number of operational taxonomic units (OTUs) and in the Shannon diversity index (p = .0009 and .01, respectively) of soil prokaryotic community. Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla in CS, while ES soil showed a more heterogeneous composition of phyla. Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that fish-processing effluent discharges promoted an enrichment of Firmicutes and Bacteroidetes, which are active contributors to organic matter mineralization, along with a decrease of oligotrophic phyla such as Acidobacteria, Chloroflexi, Armatimonadetes and Nitrospirae, commonly found in nutrient-poor arid soils. The concentrations of inorganic C and ammonium, the EC and the soil moisture explained 73% of the total variation within the community composition. Due to its salinity and nutrients, fish-processing effluents have potential mainly for native salt-tolerant plant irrigation, however the impacts of soil prokaryotic community shifts over plant growth remain to be determined.

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