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The mechanisms of the maintenance of plant diversity in forests have been extensively studied because of their ecological importance. The study of the regeneration and growth dynamics of herbaceous understory communities in forests is relatively more common than that of woody plant overstory and understory communities. To investigate which environmental factors (plant roots, forest litter, or both) control seedling survival, growth, and production in the herbaceous layer in the context of increasingly severe seasonal drought caused by global climate change, we performed a seedling growth experiment of the herbaceous layer influenced by the interaction of plant roots and forest litter through a manipulative complete block experiment, crossed with an irrigation experiment, in a montane subtropical moist evergreen broad-leaved forest of southwestern China. Within both the control and watered plots, we established four experimental subplots with plant roots and forest litter included (R+L+); plant roots included, but forest litter excluded (R+L−); plant roots excluded, but forest litter included (R−L+); and both plant roots and forest litter excluded (R−L−). After one year, the R+L+ treatment in the control plot had statistically less species richness and plant individuals, shorter mean and maximum seedling heights, and less dry biomass of plant seedlings than those in the other seven experimental treatments. Across all the experimental replicates, the pooled data showed that plant roots, forest litter, and seasonal drought, together, inhibited all the dependent herbaceous growth variables. Our study demonstrates how plant roots, forest litter, and seasonal drought synergistically regulate seedling establishment and the growth of the herbaceous layer in tropical and subtropical forest understory. This synergistic regulation changes plant physiological responses and forest evolution through controlling plant diversity and the individual richness of the herbaceous layer in the context of sustained global climate change.

We investigated how differences in mangrove island micro-elevation (i.e., habitat, center vs. edge) affect tree physiology in a scrub mangrove forests of the southeastern Everglades. We measured leaf gas exchange rates of scrub Rhizophora mangle L. trees monthly during 2019, hypothesizing that CO2 assimilation (Anet) and stomatal conductance (gsw) would decline with increasing water levels and salinity, expecting more-considerable differences at mangrove-island edges than centers, where physiological stress is greatest. Water levels varied between 0 and 60 cm from the soil surface, rising during the wet season (May-October) relative to the dry season (November-April). Porewater salinity ranged from 15 to 30 ppt, being higher at mangrove-island edges than centers. Anet maximized at 15.1 μmol m-2 s-1, and gsw was typically -2 s-1, both of which were greater in the dry than the wet season and greater at island centers than edges, with seasonal variability being roughly equal to variation between habitats. After accounting for season and habitat, water level positively affected Anet in both seasons but did not affect gsw. Similarly, porewater salinity had a slightly positive marginal effect on Anet but a negligible effect on gsw. Our findings suggest that inundation stress (i.e., water level) is the primary driver of variation in leaf gas exchange rates of scrub mangroves in the Florida Everglades, while also constraining Anet more than gsw. The interaction between inundation stress due to permanent flooding and habitat varies with season as physiological stress is alleviated at higher-elevation mangrove-island center habitats during the dry season. Freshwater inflows during the wet season, increase water levels and inundation stress at higher-elevation mangrove-island centers, but also potentially alleviate salt and sulfide stress in soils. Thus, habitat heterogeneity leads to differences in nutrient and water acquisition and use between trees growing in island centers versus edges, creating distinct physiological controls on photosynthesis, which likely affect carbon flux dynamics of scrub mangroves in the Everglades.

Accounting for intraspecific trait variation (ITV) is crucial to plant ecology for vegetation modeling efforts. ITV can be substantial; however, it remains unclear how ITV influences community-weighted mean (CWM) trait estimates. We use leaf and root trait data from 423 trees of 72 species from 15 Angiosperm families in combination with community data from 164 25×25m plots comprising 580 species to evaluate the contributions of ITV and compositional turnover to CWMs, comparing unlogged primary tropical forest to selectively-logged and clear-cut secondary tropical forest. We also examine the effect of imputing missing trait values using phylogenetic generalized linear modeling (PhyloPars) on CWMs. For six of the seven traits, ITV negatively covaried with community compositional turnover to generate larger CWM differences between forest types than observed if ITV was not integrated. For example, plot average weighted mean specific leaf area was 10.7 and 10.4 m2 kg-1 for primary and secondary forests, not accounting for ITV, but shifted to 9.8 and 11.1 m2 kg-1 after doing so. Our results from 72-species assemblages were largely consistent with results using phylogenetically-imputed traits for the entire community. The contribution of ITV to CWMs ranged from 25 to 75%, with nearly all trait variation due to forest type attributable to ITV. CWM trait estimates became more conservative with forest age, whereas ITV for many traits showed an opposing acquisitive shift (i.e., increasing in leaf area or root length), and because of negative covariation between ITV and species turnover, forest age-related weighted-mean trait differences increased.

Accounting for intraspecific trait variation (ITV) is central to plant ecology and crucial for vegetation modeling efforts. ITV can be substantial; however, it remains unclear how ITV influences community-weighted mean (CWM) trait estimates. We use leaf and root trait data from 423 trees of 72 species from 15 Angiosperm families in combination with community data from 164 25×25m plots comprising 580 species to evaluate the contribution of ITV to CWMs, comparing unlogged primary tropical forest to selectively-logged and clear-cut secondary tropical forest. We examine the effect of gap-filling missing trait values using phylogenetic generalized linear modeling (PhyloPars) on CWMs. For six of the seven traits, ITV negatively covaried with species turnover to generate larger CWM differences between forest types than observed if ITV was not integrated. For example, plot average assemblage-weighted mean specific leaf area was 10.7 and 10.4 m2 kg-1 for primary and secondary forests, not accounting for ITV, but shifted to 9.8 and 11.1 m2 kg-1 after doing so. Our results from 72-species assemblages were largely consistent with results using phylogenetically-imputed traits for the entire community. The contribution of ITV to CWMs ranged from 25 to 75%, with nearly all trait variation due to forest type attributable to ITV. CWM trait estimates became more conservative with forest age, whereas ITV for many traits showed an acquisitive shift (i.e., increasing in leaf area or root length), and because of negative covariation between ITV and species turnover, forest age-related CWM differences increased.

Background: Although it is well known that microbial communities are extremely diverse, how and why levels of biodiversity are generated and maintained are enduring ecological questions. Janzen’s mountain passes hypothesis assumes that the relatively stable climate regimes of tropical mountains means that species have narrower ranges than montane regions in cooler climates, allowing disproportionately high levels of species coexistence and diversity. We test this hypothesis for soil bacteria and fungi, to explore the relative importance of niche and neutral dynamics in governing of microbial diversity on mountains. Results: We found that the tropical mountain showed greater climatic barriers that effectively limited the dispersal of microbes but had no similar soil barriers. Our results show that tropical mountains have higher β-diversity and greater species turnover rates along elevations than subtropical and subalpine mountains both for fungi and bacteria. β-diversity patterns along elevational gradients are mainly shaped by dispersal limitation coupled with ecological drift and homogeneous selection, particularly in the tropics. Conclusions: Therefore, stronger effects of climatic barriers in tropical mountains in conjunction with biogeographic species distributions and dispersal limitation permit greater biological diversity of soil bacteria and fungi, which supports the predictions of Janzen’s hypothesis. This study advances our understanding of mechanisms underpinning the community assembly of soil microorganisms by demonstrating that climatic-dependent dispersal limitations also operate in tropical soil microbial communities.

Tropical cyclones drive coastal ecosystem dynamics, and their frequency, intensity, and spatial distribution are predicted to shift with climate change. Patterns of resistance and resilience were synthesized for 4138 ecosystem time series from n = 26 storms occurring between 1985 and 2018 in the Northern Hemisphere to predict how coastal ecosystems will respond to future disturbance regimes. Data were grouped by ecosystems (fresh water, salt water, terrestrial, and wetland) and response categories (biogeochemistry, hydrography, mobile biota, sedentary fauna, and vascular plants). We observed a repeated pattern of trade-offs between resistance and resilience across analyses. These patterns are likely the outcomes of evolutionary adaptation, they conform to disturbance theories, and they indicate that consistent rules may govern ecosystem susceptibility to tropical cyclones.

Linking drought to the timing of physiological processes governing tree growth remains one limitation in forecasting climate change effects on tropical trees. Using dendrometers, we measured fine-scale growth for 96 trees of 25 species from 2013 to 2016 in an everwet forest in Puerto Rico. Rainfall over this time span varied, including an unusual, severe El Niño drought in 2015. We assessed how growing season onset, median day, conclusion, and length varied with absolute growth rate and tree size over time. Stem growth was seasonal, beginning in February, peaking in July, and ending in November. Species growth rates varied between 0 and 8 mm/year and correlated weakly with specific leaf area, leaf phosphorus, and leaf nitrogen, and to a lesser degree with wood specific gravity and plant height. Drought and tree growth were decoupled, and drought lengthened and increased variation in growing season length. During the 2015 drought, many trees terminated growth early but did not necessarily grow less. In the year following drought, trees grew more over a shorter growing season, with many smaller trees showing a post-drought increase in growth. We attribute the increased growth of smaller trees to release from light limitation as the canopy thinned because of the drought, and less inferred hydraulic stress than larger trees during drought. Soil type accounted for interannual and interspecific differences, with the finest Zarzal clays reducing tree growth. We conclude that drought affects the phenological timing of tree growth and favors the post-drought growth of smaller, sub-canopy trees in this everwet forest.

Accounting for intraspecific trait variation (ITV) is central to plant ecology and crucial for vegetation modeling efforts. ITV can be substantial; however, it remains unclear how ITV influences community-weighted mean (CWM) trait estimates. We use leaf and root trait data from 423 trees of 72 species from 15 Angiosperm families in combination with community data from 164 small plots comprising 582 species to evaluate the contribution of ITV to CWMs, comparing unlogged, primary forest to selectively-logged and clear-cut secondary forest. We examine the effect of gap-filling missing trait values via phylogenetic generalized linear modeling (PhyloPars) on CWMs. For six of seven traits, ITV negatively covaried with species turnover to generate larger CWM differences than observed if ITV was not integrated. For example, plot average CWM specific leaf area was 10.7 and 10.4 m2 kg− 1 for primary and secondary forest, not accounting for ITV, but shifted to 9.8 and 11.1 m2 kg− 1 after doing so. Specific root length showed a similar trend. Our results from 72-species assemblages were supported by the results from the gap-filled analysis using the entire community, where the contribution of ITV to CWMs ranged from 25 to 75%, with nearly all trait variation due to forest type attributable to ITV. Therefore, CWM trait estimates became more-conservative with forest age, whereas ITV for many traits showed an acquisitive shift, and because of negative covariation between ITV and species turnover, forest age-related CWM differences increased. Differences were unaffected, if not strengthened, by gap-filling incomplete functional trait matrices.

Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consultation with data collectors, data users, instrument manufacturers, and data scientists was undertaken in order to ensure that the reporting format met community needs. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format is published in the U.S. Department of Energy's ESS-DIVE data repository, with documentation and future development efforts being maintained in a version control system. publishedVersion

Legumes provide an essential service to ecosystems by capturing nitrogen from the atmosphere and delivering it to the soil, where it may then be available to other plants. However, this facilitation by legumes has not been widely studied in global tropical forests. Demographic data from 11 large forest plots (16–60 ha) ranging from 5.25° S to 29.25° N latitude show that within forests, leguminous trees have a larger effect on neighbor diversity than non-legumes. Where soil nitrogen is high, most legume species have higher neighbor diversity than non-legumes. Where soil nitrogen is low, most legumes have lower neighbor diversity than non-legumes. No facilitation effect on neighbor basal area was observed in either high or low soil N conditions. The legume–soil nitrogen positive feedback that promotes tree diversity has both theoretical implications for understanding species coexistence in diverse forests, and practical implications for the utilization of legumes in forest restoration., Xu et al. examine the effect of leguminous trees on neighbor diversity across 11 plots in tropical forests around the world, and find that in high soil nitrogen conditions, most legume species have higher neighbor diversity than non-legumes, and vice versa where soil nitrogen is low. Their results have practical implications for the utilization of legumes in forest restoration.

The tree growth and mortality trade-off is well documented and plays a key role in forests by forming the basis of many ecosystem processes and contributing to tree species coexistence. One area that requires further understanding is how the growth-mortality trade-off is influenced by biotic and abiotic interactions in the forest. In this study, we used a 5-year interval of tree growth and mortality demographic data from a 9-ha forest dynamics plot in a temperate old-growth Chinese forest to address two questions, (1) What is the nature of the growth-mortality trade-off among species in this forest? (2) Are there differences between the responses of tree growth and mortality to local neighborhood variables, both biotic and abiotic? Specifically, do these responses vary among species and with tree size? For the first question, we hypothesized that, within species, mortality rate would be negatively correlated with growth rate, whereas among species it would be positively correlated. For the second question, we expected biotic and abiotic factors to both be important for tree mortality; but expected biotic factors to be more important than abiotic factors for tree growth. The responses of tree growth and mortality to local neighborhood variables, both biotic and abiotic, varied among species. Abiotic factors were more important than biotic factors for small trees; biotic variables were stable with tree size for both small and large trees. Our results showed that there were differences between the responses of tree growth and mortality to local neighborhood variables (i.e., biotic and abiotic) in this temperate forest community. The responses of tree mortality to local neighborhood variables strongly varied across species. Abiotic factors were only important for the growth of small trees. Biotic factors were stable with tree size for growth of small and large trees, but not for mortality. Mortality was negatively correlated with growth for large trees within species; growth-mortality trade-off among species was found to be more accentuated for small trees. The responses of tree mortality to local neighborhood variables differed strongly across species, whereas the responses of tree growth to local neighborhood variables varied among size classes. Tree growth and mortality is tightly correlated both within (negatively) and among species (positively), and their relationships are both size dependent in this temperate forest. Our findings highlight that differential responses of tree growth and mortality to local neighborhood variables continue to shape the forest community well after sapling establishment in this temperate forest community.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles—open data, open source and open methods—is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.

A growing body of research documents how the El Niño Southern Oscillation (ENSO) results in short-term changes in terrestrial environmental conditions, with the potential to drive ecosystem processes as the duration and severity of ENSO events increases with anthropogenic climate change. An ENSO positive phase results in anomalous patterns of rainfall and temperature throughout the tropics that coincide with leaf flush and increased fruit production in tropical forests worldwide. However, our understanding of possible mechanisms underlying this natural phenomenon is limited. Furthermore, flowering in tropical trees anticipates ENSO development, motivating the continued search for a global phenological cue for tropical angiosperm reproduction. We propose the solar energy flux hypothesis: that a physical energy influx in the Earth’s upper atmosphere and magnetosphere generated by a positive anomaly in the solar wind preceding ENSO development, cues tropical trees to increase allocation of resources to reproduction. We show that from 1994-2013, the solar wind energy flux into the Earth’s magnetosphere (Ein) is more strongly correlated with the number of trees in fruit or flower in a Puerto Rican wet forest than the Niño 3.4 climate index, despite Niño 3.4 being a previously identified driver of interannual increases in reproduction. We discuss the idea that changes in the global magnetosphere and thermosphere conditions via solar wind-effects on global atmospheric circulation, principally a weaker Walker circulation, cue interannual increases tropical tree reproduction. This may be a mechanism that synchronizes the reproductive output of the tropical trees to changes in environmental conditions that coincide with ENSO. Thus, space weather patterns may help explain terrestrial biological phenomena that occur at quasi-decadal scales.

In the version of this Perspective originally published, the first author of reference 39 was incorrectly listed as W. Cornwell and the publication year was incorrect. The reference should have read as follows: “Flores-Moreno, H. et al. fungaltraits aka funfun: a dynamic functional trait database for the world's fungi (GitHub, 2019); https://doi.org/10.5281/zenodo.1216257”. This has now been corrected.

Functional traits are increasingly used to understand the ecology of plants and to predict their responses to global changes. Unfortunately, trait data are unavailable for the majority of plant species. The lack of trait data is especially prevalent for hard-to-measure traits and for tropical plant species, potentially due to the many inherent difficulties of working with species in remote, hyperdiverse rainforest systems. The living collections of botanic gardens provide convenient access to large numbers of tropical plant species and can potentially be used to quickly augment trait databases and advance our understanding of species' responses to climate change. In this review, we quantitatively assess the availability of trait data for tropical versus temperate species, the diversity of species available for sampling in several exemplar tropical botanic gardens and the validity of garden-based leaf and root trait measurements. Our analyses support the contention that the living collections of botanic gardens are a valuable scientific resource that can contribute significantly to research on plant functional ecology and conservation.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.

Understanding the ecological processes that regulate microbial community assembly in different habitats is critical to predict microbial responses to anthropogenic disturbances and environmental changes. Rubber (Hevea brasiliensis) and Eucalypt (Eucalyptus urophylla) plantations (thereafter RP and EP) are rapidly established at the expense of forests in tropical China, greatly affecting tropical soils and their processes. However, the assembly processes of soil microbial communities after forest conversions remain unclear. We investigated soil microbial communities&rsquo, attributes and quantified the portion of deterministic assembly variation in two RP (a 3- and a 5-year-old) and two EP (a 2- and a 4-year-old) in Southern China. Shannon and Faith&rsquo, s Phylogenetic &alpha, diversity of both bacterial and fungal communities were higher in RP than in EP, regardless of plantation age or soil depth (0&ndash, 50 cm). Bacterial and fungal community structure was significantly different among the four plantations. The dominant microbial taxa in RP closely tracked the availability of nitrogen, phosphorus and potassium (K) while those in EP were closely related to the high total K content. Microbial co-occurrence networks in RP were more modular than those in EP, as governed by more keystone taxa that were strongly dependent on soil available nutrients. Environmental filtering imposed by soil nutrients heterogeneity contributed a considerable portion (33&ndash, 47%) of bacterial assembly variation in RP, but much less (8&ndash, 14%) in EP. The relative contribution of environmental selection on fungal assembly was also greater in RP than in EP. Our findings suggest that in RP clear microbial community patterns exist with respect to soil nutrients, whereas in EP microbial community assembly patterns are more stochastic and variable. The large variation in soil microbial community assembly patterns in EP could lead to fragile and unstable microbial-soil relationships, which may be one factor driving soil degradation in EP.

Functional traits are increasingly used to understand the ecology of plants and to predict their responses to global changes. Unfortunately, trait data are unavailable for the majority of plant species. The lack of trait data is especially prevalent for hard-to-measure traits and for tropical plant species, potentially owing to the many inherent difficulties of working with species in remote, hyperdiverse rainforest systems. The living collections of botanic gardens provide convenient access to large numbers of tropical plant species and can potentially be used to quickly augment trait databases and advance our understanding of species' responses to climate change. In this review, we quantitatively assess the availability of trait data for tropical versus temperate species, the diversity of species available for sampling in several exemplar tropical botanic gardens and the validity of garden-based leaf and root trait measurements. Our analyses support the contention that the living collections of botanic gardens are a valuable scientific resource that can contribute significantly to research on plant functional ecology and conservation. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.

As cyclonic wind storms (hurricanes and typhoons) increase in frequency and intensity with climate change, it is important to understand their effects on the populations and communities of tropical trees they impact. Using tree demographic data from four large, tropical forest dynamics plots that differ in cyclonic storm frequency, we compare tree population and community dynamics. Additionally, we assess the effect of cyclonic storms on three functional traits, specific leaf area, wood density, and tree height of the dynamic tree assemblages. Mortality, growth and recruitment rates and the intrinsic rates of population growth of species differed across the plots, and were most dynamic, especially for stems 1&ndash, 2 cm in diameter, at the plot which had an intermediate level of cyclonic storm frequency. Functional assemblages of species had the greatest degree of temporal variation in relation to disturbance, as measured by the change in functional divergence for the two plots with more intermediate cyclonic storm recurrence. Therefore, cyclonic storms affecting these plots generally have a greater effect on forest composition and dynamism than comparable cyclonic storms do on the plot which experiences cyclonic storms more frequently. Thus, we provide some evidence that community-wide demographic resistance to cyclonic storms is generally lower at an intermediate frequency of storms. While cyclonic storm strength and timing are important determinants of the within forest variation in tree dynamics and functional trait assemblages, we also show that cyclonic storm timing and frequency shapes tropical forest dynamics and functional composition across forests. We conclude that, over a given time interval, sites with intermediate levels of damaging cyclonic wind disturbance express a greater potential for life-history variation in the forest community, when compared to sites with less or more frequent disturbance.