Host specificity of plant-associated bacteria is negatively associated with genome size and host abundance along a latitudinal gradient.

Host specialization plays a critical role in the ecology and evolution of plant-microbe symbiosis. Theory predicts that host specialization is associated with microbial genome streamlining and is influenced by the abundance of host species, both of which can vary across latitudes, leading to a latitudinal gradient in host specificity. Here, we quantified the host specificity and composition of plant-bacteria symbioses on leaves across 329 tree species spanning a latitudinal gradient. Our analysis revealed a predominance of host-specialized leaf bacteria. The degree of host specificity was negatively correlated with bacterial genome size and the local abundance of host plants. Additionally, we found an increased host specificity at lower latitudes, aligning with the high prevalence of small bacterial genomes and rare host species in the tropics. These findings underscore the importance of genome streamlining and host abundance in the evolution of host specificity in plant-associated bacteria along the latitudinal gradient.

Diversity and biogeography of plant phyllosphere bacteria are governed by latitude-dependent mechanisms.

Predicting and managing the structure and function of plant microbiomes requires quantitative understanding of community assembly and predictive models of spatial distributions at broad geographic scales. Here, we quantified the relative contribution of abiotic and biotic factors to the assembly of phyllosphere bacterial communities, and developed spatial distribution models for keystone bacterial taxa along a latitudinal gradient, by analyzing 16S rRNA gene sequences from 1453 leaf samples taken from 329 plant species in China. We demonstrated a latitudinal gradient in phyllosphere bacterial diversity and community composition, which was mostly explained by climate and host plant factors. We found that host-related factors were increasingly important in explaining bacterial assembly at higher latitudes while nonhost factors including abiotic environments, spatial proximity and plant neighbors were more important at lower latitudes. We further showed that local plant-bacteria associations were interconnected by hub bacteria taxa to form metacommunity-level networks, and the spatial distribution of these hub taxa was controlled by hosts and spatial factors with varying importance across latitudes. For the first time, we documented a latitude-dependent importance in the driving factors of phyllosphere bacteria assembly and distribution, serving as a baseline for predicting future changes in plant phyllosphere microbiomes under global change and human activities.

Species packing and the latitudinal gradient in beta-diversity.

The decline in species richness at higher latitudes is among the most fundamental patterns in ecology. Whether changes in species composition across space (beta-diversity) contribute to this gradient of overall species richness (gamma-diversity) remains hotly debated. Previous studies that failed to resolve the issue suffered from a well-known tendency for small samples in areas with high gamma-diversity to have inflated measures of beta-diversity. Here, we provide a novel analytical test, using beta-diversity metrics that correct the gamma-diversity and sampling biases, to compare beta-diversity and species packing across a latitudinal gradient in tree species richness of 21 large forest plots along a large environmental gradient in East Asia. We demonstrate that after accounting for topography and correcting the gamma-diversity bias, tropical forests still have higher beta-diversity than temperate analogues. This suggests that beta-diversity contributes to the latitudinal species richness gradient as a component of gamma-diversity. Moreover, both niche specialization and niche marginality (a measure of niche spacing along an environmental gradient) also increase towards the equator, after controlling for the effect of topographical heterogeneity. This supports the joint importance of tighter species packing and larger niche space in tropical forests while also demonstrating the importance of local processes in controlling beta-diversity.

Direct and indirect effects of climate on richness drive the latitudinal diversity gradient in forest trees.

Climate is widely recognised as an important determinant of the latitudinal diversity gradient. However, most existing studies make no distinction between direct and indirect effects of climate, which substantially hinders our understanding of how climate constrains biodiversity globally. Using data from 35 large forest plots, we test hypothesised relationships amongst climate, topography, forest structural attributes (stem abundance, tree size variation and stand basal area) and tree species richness to better understand drivers of latitudinal tree diversity patterns. Climate influences tree richness both directly, with more species in warm, moist, aseasonal climates and indirectly, with more species at higher stem abundance. These results imply direct limitation of species diversity by climatic stress and more rapid (co-)evolution and narrower niche partitioning in warm climates. They also support the idea that increased numbers of individuals associated with high primary productivity are partitioned to support a greater number of species.

Determinants of change in subtropical tree diameter growth with ontogenetic stage.

We evaluated the degree to which relative growth rate (RGR) of saplings and large trees is related to seven functional traits that describe physiological behavior and soil environmental factors related to topography and fertility for 57 subtropical tree species in Dinghushan, China. The mean values of functional traits and soil environmental factors for each species that were related to RGR varied with ontogenetic stage. Sapling RGR showed greater relationships with functional traits than large-tree RGR, whereas large-tree RGR was more associated with soil environment than was sapling RGR. The strongest single predictors of RGR were wood density for saplings and slope aspect for large trees. The stepwise regression model for large trees accounted for a larger proportion of variability (R(2) = 0.95) in RGR than the model for saplings (R(2) = 0.55). Functional diversity analysis revealed that the process of habitat filtering likely contributes to the substantial changes in regulation of RGR as communities transition from saplings to large trees.

Seed rain composition responds to climate change in a subtropical forest.

Recent climate change has been shown to alter aspects of forest plant demography, such as growth and mortality, but less attention has been focused on how climate change alters the reproduction of plant populations through time. We hypothesized that the plant seed production would respond to climate change, and that the response would differ according to plant life form and functional traits. We tested this hypothesis by examining climate change from 2005 to 2020 and by determining the temporal trends of seed rain and seed production from plants with different life forms (e.g., herbs, vines, trees, palms) and of tree species with different statures as well as leaf, seed and wood traits during 2014-2020. We also tested the correlation between meteorological variables and time series of seed rain using cross correlation analysis. We found increasing wetness (lower vapor pressure deficit) through time but with decreasing minimum relative humidity, which is a pattern consistent with trends seen in many other parts of the world. During the study period, seed production of shrubs and relative contribution of woody vines to total seed rain decreased, while relative contribution of palms to total seed rain and tree species with more conservative leaf traits increased their contribution to total seed rain. Overall, these trends were well explained by the trends of meteorological variables and the responses of these life forms to climate change in previous studies. Additionally, the increasingly conservative leaf traits were also consistent with shifts in traits following recovery from disturbance. Our results suggest that a trait-based approach may help to unveil trends that are not readily apparent by examining seed counts alone. The compositional change found in the seed rain may indicate future shifts in forest species composition and should be incorporated into future studies of forest modelling and projections under climate change.

Draft genome of Castanopsis chinensis, a dominant species safeguarding biodiversity in subtropical broadleaved evergreen forests.

OBJECTIVES: Castanopsis is the third largest genus in the Fagaceae family and is essentially tropical or subtropical in origin. The species in this genus are mainly canopy-dominant trees, and the key components of evergreen broadleaved forests play a crucial role in the maintenance of local biodiversity. Castanopsis chinensis, distributed from South China to Vietnam, is a representative species. It currently suffers from a high disturbance of human activity and climate change. Here, we present its assembled genome to facilitate its preliminary conservation and breeding on the genome level. DATA DESCRIPTION: The C. chinensis genome was assembled and annotated by Nanopore and MGI whole-genome sequencing and RNA-seq reads using leaf tissues. The assembly was 888,699,661 bp in length, consisting of 133 contigs and a contig N50 of 23,395,510 bp. A completeness assessment of the assembly with Benchmarking Universal Single-Copy Orthologs (BUSCO) indicated a score of 98.3%. Repetitive elements comprised 471,006,885 bp, accounting for 55.9% of the assembled sequences. A total of 51,406 genes that coded for 54,310 proteins were predicted. Multiple databases were used to functionally annotate the protein sequences.

Genome assembly of Erythrophleum Fordii, a special "ironwood" tree in China.

OBJECTIVES: Erythrophleum is a genus in the Fabaceae family. The genus contains only about 10 species, and it is best known for its hardwood and medical properties worldwide. Erythrophleum fordii Oliv. is the only species of this genus distributed in China. It has superior wood and can be used in folk medicine, which leads to its overexploitation in the wild. For its effective conservation and elucidation of the distinctive genetic traits of wood formation and medical components, we present its first genome assembly. DATA DESCRIPTION: This work generated ~ 160.8 Gb raw Nanopore whole genome sequencing (WGS) long reads, ~ 126.0 Gb raw MGI WGS short reads and ~ 29.0 Gb raw RNA-seq reads using E. fordii leaf tissues. The de novo assembly contained 864,825,911 bp in the E. fordii genome, with 59 contigs and a contig N50 of 30,830,834 bp. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed 98.7% completeness of the assembly. The assembly contained 471,006,885 bp (54.4%) repetitive sequences and 28,761 genes that coded for 33,803 proteins. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.

A DNA barcode library for woody plants in tropical and subtropical China.

The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.

Effects of soil resource availability on patterns of plant functional traits across spatial scales.

Identifying patterns and drivers of plant community assembly has long been a central issue in ecology. Many studies have explored the above questions using a trait-based approach; however, there are still unknowns around how patterns of plant functional traits vary with environmental gradients. In this study, the responses of individual and multivariate trait dispersions of 134 species to soil resource availability were examined based on correlational analysis and torus-translation tests across four spatial scales in a subtropical forest, China. Results indicated that different degrees of soil resource availability had different effects on trait dispersions. Specifically, limited resource (available phosphorus) showed negative relationships with trait dispersions, non-limited resource (available potassium) showed positive relationships with trait dispersions, and saturated resource (available nitrogen) had no effect on trait dispersions. Moreover, compared with the stem (wood density) and architectural trait (maximum height), we found that leaf functional traits can well reflect the response of plants to nutrient gradients. Lastly, the spatial scale only affected the magnitude but not the direction of the correlations between trait dispersions and environmental gradients. Overall, the results highlight the importance of soil resource availability and spatial scale in understanding how plant functional traits respond to environmental gradients.

Plastome-based phylogeny improves community phylogenetics of subtropical forests in China.

Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

Functional Traits Are Good Predictors of Tree Species Abundance Across 101 Subtropical Forest Species in China.

What causes variation in species abundance for a given site remains a central question in community ecology. Foundational to trait-based ecology is the expectation that functional traits determine species abundance. However, the relative success of using functional traits to predict relative abundance is questionable. One reason is that the diversity in plant function is greater than that characterized by the few most commonly and easily measurable traits. Here, we measured 10 functional traits and the stem density of 101 woody plant species in a 200,000 m2 permanent, mature, subtropical forest plot (high precipitation and high nitrogen, but generally light- and phosphorus-limited) in southern China to determine how well relative species abundance could be predicted by functional traits. We found that: (1) leaf phosphorus content, specific leaf area, maximum CO2 assimilation rate, maximum stomata conductance, and stem hydraulic conductivity were significantly and negatively associated with species abundance, (2) the ratio of leaf nitrogen content to leaf phosphorus content (N:P) and wood density were significantly positively correlated with species abundance; (3) neither leaf nitrogen content nor leaf turgor loss point were related to species abundance; (4) a combination of N:P and maximum stomata conductance accounted for 44% of the variation in species' abundances. Taken together, our findings suggested that the combination of these functional traits are powerful predictors of species abundance. Species with a resource-conservative strategy that invest more in their tissues are dominant in the mature, subtropical, evergreen forest.

Correction: The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China.

[This corrects the article DOI: 10.1371/journal.pone.0238478.].

Consequences of spatial patterns for coexistence in species-rich plant communities.

Ecology cannot yet fully explain why so many tree species coexist in natural communities such as tropical forests. A major difficulty is linking individual-level processes to community dynamics. We propose a combination of tree spatial data, spatial statistics and dynamical theory to reveal the relationship between spatial patterns and population-level interaction coefficients and their consequences for multispecies dynamics and coexistence. Here we show that the emerging population-level interaction coefficients have, for a broad range of circumstances, a simpler structure than their individual-level counterparts, which allows for an analytical treatment of equilibrium and stability conditions. Mechanisms such as animal seed dispersal, which result in clustering of recruits that is decoupled from parent locations, lead to a rare-species advantage and coexistence of otherwise neutral competitors. Linking spatial statistics with theories of community dynamics offers new avenues for explaining species coexistence and calls for rethinking community ecology through a spatial lens.

The complete chloroplast genome sequence of Ormosia formosana.

Ormosia formosana is an important hardwood species and its seeds are popular as decorative jewelry. Currently, this species is threatened in the natural forests due to habitat destruction. Here, we first report the chloroplast genome of O. formosana for future studies in ecology, phylogeny, and conservation. The chloroplast genome of O. formosana is 173,587 bp in length with a GC content of 35.80%. It includes a large single-copy region of 73,550 bp, a small single-copy region of 18,683 bp, and two inverted repeat regions of 40,696 bp and 40,658 bp, respectively. The genome was totally annotated with 135 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis indicated that O. formosana is most genetically similar to O. boluoensis.

The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China.

Environments in both biotic and abiotic ecosystems have been affected by the colonization of non-native flora. In this study, we examined the effect of Bidens alba invasion on different land-use types along a coastline in southern China. Bacterial communities in each site were determined using 16S rDNA sequencing, and soil physicochemical properties were analyzed using standard methods. Although our results indicated that B. alba invasion did not have a significant effect on the alpha diversity of bacteria, it caused significant differences in soil bacterial community composition between invaded and uninvaded soil across different land-use types. Beta diversity and several physicochemical properties in forest, orchard and waterfront environments were recorded to be more susceptible to B. alba invasion. A high proportion of the variation of bacterial communities can be explained by a combination of environmental variables, indicating that environmental selection rather than plant invasion is a more effective process in coastal microbial assemblages. By comparing topological roles of shared OTUs among invaded and uninvaded soil, keystone taxa in invaded soil were identified. Acidobacteria was the major phyla involved in the invasive process which could be driven by environmental selection. How key phyla react in our experiment should be verified by further studies.

Soil nitrogen concentration mediates the relationship between leguminous trees and neighbor diversity in tropical forests.

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.

Testing the competition-colonization trade-off and its correlations with functional trait variations among subtropical tree species.

The competition-colonization trade-off, by which species can partition spatial niches, is a potentially important mechanism allowing the maintenance of species diversity in plant communities. We examined whether there was evidence for this trade-off among tree species in a subtropical forest and how it correlated with eight functional traits. We developed and estimated a metric for colonization ability that incorporates both fecundity and seed dispersal based on seed trap data and the sizes and distributions of adult trees. Competitive ability was estimated as survival probability under high crowding conditions based on neighborhood models. Although we found no significant relationship between colonization and competitive abilities, there was a significant negative correlation between long distance dispersal ability and competitive ability at the 5 cm size class. Colonizers had traits associated with faster growth, such as large leaves and low leaf lamina density, whereas competitors had traits associated with higher survival, such as dense wood. Our results imply that any trade-off between competition and colonization may be more determined by dispersal ability than by fecundity, suggesting that seed dispersal is an important contributor to diversity maintenance. Future work should test how competitive ability covaries with the components of colonization ability, as we did here.

Contributions of precipitation and temperature to the large scale geographic distribution of fleshy-fruited plant species: Growth form matters.

Fruit type, an important reproductive trait, is closely related to reproduction strategy, community dynamics and biotic interactions. However, limited research has explored the geographic distribution of fruit type and the underlying abiotic factors influencing this on a large scale. Here we aim to study large-scale distribution patterns of fleshy-fruited plant species and the most important environmental drivers for different growth forms in utilizing the fruit type and distribution data for over 27000 plant species in China. Results indicated that the proportion of fleshy-fruited species was higher in southeast China, and this pattern was consistent between different growth forms. Overall, the proportion of fleshy-fruited species was higher in wet, warm, and stable environments. Notably, mean annual precipitation had the greatest predictive contribution to woody fleshy-fruited species distributions, but mean annual temperature best predicted the herbaceous fleshy-fruited species distributions. We provide the first map of a large-scale distribution of fleshy-fruited plant species for different growth forms in the northern hemisphere and show that these geographic patterns are mainly determined by contrasting climatic gradients. Recognizing that climate factors have different relationships with different growth forms of fleshy-fruited species advances our knowledge about fruit type and environment. This work contributes to predictions of the global distribution of fleshy-fruited species under future climate change scenarios and provides a reference for continued research on the complex interactions between plants, frugivores and the environment.

Forest dynamics and its driving forces of sub-tropical forest in South China.

Tree mortality and recruitment are key factors influencing forest dynamics, but the driving mechanisms of these processes remain unclear. To better understand these driving mechanisms, we studied forest dynamics over a 5-year period in a 20-ha sub-tropical forest in the Dinghushan Nature Reserve, South China. The goal was to identify determinants of tree mortality/recruitment at the local scale using neighborhood analyses on some locally dominant tree species. Results show that the study plot was more dynamic than some temperate and tropical forests in a comparison to large, long-term forest dynamics plots. Over the 5-year period, mortality rates ranged from 1.67 to 12.33% per year while recruitment rates ranged from 0 to 20.26% per year. Tree size had the most consistent effect on mortality across species. Recruitment into the ≥1-cm size class consistently occurred where local con-specific density was high. This suggests that recruitment may be limited by seed dispersal. Hetero-specific individuals also influenced recruitment significantly for some species. Canopy species had low recruitment into the ≥1-cm size class over the 5-year period. In conclusion, tree mortality and recruitment for sixteen species in this plot was likely limited by seed dispersal and density-dependence.