Jian Gao

Over the last decade, the mechanisms underlying changes in bacterial biodiversity in forest soils based on 16S rRNA sequencing have gained considerable attention in ecological and geographical research (Bahram et al., 2018;Piton et al., 2023). Soil pH plays a pivotal role in the development of soil bacterial biodiversity (Ramoneda et al., 2023;Luan et al., 2023;He et al., 2023). To explore the mechanism underlying the changes in bacterial biodiversity in forest soils with varying pH, researchers have evaluated bacterial 16S diversity. Wang et al. (2023) analysed the 16S and bacterial metagenomic data from soil samples obtained at 12 forest sites in China and concluded that on a pH gradient, the mismatch between taxonomic and functional diversity may be attributed to changes in genome size. That is, a small community of large-genome taxa could harbour higher functional diversity than a large community of small-genome taxa. Biodiversity in resource-limited conditions with acidic pH environments (commonly found at low latitudes) should be lower than that in resource-abundant conditions with neutral pH environments (commonly found at high latitudes). Yet this proposed decoupling stands in contrast to the theoretical expectation that genome size and biodiversity exhibit a positive correlation under natural ecological conditions (Lynch & Conery, 2003;Joyce, 2002;Pellicer et al., 2023). 2020), all of whom utilized identical sampling sites, methods, and experimental conditions. Since the measurements and primary analyses were conducted by the same research group, the datasets are highly comparable. All statistical analyses were performed in IBM SPSS Statistics 27.0, and line graph plotting was conducted using OriginPro 2022 (v9.9.0.225).Forest soil pH in China peaks near 40°N (Zheng et al., 2022). While Wang et al. reported a positive linear correlation, our analysis revealed a nonlinear relationship, particularly near neutral pH (Wang et al., 2023). Previous studies have also shown that if Wang et al. could add more sampling sites in the north of 40 °N, the unimodal curve could be more clearly observed (Song, 2023). In our study, bacterial biodiversity showed a significant unimodal relationship with latitude. (Figure S1a). Furthermore, unimodal relationships between bacterial functional diversity, genome size, and carbohydrate-active enzyme gene diversity and latitude were observed through metagenomic annotation and quantification of diversity indices based on richness (Figure S1b-d); all plot visualizations were generated in OriginPro 2022. Our work aligns with previous studies showing a unimodal pattern of bacterial biodiversity around 40°N (Liu et al., 2020). Therefore, the interpretation presented by Wang et al. may be affected by the fact that they only selected three sites north of 40°N, which may have been insufficient to clearly reveal the unimodal pattern (Wang et al., 2023).Meanwhile, both bacterial functional diversity and genome size display a significant decreasing -increasing relationship with latitude, also turning near 40°N (Figure S1b-d).Bacterial biodiversity is primarily linked to latitude, whereas functional diversity and genome size correlate more closely with pH. Thus, the observed large genomes and high functional diversity in acidic soils likely reflect the prevalence of such soils in climatically favorable low-latitude forests, not a direct stress response, leading to the earlier misinterpretation.Fungi, particularly mycorrhizal fungi, are widely recognized as key drivers of microbial diversity in forest soils of China due to their central role in nutrient cycling and cannot be overlooked (Chen et al., 2022). We found that latitude indirectly affects fungal diversity by positively influencing plant nitrogen and phosphorus reuptake rates (NR/PR), and NR/PR reflects N/P limitation (Du et al., 2020). A possible explanation for this pattern is that when plants are limited by phosphorus, they become more reliant on symbiotic fungi for nutrient supply (Zheng et al., 2022). This may create a cascading effect on the dependence of the plants on symbiotic fungi, thereby shaping the latitudinal variation pattern of fungal diversity S2a), no such correlation exists for functional diversity. Fungal diversity and bacterial carbohydrate-active enzyme gene diversity (Figure S2b) and genome size (Figure S2c) were analyzed for pairwise correlations via SPSS Statistics 27.0, with diversity metrics based on richness for all microbial indices. In contrast to the taxonomic pattern, fungal diversity is negatively correlated with the diversity of bacterial carbohydrate-active enzyme genes (Figure S2b). This observational pattern is consistent with the dominant role of mycorrhizal fungi in the carbon cycle, where they directly exchange carbon, nitrogen, and phosphorus with plant roots (Chen et al., 2022; Lebreton et al., 2021). Their symbiotic advantage suggests they may occupy key carbon-metabolism niches, potentially contributing to competitive exclusion of bacteria from these functions (Song et al., 2023). However, the nutrients processed and released by fungi into the soil create new ecological niches, which we interpret as consistent with a "trickle-down effect" that promotes bacterial taxonomic diversity and may account for the observed positive correlation (Jacoby & Kopriva, 2019). Notably, fungal diversity shows no linkage to bacterial genome size (Figure S2c), suggesting that these putative fungal-driven processes operate largely independently of genome size evolution in bacteria.To verify whether our inference is consistent with the actual situation, we used structural equation modelling in R 4.4.1 (packages lavaan v0.6-11 and piecewiseSEM v2.1.0) to examine the ecological processes suggested by (H1) Wang et al. and (H2) this study (Figure 1a,b). The results showed that H2 had a higher degree of explanation for bacterial diversity than H1. Because in the...

Recent studies have suggested that large-scale afforestation may disrupt the national water cycle in China. However, contemporary scientific approaches, such as 'determining greenery based on water' and deploying drought-resistant species, can improve soil water retention and ecological stability, making afforestation an efficient strategy for water resource management and ecological investment. Here, we reassess the role of afforestation in China's water cycle from a scale-aware and multi-driver perspective. We argue that afforestation can enhance soil water retention and ecosystem stability at local scales, while its influence on large-scale hydrological processes is intertwined with climate variability, atmospheric circulation, cryospheric processes, and human water management. Rather than acting as a dominant driver, afforestation may contribute to regional hydrological adjustments alongside other key environmental factors. This perspective highlights the importance of integrating scale and multiple drivers when evaluating land–water interactions under global change. Furthermore, regional afforestation strategies focus on curbing desert expansion and restoring degraded lands rather than attempting to eliminate natural deserts. From a long-term, regional perspective, these efforts may have contributed to mitigating soil erosion and desertification, improving river and lake health, and enhancing the resilience of ecosystems in East Asia. Cumulative evidence suggests that afforestation produces both ecohydrological benefits and hydrological trade-offs, with their net outcomes depending on regional climate, water limitation, management practices, and spatial scale.

Stover mulching, as a sustainable agricultural conservation practice, has been shown to effectively increase soil organic matter and enhance crop yields. The impact of stover mulching on soil microorganisms has been extensively studied. However, less attention has been given to endophytic and rhizospheric microorganisms that have closer relationships with crops. How do the quality and frequency of stover mulching affect the composition and structure of these endosphere and rhizosphere microbial communities? And what is their influence on critical indicators of soil health such as bacterial plant pathogen and Rhizobiales? These questions remain unresolved. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching qualities (0%, 33%, 67%, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. Results showed significant correlations between Bacillales and Rhizobiales orders and soil SOC, NO₃⁻N, and NH₄⁺N; Hypocreales and Eurotiales orders were significantly correlated with soil NO₃⁻N, with the Aspergillus genus also showing a significant correlation with soil SOC. The frequency and quality of stover mulching had a significant effect on root and rhizospheric microbial communities, with the lowest relative abundance of bacterial plant pathogens and highest relative abundance of nitrogen-fixing bacteria such as Rhizobiales and Hypocreales observed under F1/3 and F2/3 conditions. The most complex structures in endosphere and rhizospheric microbial communities were found under Q33 and Q67 conditions, respectively. This research indicates that from a soil health perspective, low-frequency high-coverage stover mulching is beneficial for the composition of endosphere and rhizosphere microbial communities, while moderate coverage levels are conducive to more complex structures within these communities. This study holds significant ecological implications for agricultural production and crop protection.

Introduction: Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP).Methods: Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing.Results: Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms.Conclusion: Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.

Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124–156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103–158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76–103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.

The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient for the enhancement of the understanding of phylogenetic relationships and taxonomic revision. Here, we report complete cp genomes of five species of Acer sect. Platanoidea. The length of Acer sect. Platanoidea cp genomes ranged from 156,262 bp to 157,349 bp and detected the structural variation in the inverted repeats (IRs) boundaries. By conducting a sliding window analysis, we found that five relatively high variable regions (trnH-psbA, psbN-trnD, psaA-ycf3, petA-psbJ and ndhA intron) had a high potential for developing effective genetic markers. Moreover, with an addition of eight plastomes collected from GenBank, we displayed a robust phylogenetic tree of the Acer sect. Platanoidea, with high resolutions for nearly all identified nodes, suggests a promising opportunity to resolve infrasectional relationships of the most species-rich section Platanoidea of Acer.

Adaptive divergence, which usually explains rapid diversification within island species, might involve the positive selection of genes. Anthocyanin biosynthetic pathway (ABP) genes are important for floral diversity, and are related to stress resistance and pollination, which could be responsible for species diversification. Previous studies have shown that upstream genes of ABP are subject to selective constraints and have a slow evolutionary rate, while the constraints on downstream genes are lower. In this study, we confirmed these earlier observations of heterogeneous evolutionary rate in upstream gene CHS and the downstream gene UFGT, both of which were expressed in Scutellaria sp. inflorescence buds. We found a higher evolutionary rate and positive selection for UFGT. The codons under positive selection corresponded to the diversified regions, and the presence or absence of an α-helix might produce conformation changes in the Rossmann-like fold structure. The significantly high evolutionary rates for UFGT genes in Taiwanese lineages suggested rapid accumulation of amino acid mutations in island species. The results showed positive selection in closely related species and explained the high diversification of floral patterns in these recently diverged species. In contrast, non-synonymous mutation rate decreases in long-term divergent species could reduce mutational load and prevent the accumulation of deleterious mutations. Together with the positive selection of transcription factors for ABP genes described in a previous study, these results confirmed that positive selection takes place at a translational level and suggested that the high divergence of ABP genes is related to the floral diversity in island Scutellaria species.