Does genome size drive the pH-related shifts in bacterial biodiversity within forest soils?

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 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 2) ensuring the selection of representative sampling sites; and 3) employing transect-based or controlled experiments to better isolate environmental drivers.