Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline

pH Nonlinearly Dominates Soil Bacterial Community Assembly along an Altitudinal Gradient in Oak-Dominant Forests

Soil bacteria, the predominant microbiota in soil, are subject to the law of minimum and the law of tolerance, but the assembly patterns of soil bacteria in response to environmental factors remain far from clear. Here, we took advantage of an altitudinal gradient (1020-1770 asl) in oak-dominant forests and assessed whether soil bacteria linearly or nonlinearly respond to environmental properties through the changes in the community diversity and composition. We found that soil bacteria decreased with increasing altitude in terms of the species richness and phylogenetic structure, while they were unchanged with increasing altitude in terms of community composition. The species richness was nonlinearly affected by the soil pH (19.9%), C:N ratio (14.3%), SOC (11.4%), and silt + clay content (9.9%). Specifically, the species richness peaked at a pH of 5.5-6.5, and an SOC of 25-50 g kg-1, and it showed abrupt decreases and increases at a C:N ratio of 14.5 and a silt + clay content of 70%. The community composition was significantly affected by the soil pH (28.2%), then by the SOC (3.6%), available phosphorus (1.0%), and silt + clay content (0.5%), and it showed less turnovers at a pH of 6.0, SOC of 50 g kg-1, and available phosphorus > 3.0 g kg-1. These findings imply that environmental filtering processes nonlinearly shape bacterial communities.

The spatial patterns of diversity and their relationships with environments in rhizosphere microorganisms and host plants differ along elevational gradients

Introduction

Identifying spatial patterns of biodiversity along elevational gradients provides a unified framework for understanding these patterns and predicting ecological responses to climate change. Moreover, microorganisms and plants are closely interconnected (e.g., via the rhizosphere) and thus may share spatial patterns of diversity and show similar relationships with environments.

Methods

This study compared diversity patterns and relationships with environments in host plants and rhizosphere microorganisms (including various functional groups) along elevational gradients across three climatic zones.

Results

We found that above-and belowground diversity decreased monotonically or showed a hump-shaped or U-shaped pattern along elevation gradients. However, the diversity patterns of plants, bacteria, and fungi varied depending on the taxon and climatic zone. Temperature and humidity strongly contribute to above-and belowground diversity patterns and community composition along elevational gradients. Nonetheless, soil factors might be important regulators of diversity patterns and the community composition of plants and microorganisms along these gradients. Structural equation modeling revealed that environmental factors had a stronger direct effect on rhizosphere microbial diversity than host plant diversity.

Discussion

In sum, spatial patterns of diversity and their relationships with environments in rhizosphere microorganisms and their host plants differed at the regional scale. Different functional groups (e.g., pathogen, mycorrhiza and nitrifier) of soil microorganisms may have divergent elevational patterns and environmental responses. These data improve our understanding of elevational diversity patterns, and provide new insights into the conservation of biodiversity and ecosystem management, especially under climate change.

Diversity and distribution of CO2-fixing microbial community along elevation gradients in meadow soils on the Tibetan Plateau

Soil CO₂-fixing microbes play a significant role in CO₂-fixation in the terrestrial ecosystems, particularly in the Tibetan Plateau. To understand carbon sequestration by soil CO₂-fixing microbes and the carbon cycling in alpine meadow soils, microbial diversity and their driving environmental factors were explored along an elevation gradient from 3900 to 5100 m, on both east and west slopes of Mila Mountain region on the Tibetan Plateau. The CO₂-fixing microbial communities were characterized by high-throughput sequencing targeting the cbbL gene, encoding the large subunit for the CO₂-fixing protein ribulose 1, 5-bisphosphate carboxylase/oxygenase. The overall OTU (Operational Taxonomic Unit) abundance is concentrated at an altitude between 4300  and  4900 m. The diversity of CO₂-fixing microbes is the highest in the middle altitude area, and on the east slope is higher than those on the west slope. In terms of microbial community composition, Proteobacteria is dominant, and the most abundant genera are Cupriavidus, Rhodobacter, Sulfurifustis and Thiobacillus. Altitude has the greatest influence on the structural characteristics of CO₂-fixing microbes, and other environmental factors are significantly correlated with altitude. Therefore, altitude influences the structural characteristics of CO₂-fixing microbes by driving environmental factors. Our results are helpful to understand the variation in soil microbial community and its role in soil carbon cycling along elevation gradients.

Embracing mountain microbiome and ecosystem functions under global change

Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services to humans. They have provided classic model natural systems for plant and animal diversity gradient studies for over 250 years. In the recent decade, the exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review the literature on microbial diversity across taxonomic groups and ecosystem types on global mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which are largely consistent with traditional climatic hypotheses. However, elevational patterns are complicated for species richness without general rules in terrestrial and aquatic environments and are driven mainly by deterministic processes caused by abiotic and biotic factors. We see a major shift from documenting patterns of biodiversity towards identifying the mechanisms that shape microbial biogeographical patterns and how these patterns vary under global change by the inclusion of novel ecological theories, frameworks and approaches. We thus propose key questions and cutting-edge perspectives to advance future research in mountain microbial biogeography by focusing on biodiversity hypotheses, incorporating meta-ecosystem framework and novel key drivers, adapting recently developed approaches in trait-based ecology and manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships and finally modelling and predicting their global change responses.

Distinct soil bacterial patterns along narrow and broad elevational gradients in the grassland of Mt. Tianshan, China

Bacteria are essential regulators of soil biogeochemical cycles. While several studies of bacterial elevational patterns have been performed in recent years, the drivers of these patterns remain incompletely understood. To clarify bacterial distribution patterns and diversity across narrow- and broad-scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan in China along three elevational transects and the overall elevation transect: (1) 6 sites at elevations of 1047–1587 m, (2) 8 sites at 876–3070 m, and (3) 8 sites at 1602–2110 m. The bacterial community diversity across the overall elevation transects exhibited a hump-like pattern, whereas consistent patterns were not observed in the separate elevational transects. The bacterial community composition at the phylum level differed across the transects and elevation sites. The Actinobacteria was the most abundant phylum overall (41.76%) but showed clear variations in the different transects. Furthermore, heatmap analyses revealed that both pH and mean annual temperature (MAT) were significantly (P < 0.05) correlated with bacterial community composition as well as the dominant bacterial phyla, classes, and genera. These findings provide an inclusive view of bacterial community structures in relation to the environmental factors of the different elevational patterns.

Seasonal dynamics of soil microbial diversity and functions along elevations across the treeline

Although microbial diversity patterns along elevations have been extensively studied, little is known about whether the patterns are influenced by seasonality. To test the seasonal and elevational effects on microbial communities and functions, we collected soil samples across a mountain gradient above and below the treeline in three seasons (spring, summer and autumn). Microbial diversity based on the sequencing of 16S rRNA, 18S rRNA and nifH genes was measured, and microbial functions represented by soil basal respiration and microbial biomass were analyzed. As expected, we found significant seasonal and elevational effects on microbial α- and β-diversity and functions, and the effects of elevations were greater than seasonal effects. Elevational patterns of microbial β-diversity and functions were not influenced by seasonality. However, the elevational α-diversity patterns showed by specific groups (bacteria, protist and metazoa) changed among seasons. Further, we identified key soil properties (i.e. moisture, total carbon, total nitrogen and nitrate) which had higher seasonal and elevational variations, mainly contributing to the spatiotemporal variations of microbial diversity and functions. The findings of higher soil nutrients, archaeal and metazoan richness, and microbial functions at the treeline elevation, imply a strong edge effect of treeline on microbial diversity and functions. Together, our study highlights that seasonality influences the elevational patterns of soil microbial α-diversity, rather than that of β-diversity and functions, thus provides new insights into the seasonal and elevational effects on microbial communities and functions.

Contrasting Patterns and Drivers of Soil Fungal Communities between Two Ecosystems Divided by the Treeline

The treeline is a sensitive region of the terrestrial ecosystem responding to climate change. However, studies on the composition and formation mechanisms of soil fungal communities across the treeline are still lacking. In this study, we investigated the patterns of soil fungal community composition and interactions among functional guilds above and below the treeline using Illumina high-throughput sequencing and ecological network analysis. The results showed that there were significant differences in the soil environment and soil fungal community composition between the two ecosystems above and below the treeline. At the local scale of this study, geographic distance and environmental factors affected the composition of the soil fungal community. Soil temperature was an important environmental predictor of soil fungal community composition. Species in soil fungal communities in the subalpine meadow were more closely related to each other compared to those in the montane forest. Furthermore, the soil fungal community in montane forest was more stable. Our findings contribute to a better understanding of how mountain ecological functions respond to global climate change.

Winogradsky columns as a strategy to study typically rare microbial eukaryotes

Winogradsky columns have been widely used to study soil microbial communities, but the vast majority of those investigations have focused on the ecology and diversity of bacteria. In contrast, microbial eukaryotes (ME) have been regularly overlooked in studies based on experimental soil columns. Despite the recognized ecological relevance of ME in soil communities, investigations focused on ME diversity and the abundance of certain groups of interest are still scarce. In the present study, we used DNA metabarcoding (high-throughput sequencing of the V4 region of the 18S rRNA locus) to survey the ME diversity and abundance in an experimental Winogradsky soil column. Consistent with previous surveys in natural soils, our survey identified members of Cercozoa (Rhizaria; 31.2%), Apicomplexa and Ciliophora (Alveolata; 12.5%) as the predominant ME groups, but at particular depths we also detected the abundant presence of ME lineages that are typically rare in natural environments, such as members of the Vampyrellida (Rhizaria) and Breviatea (Amorphea). Our survey demonstrates that experimental soil columns are an efficient enrichment-culture approach that can enhance investigations about the diversity and ecology of ME in soils.

Contrasting patterns and drivers of soil bacterial and fungal diversity across a mountain gradient

Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient-bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed-effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems.

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

Soil pH dominates elevational diversity pattern for bacteria in high elevation alkaline soils on the Tibetan Plateau

Although studies of elevational diversity gradient for microbes have attracted considerable attention, the generality of these patterns and their underlying drivers are still poorly understood. Here, we investigated bacterial distribution across a high elevational gradient (4328-5228 m a.s.l.) along the Nyainqêntanglha mountains on the Southwestern Tibetan Plateau. We found a decreasing diversity trend with increasing elevation, with pH contributing most to the diversity variation, followed by elevation and mean annual temperature (MAT). Bacterial community composition differed taxonomically and phylogenetically with elevation. Furthermore, partial Mantel analyzes showed that bacterial community composition was significantly influenced by elevation, pH and MAT. Phylogenetic structure analysis indicated that deterministic processes (related to pH) determined bacterial community assembly along this elevation gradient. Our results reinforce the observed rule that pH is of foremost importance in driving bacterial elevational diversity patterns. We also suggest that absence of tree cover and of human disturbance might be important in allowing an underlying elevational trend to reveal itself. Review of other studies suggests that the trend of decreasing diversity at higher elevations might be generally true above the tree line.

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients

The importance of assembly processes in shaping biological communities is poorly understood, especially for microbes. Here, we report on the forces that structure soil bacterial communities along a 2000 m elevational gradient. We characterized the relative importance of habitat filtering and competition on phylogenetic structure and turnover in bacterial communities. Bacterial communities exhibited a phylogenetically clustered pattern and were more clustered with increasing elevation. Biotic factors (i.e., relative abundance of dominant bacterial lineages) appeared to be most important to the degree of clustering, evidencing the role of the competitive ability of entire clades in shaping the communities. Phylogenetic turnover showed the greatest correlation to elevation. After controlling the elevation, biotic factors showed greater correlation to phylogenetic turnover than all the habitat variables (i.e., climate, soil and vegetation). Structural equation modelling also identified that elevation and soil organic matter exerted indirect effects on phylogenetic diversity and turnover by determining the dominance of microbial competitors. Our results suggest that competition among bacterial taxa induced by soil carbon contributes to the phylogenetic pattern across elevational gradient in the Tibetan Plateau. This highlights the importance of considering not only abiotic filtering but also biotic interactions in soil bacterial communities across stressful elevational gradients.

Relative influence of sediment variables on mangrove community assembly in Leizhou Peninsula, China

Effective conservation of mangroves requires a complete understanding of vegetation structure and identification of the variables most important to their assembly. Using canonical correspondence analysis (CCA) combined with variation partition, we determined the independent and joint effects of sediment variables, including physicochemical characteristics and heavy metals, on mangrove community assemblies in the overstory and understory in Leizhou Peninsula, China. The results indicated that the contributions of sediment physicochemical variables to community assembly were greater than were those of heavy metals, particularly in overstory vegetation. However, the independent contributions of heavy metals were higher in understory mangrove vegetation than in the overstory. The TOC, TP, and salinity of the sediment, distance from the coastline, and concentration of As were limiting factors for mangrove assembly in overstory vegetation, while understory vegetation may be affected to a greater degree by the distance from the coastline, electrical conductivity, and concentration of As and Pb in the sediment.