Wetlands, regarded as the kidneys of the Earth, are important ecosystems for flora and fauna biodiversity, providing food, regulating climate, and purifying water [1, 2]. However, global wetlands are facing many ecological problems (e.g., biodiversity loss, reclamation, and water pollution) due to climate change and anthropogenic disturbance [3–5]. Therefore, microbial community in wetlands might also be subject to diversity loss and as a consequence the ecological function of biogeochemical processes will be affected. Microorganisms in wetland soils are one of the largest world reservoirs of biodiversity and drive numerous ecological processes in terrestrial ecosystems [6–8]. Specifically, bacteria and fungi are responsible for the turnover and cycling of important elements, including carbon, nitrogen, and phosphorus [9–11]. Microbial diversity is closely correlated with multiple ecosystem functions [6, 10], therefore understanding microbial diversity might be beneficial for evaluating the health of wetland ecosystems.
Deciphering the fundamental mechanisms for generating and maintaining microbial diversity is a core objective in community ecology, and some interesting patterns have been discovered. For instance, distance-decay relationships (DDRs) mean that microbial community similarity generally decreases with an increase in geographical distance [12, 13]. Microbial β-diversity varies along environmental gradients (e.g., pH and salinity) [14, 15]. Many ecological theories that attempt to explain diversity-environment interconnections mainly consider species interaction models (e.g., competition and cooperation) and its in-situ resource (e.g., space and nutrient availability) [13, 16, 17]. Heterogeneity in substrate preference and environmental stress adaptations of microorganisms results in differences in microbial growth and biomass yield [14, 15, 18]. This can lead to a skewed abundance distribution in a local microbial community, with relatively few dominant and a large number of rare species (alternatively known as a “rare biosphere”) [17, 19, 20]. Previous studies have reported that rare and abundant species often show different distribution patterns and functional traits [21–23]. Therefore, disentangling the biogeography and community assembly of rare and abundant microbial taxa is essential for understanding microbe-driven ecosystem processes and functions.
Recent studies have described the biogeography of rare and abundant microbial taxa in various environments [17, 20], with both spatial effects and environmental factors influencing soil microbial diversity [17, 20, 24]. For instance, local physicochemical properties have greater effects on both rare and abundant bacterial β-diversity compared to geospatial factors [20]. However, most studies investigate the biogeography of rare and abundant bacterial communities in agricultural soils [17, 22, 24, 25], and little is known about rare and abundant bacterial and fungal taxa in natural wetlands.
Environmental filtering is an important determinant in shaping species distribution patterns and affecting abundance [26–28]. The relative abundance of a rare or abundant taxon is the result of a tradeoff between its growth and death rates [29]. Rare and abundant microbial taxa show diverse responses to environmental change [22, 25]. Environmental thresholds of arbuscular mycorrhizal fungi in European grassland are estimated using the accumulated values of change points of all the species in a given microbial community [30]. Procurable environmental thresholds rarely integrate the abundance, occurrence, and directionality of microbial responses at the species level, and little research is based on standardized phylogenetic and molecular evolutionary analysis of natural sites on a large spatial scale [17, 31]. Additionally, the responses of microbes to environmental change exhibit phylogenetic conservatism, and in this case microbes are not distributed randomly across the tree of life [32, 33]. For example, ectomycorrhizal fungal of Craterellus show strong conservatism of positive response to nitrogen deposition, while Cortinarius, Tricholoma, Piloderma, and Suillus exhibit strong conservatism of consistently negative responses to nitrogen deposition [34]. Soil pH and salinity are regarded as crucial determinants in shaping terrestrial bacterial biogeographic patterns [28, 35, 36], and the response traits of pH and salinity preference are found to be relatively deeply conserved [32]. Therefore, understanding the phylogenetic patterns of microbial response traits provides predictions for microbial biogeography and their responses to environmental change, and for changes in biodiversity-driven ecosystem multifunctioning [6, 17, 37, 38]. However, phylogenetic distributions and response thresholds of both bacterial and fungal communities to ongoing environmental change, especially abundant and rare taxa, have not been evaluated in wetlands of high elevation geographic regions.
Ecological community assembly, regarded as a significant ecological issue, estimates the relative contributions of stochastic processes (i.e., dispersal limitation and homogenizing dispersal) and deterministic processes (i.e., variable selection and homogeneous selection) to microbial communities [13, 39–41]. Both stochastic and deterministic processes determine microbial communities and are considered to be obligatory in coupling microbial community structure with the ecosystem functions they supply [40, 42]. Abundant microbial taxa are limited by dispersion more than rare taxa in agricultural soils [17, 21] and in inland freshwater ecosystems across China [43]. By contrast, the dispersal of rare bacterial taxa is more limited than that of abundant bacterial taxa in three subtropical bays of China [44]. The balance between stochastic and deterministic processes is regulated by environmental factors [13, 45, 46]. For instance, the divergence in soil pH and salinity could change the relative contributions of different ecological assembly processes in shaping bacterial communities [8, 21, 36, 46]. Moreover, extreme pH even results in a deterministic community assembly of soil bacteria [46]. However, whether similar environmental variables mediating the dominance of stochasticity and determinism in community assembly of rare and abundant microbes in wetlands remains unclear.
The 33 wetlands in the Qinghai-Tibetan Plateau, with altitudes ranging from 2547 to 4745 m, were chosen as our study areas. The mean annual temperature and mean annual precipitation of these wetlands are − 4.49–17.62 °C and 89–1038 mm, respectively, and detailed terrain properties are described (Additional file 1: Table S1). These wetlands have been largely protected from human activities. However, some factors including climate change might engender some unknown impacts on these wetlands. This situation caught our interest to predict and evaluate the responses of wetland ecosystems to environmental change, and in order to understand protection of wetlands by mitigating the impact of climate change in the future. In the present study, we aimed to (i) assess the potential environmental thresholds and phylogenetic distributions of rare and abundant bacteria and fungi across diverse environmental gradients in wetlands across Qinghai-Tibetan Plateau, and (ii) reveal the major environmental variables affecting the assembly of rare and abundant microbial sub-communities. In view of the low competition potential and growth rate of rare taxa [47, 48], we hypothesized that rare microbial taxa would present relatively narrow environmental thresholds and relatively weak phylogenetic signals for traits compared with abundant microbial taxa. In addition, the ecological assembly processes dominating rare and abundant microbial sub-communities would be affected by different environmental variables. To achieve our goals and validate our hypothesis, we employed amplicon sequencing datasets of soil bacteria and fungi along with 14 environmental factors.