BackgroundThe relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of spatial scale on the relative role of stochasticity and determinism in agricultural monocultures consisting only of wheat, thereby minimizing the influence of differences in plant species cover and in cultivation/disturbance regime, extending across a wide range of soils and climates of the North China Plain (NCP). We sampled 243 sites across 1092 km and sequenced the 16S rRNA bacterial gene using MiSeq. We hypothesized that determinism would play a relatively stronger role at the broadest scales, due to the strong influence of climate and soil differences in selecting many distinct OTUs of bacteria adapted to the different environments. In order to test the more general applicability of the hypothesis, we also compared with a natural ecosystem on the Tibetan Plateau.ResultsOur results revealed that the relative importance of stochasticity vs. determinism did vary with spatial scale, in the direction predicted. On the North China Plain, stochasticity played a dominant role from 150 to 900 km (separation between pairs of sites) and determinism dominated at more than 900 km (broad scale). On the Tibetan Plateau, determinism played a dominant role from 130 to 1200 km and stochasticity dominated at less than 130 km. Among the identifiable deterministic factors, soil pH showed the strongest influence on soil bacterial community structure and diversity across the North China Plain. Together, 23.9% of variation in soil microbial community composition could be explained, with environmental factors accounting for 19.7% and spatial parameters 4.1%.ConclusionsOur findings revealed that (1) stochastic processes are relatively more important on the North China Plain, while deterministic processes are more important on the Tibetan Plateau; (2) soil pH was the major factor in shaping soil bacterial community structure of the North China Plain; and (3) most variation in soil microbial community composition could not be explained with existing environmental and spatial factors. Further studies are needed to dissect the influence of stochastic factors (e.g., mutations or extinctions) on soil microbial community distribution, which might make it easier to predictably manipulate the microbial community to produce better yield and soil sustainability outcomes.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0409-4) contains supplementary material, which is available to authorized users.

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c pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity. Bacterioplankton are a crucial component of aquatic ecosystems, and they play an important role in the ecological processes of freshwater lakes (1, 2). Understanding the mechanisms governing bacterioplankton community assembly (e.g., community composition, diversity, and phylogenetic structure) in natural freshwater lakes is a longstanding challenge in microbial community ecology. There is increasing evidence that the community structure of freshwater lake bacterioplankton is influenced by niche-related (deterministic) and neutral (stochastic) processes (2-4). Niche-related processes (5) include selection imposed by the abiotic environment (environmental filtering) and species interactions (competition, facilitation, mutualism, and predation), whereas neutral effects (6) include stochastic processes, such as unpredictable disturbances, probabilistic dispersal, and random birth/death events (7,8). Neutral processes likely result in random fluctuations in community composition along a given environmental gradient (9). The observation that both niche and neutral processes are important in shaping bacterioplankton community assembly raises the question of what affects the relative contributions and interplay between stochastic and deterministic processes in structuring lacustrine bacterioplankton assembly.Multiple environmental factors regulate the distribution of bacterioplankton communities in freshwater lakes (10-16). pH is proposed to be an important environmental factor influencing both overall bacterioplankton community composition (BCC) (2, ...