Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

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Sedimentological, geochemical and palynological data from Wulungu Lake in northern Xinjiang, China, are used to reconstruct environmental and climate changes since 9550 cal yr BP. High abundance of Sparganium and Poaceae, low Md (median diameter) and δ13Corganic values indicate aridity between 9550 and 6730 cal yr BP. High Md and δ13Corganic values, and the prevalence of desert-steppe and steppe vegetation between 4200 and 560 cal yr BP, indicate that effective moisture increased after 6730 cal yr BP, peaking at 4200 and 560 cal yr BP. Low Md values, a negative excursion of δ13Corg, and the transition from steppe to desert vegetation since 560 cal yr BP reflect a decrease in effective moisture during the latest Holocene. Late Holocene human activities were indicated by sharp increase in the abundance of Pediastrum then. Variations in carbonate contents indicate that temperature was generally high between 9550 and 7740 cal yr BP, low between 7740 and 6730 cal yr BP, intermediate between 6730 and 560 cal yr BP, and low during the last 560 yr. Regional comparison indicates that the Asian monsoon did not extend to Wulungu Lake and westerlies were the main factor in determining the moisture availability during the Holocene.