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Bacterial community has been significantly enrolled in the biogeochemical cycling of the coastal subsurface ecosystem. The bacterial community variations with salinity have been extensively investigated in the surface environment, such as lake, soil, and estuary, but not in the subsurface environment. Here we explore the responses of bacterial populations to the salinity and other environmental factors (EFs) by considering both the abundant and rare sub-community in a coastal Holocene groundwater system. Our study results indicate that the bacterial diversity was independent of the salinity in both the abundance and rare sub-community. Besides diversity, no flourishing of abundant bacteria relative abundance is observed with increasing or decreasing salinity. Yet the rare taxa exhibit a bio-growth with salinity, which has a significant correlation (p < 0.001) with sulfate concentration. The responses of the abundant sub-community taxa to nutrients, temperature, pH, and dissolved oxygen are insensitive. However, the correlation between δ18O, δD and the entire community diversity is significant, which demonstrates the bacterial community is affected by the groundwater origin. Besides, not all the species in one class or order are necessarily shaped by the same factor. To quantify the impact of EFs on the community properties, analyses in different taxonomic levels is suggested. These findings imply that the spatial organization of microbial communities is complicated and influenced by multiple factors on a regional scale. The investigated results are useful for understanding biogeochemical processes in the coastal groundwater. Unlabelled Image • The entire bacterial abundance and diversity are independent of the salinity in the saltwater aquifer. • Bacterial community composition is affected by the groundwater origin. • No flourishing of abundant bacteria relative abundance was observed with salinity variations. • The rare sub-community diversity has a bio-growth with salinity. [ABSTRACT FROM AUTHOR]

Bacterioplanktonic communities, consisting of a few abundant taxa (AT) and many rare taxa (RT), are essential component of riverine ecosystems. Nonetheless, the biogeographic patterns of bacterioplankton and roles of AT and RT in community structuring and functional composition remain uncertain in large rivers. Here, we employ the Yangtze River, which is the third-longest river in the world, as model system. By using high-throughput sequencing and bioinformatics tool of Tax4Fun, the geographical patterns of bacterioplanktonic taxonomic and predicted functional communities are investigated, and the relative importance of abundant and rare subcommunities in community structuring are explored. Results showed a clear spatial variation that the bacterioplanktonic communities of upper, middle and lower reaches of the river are significantly different from each other. Besides, the Three Gorges Dam exhibited impact on the bacterioplankton of upper reach whose community is relatively closer to that of the Poyang Lake. Both the abundant and rare subcommunities showed spatial variation along the river, which is similar to the total bacterioplanktonic community. The rare subcommunity comprised a majority of community diversity with 23.6% of the total sequences and 94.2% of the total OTUs. The rare subcommunity contributes a major part (56.8%) versus abundant subcommunity (16.3%) of the spatial variation of the total community. In addition, the non-RT exhibits more interactions with RT than with themselves, and all of the 33 keystone species are belonged to RT. Hence, the RT is critical for community structuring and assembling. By contrast, no obvious spatial effect was observed for the predicted functional community. The predicted functions of abundant and rare subcommunities are consistent with that of total community, despite their contrasting community composition. In summary, the rare subcommunity show significantly impact on the community structure and assembling, and play an important role in predicted function as 'seed bank' in the Yangtze River. Unlabelled Image • Bacterioplankton exhibits clear spatial variations along the Yangtze River. • Rare subcommunity is critical for community structuring and assembling. • Predicted functions do not show biogeographic pattern. • Rare subcommunity is consistent with abundant subcommunity in predicted functions. [ABSTRACT FROM AUTHOR]

Bacteria are critical ecosystem drivers in both aquatic and terrestrial ecosystems. However, our understanding of the mechanisms generating and maintaining biodiversity on large spatial scales remains limited, especially mechanisms involving rare taxa in soil ecosystems. In the present study we took paddy soils in China as model ecosystems and studied the ecological diversity and assembly mechanisms of both the rare and abundant bacterial subcommunities. We collected 339 paddy soil samples from 113 sites across 19 Chinese provinces that span distances of up to 3869 km. The bacterial community was characterized by high-throughput sequencing of the 16S rRNA gene. The α-diversity of rare and abundant subcommunities showed opposite quadratic correlations with the key environmental factor soil pH. Rare taxa exhibited a stronger distance-decay relationship than the abundant subcommunity. Moreover, deterministic selection processes dominated in the assembly of the abundant subcommunity while stochastic processes dominated in that of the rare subcommunity based on both variation partitioning analysis and the phylogenetic null model. Soil pH was also the main deterministic factor driving the geographical distributions of both the rare and abundant subcommunity. Besides, mean annul temperature and soil texture were also found to be important factors affecting the biogeography and diversity patterns of abundant and rare subcommunities. These results indicate that the mechanisms generating and maintaining the diversity of the abundant and rare subcommunities were totally different in paddy soils, suggesting that these two subcommunities may respond differently to future environmental change. Unlabelled Image • α-Diversity of abundant and rare assemblages show opposite relationships with pH. • Rare taxa show higher turnover rates than abundant taxa in paddy soils. • Communities of rare bacterial taxa are driven mainly by stochastic processes. • The assembly mechanisms of the abundant and rare subcommunities were different. [ABSTRACT FROM AUTHOR]