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Freshwater and estuarine ecosystemsare responsible forthe transport and transformation of nutrients and organic matters from the continent to the adjacent coastal zone,and therefore play critical roles in global biogeochemical cycles.They are under increasing stress from human activities,especially in China,yet there are little information available about the responses of prokaryotic communities that mediate biogeochemical processes.In the present study,we investigatedprokaryotic communities in the human-perturbedJiulongRiver Watershed(JRW),China,from river to estuarine area,by using 16S rRNA amplicon Miseq sequencing.Our results indicated that the compositions of planktonic prokaryotic communities from river and estuary were mainly shaped by nutrients and emergingchemical pollutants(PPCPs),and salinity,respectively,although they also exhibited pronouncedspatio(within or between tributaries)-temporal(hydrological seasons)variation.The distribution of functional microbial group,such as ammonia-oxidizing archaea,were influenced by anthropogenic disturbances.In river waters,several fecal indicator taxa either from Bacteria or from Archaea were frequently identified,suggesting that the watershed was under the risk of fecal pollution.Source tracker analysis demonstrated that riverine prokaryotic community was the major source of estuarine counterpart in low-salinity zone,and the contributions of different tributaries could be evaluated.However,phylogenetic null model analysis indicated that the deterministic(species-sorting)rather than stochastic(dispersal)processes was the major driver controlling the assembly of river and estuarine prokaryotic communities.Taken together,our study shed light onthe understanding of the biogeographic patterns andits ecological processes of river and estuarine prokaryoticcommunities.