Mixing of nutrient rich and often polluted freshwater with coastal seawater at estuaries forms a unique and dynamic environment, which not only supports high primary production, but also the high metabolism of diverse microorganisms. Microbes in the estuary ecosystems are the most important drivers of biogeochemical cycling, since they are responsible for the re-mineralization of river discharged organic matter and the transfer of discharged nutrients to higher trophic levels. With the increasing human activities, massive anthropogenic pollutants are inputted into the river and deposited in the estuary. Some of the pollutants, including industrial and domestic waste, are very difficult to be degraded and will have long-term effects to the estuary ecosystem. However, there is limited gen...[ Read more ]

Mixing of nutrient rich and often polluted freshwater with coastal seawater at estuaries forms a unique and dynamic environment, which not only supports high primary production, but also the high metabolism of diverse microorganisms. Microbes in the estuary ecosystems are the most important drivers of biogeochemical cycling, since they are responsible for the re-mineralization of river discharged organic matter and the transfer of discharged nutrients to higher trophic levels. With the increasing human activities, massive anthropogenic pollutants are inputted into the river and deposited in the estuary. Some of the pollutants, including industrial and domestic waste, are very difficult to be degraded and will have long-term effects to the estuary ecosystem. However, there is limited genomic information about the microorganisms inhabited in heavily polluted estuaries.

We applied metagenomic approach and isotopic measurement to investigate the inputted pollutants’ influence on the genetic changes of the estuary inhabited microorganisms. The microbial community structure was investigated through the extracted and annotated SSU rRNA genes. Besides, the distribution of microbial metabolic categories was also investigated through the annotation of the predicted functional genes. Furthermore, the draft genomes of bacteria and ammonia oxidation archaea were reconstructed from the metagenomic data, and the unique and horizontally transferred genes in them were further identified and validated. Through these approaches, we found that the sulfate reduction metabolism was preferred by the estuary inhabited microorganisms in order to resist the fluctuated oxygen concentration. The horizontally transferred antibiotic and metal resistance genes reflect the adaptation strategy used by the microorganisms in the severely polluted environments.

We also found that the ammonia-oxidizing archaea were very abundant across the bottom layer of the estuary. Nearly all ammonia-oxidizing genes in the bottom layer were contributed by archaea, and the reconstructed ammonia-oxidizing archaeal genomes were very close to the genome of an isolated pelagic archaea, SPOT01. However, the encoding genes between these two genomes are very different. This could be used to further explain the genomic difference between pelagic and coastal archaeal genomes.

Overall, these studies provide new insights into the composition, diversity and function of microorganisms inhibited in heavily polluted estuaries and extend our knowledge about the genomic change and evolution of microorganisms to such dynamic and harsh environment.