Data from: Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean

Pollution in human-made fishing ports caused by petroleum from boats, dead
fish, toxic chemicals, and effluent poses a challenge to the organisms in
seawater. To decipher the impact of pollution on the microbiome, we
collected surface water from a fishing port and a nearby offshore island
in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S
rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we
discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae
emerged as the dominant species in the fishing port, where we found many
genes harboring the functions of antibiotic resistance (ansamycin,
nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium,
iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1),
carbohydrate metabolism (biofilm formation and remodeling of bacterial
cell walls), nitrogen metabolism (denitrification, N2 fixation, and
ammonium assimilation), and ABC transporters (phosphate,
lipopolysaccharide, and branched-chain amino acids). The dominant bacteria
at the nearby offshore island (Alteromonadaceae, Cryomorphaceae,
Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly
similar to those in the South China Sea and the East China Sea.
Furthermore, we inferred that the microbial community network of the
cooccurrence of dominant bacteria on the offshore island was connected to
dominant bacteria in the fishing port by mutual exclusion. By examining
the assembled microbial genomes collected from the coastal seawater of the
fishing port, we revealed four genomic islands containing large
gene-containing sequences, including phage integrase, DNA invertase,
restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this
study, we provided clues for the possibility of genomic islands as the
units of horizontal transfer and as the tools of microbes for facilitating
adaptation in a human-made port environment.