**5. Conclusions**

In polluted freshwater environments like wastewater ditches, PNSB can form visible dense populations over PSB and GSB under specific conditions. These conditions are represented by light-exposed, sulfide-deficient water bodies with high-strength organic matter and in a limited range of ORP (−93 to 23 mV). On the other hand, coastal environments provide more favorable conditions for the massive growth of PSB or GSB because of the high availability of sulfide and lower concentrations of organic matter. In coastal colored blooms, nevertheless, PNSB with *Rhodovulum* members predominating constitute a significant proportion of the phototrophic bacterial population. These results expand our knowledge of the phototrophic community structure of marine and wastewater massive blooms and the ecological significance of PNSB in these environments. Also, the high-quality genomic information on *Rhodovulum* sp. strain MB263 and *Rdv. sulfidophilum* strain DSM 1374<sup>T</sup> obtained in this study enhances our understanding of how PNSB respond to various environmental factors in the ecosystem.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2076-2607/8/2/150/s1, Table S1: Appearance of colored blooms and microbial mats studied, Figure S2: In vivo absorption spectra of the biomass collected from pink mudflat Y1 (A), yellow-green tide pool J3 (B), and red ditch mat D3 (C), Figure S3: HPLC elution profiles of isoprenoid quinones extracted from pink mudflat Y1 (A), yellow-green tide pool J3 (B), and red ditch mat D3 (C), Figure S4: Relationship between *pufM* gene copy numbers and viable counts of PNSB + PSB in colored blooms and mats investigated, Figure S5: Maximum-likelihood phylogenetic tree of the *pufM* gene clones detected and their closest relatives, Figure S6: 16S rRNA gene sequence-based phylogenetic composition of the PSNB isolates from red mudflat J1, red tide pool J2, yellow-green tide pool J3, and red ditch mat D1, Figure S7: Harr plots showing genomic similarities between *Rhodovulum sulfidophilum* strains DSM 1374<sup>T</sup> and DSM 2351 (A) and between *Rhodovulum sulfidophilum* DSM 1374<sup>T</sup> and *Rhodovulum* sp. MB263 (B), Table S1: PCR primers used for specific gene amplification in this study, Table S2: Similarity levels of 16S rRNA gene and whole genome sequences between *Rhodovulum* sp. MB263 and authentic strains of established *Rhodovulum* species, Table S3: List of *Rhodovulum* species and strains and the accession numbers for genome sequences used for reconstruction of the phylogenomic tree based on 92 core protein-coding genes.

**Author Contributions:** Conceptualization, project administration, methodology, investigation, and writing—original draft preparation, A.H.; investigation, N.N. and C.Y.; investigation, data curation, and manuscript writing, Y.H.; writing—review, editing, and supervision, S.U., Y.K., and T.E. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research received no external funding.

**Acknowledgments:** We are grateful to Yoko Okubo, Toyohashi University of Technology, for her early contributions to this study. We also thank Takashi Kurogi for his technical assistance in qPCR and sequencing experiments.

**Conflicts of Interest:** The authors declare no conflict of interest.
