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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0612

PubMed

32071270, mBio. 2020 Feb 18;11(1):e03261-19. doi: 10.1128/mBio.03261-19.

Characterization method

liquid chromatography and mass spectrometry

Genomic accession number

RHLF01000001.1

Nucelotide position range

1252462-1269410

Substrate

alpha-glucan

Loci

ED555_05795-ED555_05845

Species

Muricauda sp. isolate Bin2/192149

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ED555_05795 RNC92589.1 0 - 1590 (+) RHLF01000001.1:1252462-1254052 -
- ED555_05800 RNC92590.1 1659 - 3291 (-) RHLF01000001.1:1254121-1255753 -
- ED555_05805 RNC92591.1 3311 - 6440 (-) RHLF01000001.1:1255773-1258902 -
- ED555_05810 RNC92592.1 6807 - 7830 (+) RHLF01000001.1:1259269-1260292 -
- ED555_05815 RNC92593.1 7863 - 10167 (+) RHLF01000001.1:1260325-1262629 -
- ED555_05820 RNC92594.1 10163 - 12035 (+) RHLF01000001.1:1262625-1264497 -
- ED555_05825 RNC92595.1 12081 - 12504 (-) RHLF01000001.1:1264543-1264966 -
- ED555_05830 RNC92596.1 12690 - 13443 (+) RHLF01000001.1:1265152-1265905 -
- ED555_05835 RNC92597.1 13442 - 14714 (+) RHLF01000001.1:1265904-1267176 -
- ED555_05840 RNC92598.1 14710 - 15442 (-) RHLF01000001.1:1267172-1267904 -
glpK ED555_05845 RNC92599.1 15452 - 16949 (-) RHLF01000001.1:1267914-1269411 2.7.1.30

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1590 (+) TC: gnl|TC-DB|P31448|2.A.21.3.21 Yes
- 1660 - 3291 (-) TC: gnl|TC-DB|Q8A1G2|8.A.46.1.1 Yes
- 3312 - 6440 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 6808 - 7830 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 7864 - 10167 (+) CAZyme: GH65 Yes
- 10164 - 12035 (+) CAZyme: GH13_38 Yes
- 12082 - 12504 (-) other Yes
- 12691 - 13443 (+) other Yes
- 13443 - 14714 (+) STP: STP|Pyr_redox_2 Yes
- 14711 - 15442 (-) TC: gnl|TC-DB|D0JBC9|1.A.8.2.9 Yes
- 15453 - 16949 (-) CDS No

PUL ID

PUL0612

PubMed

32071270, mBio. 2020 Feb 18;11(1):e03261-19. doi: 10.1128/mBio.03261-19.

Title

Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture.

Author

Zheng Q, Wang Y, Lu J, Lin W, Chen F, Jiao N

Abstract

Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of cocultivation. The associated heterotrophic bacterial assembly mostly constituted five classes, including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes, including Synechococcus and the five dominant heterotrophic bacteria, were reconstructed. The only primary producer of the coculture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TonB-dependent transporters (TBDTs), glycoside hydrolase, and peptidase proteins. Polysaccharide utilization loci present in the flavobacterial genomes influence their lifestyle preferences and close associations with phytoplankton. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low-molecular-weight dissolved organic carbon (DOC) through ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), and tripartite tricarboxylate transporter (TTT) transport systems. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking might also contribute to the maintenance of the Synechococcus-heterotroph coculture system and the interactions shaping the system.IMPORTANCE The high complexity of in situ ecosystems renders it difficult to study marine microbial photoautotroph-heterotroph interactions. Two-member coculture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. In the present study, combined metagenomic and metaproteomic data supplied the metabolic potentials and activities of uncultured dominant bacterial populations in the coculture system. The results of this study shed light on the nature of interactions between photoautotrophs and heterotrophs, improving our understanding of the complexity of in situ environments.