Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, China
- College of Earth Science, University of Chinese Academy of Sciences, China
Figures
Figure 1 with 5 supplements
Isolation, morphology, and phylogenetic analysis of Poriferisphaera heterotrophicis ZRK32.
(A) Diagram showing the strategy used to isolate the Planctomycetes bacteria. (B, C) Transmission electron microscope (TEM) observation of strain ZRK32. (D) TEM observation of ultrathin sections of …
Figure 1—figure supplement 1
Transmission electron microscope (TEM) observation of the morphology of cells from P. heterotrophicis ZRK32 (A, B).
Figure 1—figure supplement 2
Maximum likelihood phylogenetic tree of genome sequences from the P. heterotrophicis ZRK32 and other Planctomycetes bacteria constructed from the concatenated alignment of 37 single-copy genes; A. derwentensis LA107 was used as the outgroup.
The tree was inferred and reconstructed using the maximum likelihood criterion, with bootstrap values (%)>80; these are indicated at the base of each node with a gray dot (expressed as a percentage …
Figure 1—figure supplement 3
Circular diagram of the P. heterotrophicis ZRK32 genome.
Rings indicate, from outside to the center: a genome-wide marker with a scale of 0.3 MB; coding genes; gene function annotation results; ncRNA; GC content; GC skew.
Figure 1—figure supplement 4
Physiological characterizations of P. heterotrophicis ZRK32.
Growth curves of ZRK32 strains cultivated in different conditions. Temperature (A), pH (B), and NaCl concentration (C) ranges enabling growth were analyzed of ZRK32 strains cultivated in rich medium …
Figure 1—figure supplement 5
Ultrathin transmission electron microscope (TEM) sections showing some eukaryote-like structures observed in cells from P. heterotrophicis ZRK32.
Golgi-like organelles (indicated with black arrows in panels 1 and 2); endoplasmic reticula-like organelles (indicated with blue arrows in panels 3 and 4); actin filament-like organelles (indicated …
Figure 2 with 3 supplements
Growth assay and transcriptomic analysis of P. heterotrophicis ZRK32 strains cultivated in basal medium and rich medium.
(A) Growth curves of ZRK32 strains cultivated in basal medium and rich medium. Data shown as mean; error bars = SD (Standard Deviation). (B) Diagram of the tricarboxylic acid (TCA) cycle. The gene …
Figure 2—figure supplement 1
Transcriptomics analysis of the genes associated with the Embden-Meyerhof-Parnas (EMP) glycolysis pathway of P. heterotrophicis ZRK32 strains cultivated in the rich medium alone and cultivated in rich medium supplemented with either 20 mM NO3-, 20 mM NH4+, or 20 mM NO2-.
(A) Diagram of the EMP glycolysis pathway. The gene numbers shown in this schematic are the same as those shown in panels B and C. (B) Transcriptomics-based heat map showing differentially expressed …
Figure 2—figure supplement 2
Real-time quantitative reverse transcription PCR (qRT-PCR) detection of the relative expression levels of the genes associated with the tricarboxylic acid (TCA) cycle (A), NADH-quinone oxidoreductase (B), flagellar assembly (C), and Embden-Meyerhof-Parnas (EMP) glycolysis pathway (D) of P. heterotrophicis ZRK32 strains cultivated in rich medium (Rich) compared with strains cultivated in basal medium (Basal).
JD969_02150, succinate dehydrogenase; JD969_01715, fumarate hydratase; JD969_05505, malate dehydrogenase; JD969_03155, isocitrate dehydrogenase; JD969_11015, 2-oxoglutarate ferredoxin oxidoreductase;…
Figure 2—figure supplement 3
Growth curves of ZRK32 strains cultivated in the basal medium, basal medium supplemented with 5 g/L N-acetyl glucosamine, rich medium, and rich medium supplemented with 5 g/L N-acetyl glucosamine.
Data shown as mean; error bars = SD (Standard Deviation).
Figure 3
The mode of cell division utilized by P. heterotrophicis ZRK32.
(A) Ultrathin transmission electron microscope (TEM) sections showing the process of polar budding division (panels 1–8) in strain ZRK32. Images representing the different phases of cell division …
Figure 4 with 2 supplements
Nitrogen metabolism assays of P. heterotrophicis ZRK32.
(A) Growth curves of ZRK32 strains cultivated in the rich medium alone and cultivated in rich medium supplemented with either 20 mM NO3-, 20 mM NH4+, or 20 mM NO2-. Data shown as mean; error bars = …
Figure 4—figure supplement 1
Real-time quantitative reverse transcription PCR (qRT-PCR) detection of the relative expression levels of the genes associated with nitrogen metabolism (A), tricarboxylic acid (TCA) cycle (B), NADH-quinone oxidoreductase (C), flagellar assembly (D), and Embden–Meyerhof–Parnas (EMP) glycolysis pathway (E) of ZRK32 strains cultivated in the rich medium supplemented with different inorganic nitrogen sources (20 mM NO3-, 20 mM NH4+, or 20 mM NO2-) compared with strains cultivated in the rich medium alone.
‘Rich’ indicates rich medium. ‘NO3-, NH4+, and NO2-’ indicate rich medium supplemented with 20 mM NO3-, 20 mM NH4+, and 20 mM NO2-, respectively. JD969_05490, nitrate reductase; JD969_10725, nitrate …
Figure 4—figure supplement 2
Muti-omics-based central metabolism model of P. heterotrophicis ZRK32.
Based on the combination of genomic, transcriptomic, and physiological characteristics, we proposed a model toward the central metabolic traits of strain ZRK32. In this model, central metabolisms …
Figure 5 with 4 supplements
Observation and functional assay of the chronic bacteriophage induced by NO3- or NH4+ from P. heterotrophicis ZRK32.
(A) Transmission electron microscope (TEM) observation of phages extracted from the cell suspensions of ZRK32 strains that cultured in either the rich medium alone, or rich medium supplemented with …
Figure 5—figure supplement 1
Phylogenetic analysis of Phage-ZRK32, some related phages, and bacterial hosts, based on the aligned amino acid sequences of amidoligase.
The NCBI accession number for each amino acid sequence is indicated after each corresponding strain’s name. The amino acid sequences of amidoligase from nine Escherichia phages were used as the …
Figure 5—figure supplement 2
Phylogenetic analysis of Phage-ZRK32, some related phages, and bacterial hosts, based on the aligned amino acid sequences of glutamine amidotransferase.
The NCBI accession number for each amino acid sequence is indicated after each corresponding strain’s name. The amino acid sequences of glutamine amidotransferase from six Vibrio phages were used as …
Figure 5—figure supplement 3
Phylogenetic analysis of Phage-ZRK32, some related phages, and bacterial hosts, based on the aligned amino acid sequences of gamma-glutamylcyclotransferase.
The NCBI accession number for each amino acid sequence is indicated after each corresponding strain’s name. The amino acid sequences of gamma-glutamylcyclotransferase from six Lentisphaerae strains …
Figure 5—figure supplement 4
Phylogenetic analysis of Phage-ZRK32, some related phages, and bacterial hosts, based on the aligned amino acid sequences of glutathione synthase.
The NCBI accession number for each amino acid sequence is indicated after each corresponding strain’s name. The amino acid sequences of glutathione synthase from six Escherichia phages were used as …
Author response image 1
Figure 2.
Growth assay and transcriptomic analysis of P. heterotrophicis ZRK32 strains cultivated in basal medium and rich medium.
Additional files
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Supplementary file 1
Phenotypic and genotypic features of strain ZRK32 and the most closely related type strain P. corsica KS4T.
- https://cdn.elifesciences.org/articles/89874/elife-89874-supp1-v1.xlsx
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Supplementary file 2
The sugar utilization of strain ZRK32. +, Positive result or growth; −, negative result or no growth.
- https://cdn.elifesciences.org/articles/89874/elife-89874-supp2-v1.xlsx
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Supplementary file 3
Marker genes used in the phylogenetic analysis.
The DNGNGWU marker genes in phylosift refer to a suite of single-copy, protein-coding marker genes. All 37 DNGNGWU marker genes were concatenated to construct maximum likelihood phylogenetic tree.
- https://cdn.elifesciences.org/articles/89874/elife-89874-supp3-v1.xlsx
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Supplementary file 4
Primers used for real-time quantitative reverse transcription PCR (qRT-PCR).
- https://cdn.elifesciences.org/articles/89874/elife-89874-supp4-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/89874/elife-89874-mdarchecklist1-v1.docx
