Journal: Current Biology

Article Title: A light-sensing system in the common ancestor of the fungi

doi: 10.1016/j.cub.2022.05.034

Figure Lengend Snippet: Evolution of the CyclOp system across the ancestral branches of the fungi (A) Schematic representation of a maximum likelihood phylogenetic tree of the CyclOp protein gene fusion. The tree was reconstructed using 84 sequences with 3,095 amino acid positions and was inferred with IQ-TREE under the LG + F + I + G4 model with 1,000 ultrafast bootstrap replicates to assess statistical support. Dashed-lined arrows indicate the position of a given clade in the trimmed analysis (with only the type I rhodopsin domain; see ). Bootstrap support values are indicated before the nodes. Numbers within brackets on the fungal clade labels indicate the number of sequences sampled. The overall protein domain structure of the CyclOp was identified using homology-based 3D structure modeling and is represented by rhodopsin (pink) and GC domains of the fusion (blue) ( Figures S1–S3 ). (B) Depiction of candidate CyclOp-organelle systems within the zoospore ultrastructure based on the review of a wide range of microscopy data. Next to the tree, we show schematic depictions of the presence of lipid-filled organelles (red circles) in the zoospores of fungi that possess the CyclOp gene. These depictions are based on a comprehensive review of published microscopy data ( Table S2 ). Dashed red lines represent the presence of a rumposome ( Table S2 ). (C) Cladograms for the variant root hypotheses of the fungal tree and the evolution of the CyclOp system. Chytridiomycota-first (left) and Blastocladiomycota + Sanchytrids-first (right) hypotheses. Pink-blue highlight on the branches indicates the presence of the CyclOp system across the tree. See also Figures S1–S3 and Table S2 .

Article Snippet: Two Blastocladiomycota cultures ( Be ATCC 22665 and Allomyces macrogynus Australia_3) and two Chytridiomycota cultures ( Chytriomyces confervae CBS 675.73 and Rhizoclosmatium globosum JEL800) were imaged.

Techniques: Microscopy, Variant Assay

Journal: Scientific Reports

Article Title: Stimulation of carbon nanomaterials on syntrophic oxidation of butyrate in sediment enrichments and a defined coculture

doi: 10.1038/s41598-018-30745-7

Figure Lengend Snippet: Effects of the addition of CNTs and rGO on the CH 4 production ( a ) and acetate production ( b ), butyrate degradation ( c ) and butyrate degradation rate ( d ) in the defined coculture of S . wolfei with M . mariplaudis . Results are the mean and standard deviation for triplicate incubations. Different letters indicate significant differences (Duncan’s test, P < 0.05).

Article Snippet: Syntrophomonas wolfei (DSM102351) and Methanococcus maripaludis (DSM14266) were purchased from German culture collection DSMZ (Braunschweig, Germany).

Techniques: Standard Deviation

Journal: Scientific Reports

Article Title: Stimulation of carbon nanomaterials on syntrophic oxidation of butyrate in sediment enrichments and a defined coculture

doi: 10.1038/s41598-018-30745-7

Figure Lengend Snippet: FISH ( a , b ) and SEM ( c , d ) images of the defined coculture of S . wolfei with M . mariplaudis in the presence of CNTs ( a , c ) and rGO ( b , d ). The concentrations of CNTs and rGO are 2 g L −1 and 0.1 g L −1 , respectively. For the FISH images, red color indicates bacterial cell and green color indicates archaeal cell.

Article Snippet: Syntrophomonas wolfei (DSM102351) and Methanococcus maripaludis (DSM14266) were purchased from German culture collection DSMZ (Braunschweig, Germany).

Techniques:

Journal: ISME Communications

Article Title: Particle-associated bacteria differentially influence the aggregation of the marine diatom Minutocellus polymorphus

doi: 10.1038/s43705-022-00146-z

Figure Lengend Snippet: Outline of the experiments performed in this study.

Article Snippet: Stock cultures of Vibrio thalassae (DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), Pseudoalteromonas carrageenovora (DSM6820, DSMZ), and Marinobacter adhaerens HP15 [ ] were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.

Techniques: Bacteria, Sedimentation

Journal: ISME Communications

Article Title: Particle-associated bacteria differentially influence the aggregation of the marine diatom Minutocellus polymorphus

doi: 10.1038/s43705-022-00146-z

Figure Lengend Snippet: Diatom cell concentration in growth experiment 2 with axenic Minutocellus polymorphus ( a ) and diatom and bacteria cell concentration in co-culture treatments with M. polymorphus and the addition of Pseudoalteromonas carrageenovora ( b ) or Vibrio thalassae ( c ), as well as total volume of suspended micro-aggregates ( d ) and transparent exopolymeric particle (TEP) concentrations ( e ) in all treatments. Symbols and error bars denote the means and standard deviations of triplicate treatments.

Article Snippet: Stock cultures of Vibrio thalassae (DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), Pseudoalteromonas carrageenovora (DSM6820, DSMZ), and Marinobacter adhaerens HP15 [ ] were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.

Techniques: Concentration Assay, Bacteria, Co-Culture Assay

Journal: ISME Communications

Article Title: Particle-associated bacteria differentially influence the aggregation of the marine diatom Minutocellus polymorphus

doi: 10.1038/s43705-022-00146-z

Figure Lengend Snippet: Epifluorescence microscopy images of axenic Minutocellus polymorphus ( a , b ) and co-cultures of M. polymorphus and Marinobacter adhaerens HP15 ( c , d ), Vibrio thalassae ( e , f ), and Pseudoalteromonas carrageenovora ( g , h ) under blue ( a , c , e , g ) and UV ( b , d , f , h ) excitation wavelengths. Images were taken during the exponential phases of growth. Red: chlorophyll- a autofluorescence, blue: DAPI-bound nucleic acids. White arrows: diatom-attached bacteria; blue arrows: bacterial aggregates. Amorphous material is considered TEP.

Article Snippet: Stock cultures of Vibrio thalassae (DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), Pseudoalteromonas carrageenovora (DSM6820, DSMZ), and Marinobacter adhaerens HP15 [ ] were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.

Techniques: Epifluorescence Microscopy, Bacteria

Journal: ISME Communications

Article Title: Particle-associated bacteria differentially influence the aggregation of the marine diatom Minutocellus polymorphus

doi: 10.1038/s43705-022-00146-z

Figure Lengend Snippet: Transparent exopolymeric particle (TEP) production, TEP concentration normalized to diatom cell abundance, and volume of suspended micro-aggregates during the exponential, stationary, and decline growth phases of Minutocellus polymorphus in axenic cultures and in co-cultures with Marinobacter adhaerens HP15, Vibrio thalassae , or Pseudoalteromonas carrageenovora .

Article Snippet: Stock cultures of Vibrio thalassae (DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), Pseudoalteromonas carrageenovora (DSM6820, DSMZ), and Marinobacter adhaerens HP15 [ ] were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.

Techniques: Concentration Assay

Journal: ISME Communications

Article Title: Particle-associated bacteria differentially influence the aggregation of the marine diatom Minutocellus polymorphus

doi: 10.1038/s43705-022-00146-z

Figure Lengend Snippet: Abundance of aggregates formed in roller tank experiments inoculated to lower total cell abundances (10 3 cells mL −1 ).

Article Snippet: Stock cultures of Vibrio thalassae (DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), Pseudoalteromonas carrageenovora (DSM6820, DSMZ), and Marinobacter adhaerens HP15 [ ] were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.

Techniques: Sedimentation

Journal: ISME Communications

Article Title: Particle-associated bacteria differentially influence the aggregation of the marine diatom Minutocellus polymorphus

doi: 10.1038/s43705-022-00146-z

Figure Lengend Snippet: Number of visible sinking aggregates formed in roller tanks with axenic Minutocellus polymorphus , and M. polymorphus with the addition of 2.5 µm silica beads , Marinobacter adhaerens HP15, Vibrio thalassae , or Pseudoalteromonas carrageenovora in the low cell abundance experiments ( a ca. 10 cells mL −1 ; Table ) and of axenic M. polymorphus and M. polymorphus with the addition of M. adhaerens in the high cell abundance experiments ( b 10 5 cells mL −1 ; Table ). Lowercase letters indicate significant differences between treatments.

Article Snippet: Stock cultures of Vibrio thalassae (DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH), Pseudoalteromonas carrageenovora (DSM6820, DSMZ), and Marinobacter adhaerens HP15 [ ] were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.

Techniques: