Fig. 4

Genomic variation within the AL Ca. Chlorobium antarcticum population from different seasons. a Circos plot depicts read depth distribution of Ca. Chlorobium antarcticum in AL oxic-anoxic interface in summer (Dec), winter (Jul, Aug) and spring (Oct, Nov). The mean read depth of the AL_ref MAG in each merged metagenome (Additional file 1: Table S14) is shown at the beginning of each annulus (top). Outer to inner annuli and y-axis range: AL_ref MAG contigs A1–A27 ( ); Dec 2014 (, 0–10,000); Jul 2014 (, 0–800); Aug 2014 (, 0–800); Oct 2014 (, 0–100); Nov 2008 (, 0–20,000); Nov 2013 (, 0–3,000). The x-axis is shown on the outermost annulus: beginning of each contig, red tick; 10-kb length, grey tick; LCRs, labelled 1–7. Scaffolds (separated by large gaps) were represented by contigs (separated by small gaps): A1–4, A5–10, A11–12, A13–18, A19, A20, A21, A22–23, A24, A25, A26 and A27 (see MAG contigs ordering in the “Methods” section; Additional file 1: Table S3). b The relative coverages and gene composition of LCR1–7. The percentages indicate the proportion of the Ca. Chlorobium antarcticum population from each merged metagenome, including summer (red font) and winter (blue font) populations that contain the genes in the LCR. In LCR5, the arrangement of contigs A13–A17 was determined through sequence comparisons with other AL, EF and TB Ca. Chlorobium antarcticum MAGs (see MAG contigs ordering in the “Methods” section). Genes: acyl-ACP TE, acyl-acyl carrier protein thioesterase; atpA, ATP synthase subunit alpha; atpB, ATP synthase subunit a; atpC, ATP synthase subunit epsilon; atpD, ATP synthase subunit beta; atpE, ATP synthase subunit c; atpF, ATP synthase subunit b; atpG, ATP synthase subunit gamma; atpQ, ATP synthase N subunit Q; atpR, ATP synthase N subunit R; bchD, magnesium chelatase subunit D; bchH, magnesium chelatase subunit H; bchI, magnesium chelatase subunit I; brnA, antitoxin component of BrnTA type II T-A system; cbiD, cobalt-precorrin-5B C(1)-methyltransferase; cbiET, cobalamin biosynthesis bifunctional protein CbiET; cbiFG, cobalt-precorrin-4 C(11)-methyltransferase/cobalt-precorrin-5A hydrolase; cbiHC, cobalamin biosynthesis protein CbiHC; cbiJ, cobalt-precorrin-6A reductase; cbiK, sirohydrochlorin cobaltochelatase; cbiL, cobalt-precorrin-2 C(20)-methyltransferase; cbiZ, adenosylcobinamide amidohydrolase; cobN, cobaltochelatase subunit N; cysG, uroporphyrinogen-III C-methyltransferase; dnaK, molecular chaperone DnaK; fge, formylglycine-generating enzyme required for sulphatase activity; grpE, molecular chaperone GrpE; IS5, IS5 family transposase; metE, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase; nrdD, ribonucleoside-triphosphate reductase; pflA, pyruvate formate lyase activating enzyme; radC, DNA repair protein RadC; trpD, anthranilate phosphoribosyltransferase; ubiE, ubiquinone/menaquinone biosynthesis C-methylase UbiE; uvrD, DNA helicase UvrD. General function genes: AH, amidohydrolase; ATPase, AAA domain-containing ATPase; DH, dehydrogenase; Fe-S, ferredoxin domain-containing protein; helicase, superfamily I DNA and/or RNA helicase; nuclease, PD-(D/E)XK nuclease superfamily protein; PH, Pleckstrin Homology domain-containing protein; SAM, radical S-adenosyl-l-methionine superfamily protein; SPE, sugar phosphate epimerase