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. 2018 Oct 12;9:2402. doi: 10.3389/fmicb.2018.02402

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Copyright © 2018 Zhang, Xu, Liu, Cai, Luo and Li.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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(A,B) Relative abundances of the genes involved in (A) the HP/HB cycle (modified from Qin et al., 2017) and (B) the Calvin cycle between the sediment and seawater metagenomes of the Yap Trench. The pie chart of each gene indicates its relative proportion between the three sediment (yellow) and the three seawater (blue) metagenomes. (1), acetyl-CoA-propionyl-CoA carboxylase; (2), malonyl-CoA reductase (NADPH); (3), 3-hydroxypropionyl-CoA synthetase (ADP-forming); (4), 3-hydroxypropionyl-CoA dehydratase; (5), methylmalonyl-CoA epimerase; (6), methylmalonyl-CoA mutase; (7), 4-hydroxybutyryl-CoA synthetase (ADP-forming); (8), 4-hydroxybutyryl-CoA dehydratase; (9), 3-hydroxybutyryl-CoA dehydrogenase; (10), propanoyl-CoA C-acyltransferase. rbc, ribulose-bisphosphate carboxylase; pgk, phosphoglycerate kinase; gap, glyceraldehyde-3-phosphate dehydrogenase; aldo/fba, fructose-bisphosphate aldolase; fbp/glp, fructose-1,6-bisphosphatase; tkt, transketolase; glpX-SEBP, sedoheptulose-bisphosphatase; rpi, ribose 5-phosphate isomerase; prk, phosphoribulokinase. The abundance of each gene is listed in Table S3. (C) Gene abundances involved in the microbial nitrogen cycle in the six metagenomes of the Yap Trench. nif, nitrogenase; gln, glutamine synthetase; ald, alanine dehydrogenase; ure, urease; A_amo, archaeal ammonia monooxygenase; B_amo, bacterial ammonia monooxygenase; hao, hydroxylamine oxidoreductase; nxr, nitrite oxidoreductase; nap, periplasmic nitrate reductase; nar, nitrate reductase; nir, nitrite reductase; nor, nitric oxide reductase; nos, nitrous oxide reductase; hdh, hydrazine dehydrogenase; hzs, hydrazine synthase; nrf, nitrite reductase. (D) The relative gene abundances between the sediment and seawater metagenomes as depicted by the width of solid lines. The yellow line indicates abundance higher in sediments, the blue line indicates higher in seawater, and the black line indicates no difference. The dashed line indicates little to no support for a pathway. The numbers/abbreviations in red indicate statistical significant between the three sediment and the three seawater metagenomes (P < 0.05).