Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Design for Microcosm Manipulation
2.2. DNA and RNA Extraction, Sequencing and Analysis
2.3. Isolation and Identification of Model Organisms
3. Results
3.1. Community Dynamics are Dominated by Four Major Phyla, Firmly Defining the ‘Core Microbiome’ Involved in Methane Consumption
3.2. Community Dynamics within Methylococcaceae and Methylophilaceae Reveal Differential Response to Dioxygen Supply
3.3. Metagenome-Based Genome Assemblies Provide Proxies for Major Players in the Communal Methane Consumption
3.4. Organisms Representing the Core Microbiota, Burkholderiales and Bacteropidetes Isolated from Methane-Consuming Microcosms Provide High-Quality Genomic Scaffolds
3.5. Comparative Analysis of Single Genomes and MAGs Identifies the Cultivated Proxies for Community Analysis
3.6. Evidence for Simultaneous Expression of Genes for Alternative Methanol Dehydrogenases in Both Methylococcaceae and Methylophilaceae
3.7. Hypoxia Stress Response Suggests Competition for Dioxygen
3.8. Metatranscriptome Analysis Uncovers Highly Transcribed Pathways in Burkholderiales and Bacteroidetes, Likely Pinpointing the Mechanisms for the Interspecies Carbon Transfer
3.9. Insights into Metabolisms of Novel Community Members Represented by MAGs
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Normalized Reads | Protein Annotation |
---|---|
4406.72 | nitrous-oxide reductase |
4361.95 | nitric oxide reductase, NorB subunit |
4017.11 | dissimilatory nitrite reductase (NO-forming) |
2591.06 | cytochrome c oxidase cbb3-type subunit 1 |
2058.85 | nitric oxide reductase, NorC |
1840.81 | L-glutamine synthetase |
1577.16 | nitrate reductase alpha subunit |
1514.15 | cytochrome c oxidase cbb3-type subunit 2 |
1511.56 | isocitrate lyase |
1464.03 | respiratory nitrate reductase beta subunit |
941.95 | nitrogen regulatory protein P-II family |
723.80 | nitrate/nitrite transporter NarK |
704.82 | Aconitase |
685.12 | malate dehydrogenase (NAD) |
667.33 | nitrate reductase gamma subunit |
642.85 | nitric oxide reductase NorQ |
621.24 | type IV pilus assembly protein PilA |
617.12 | succinyl-CoA synthetase alpha subunit |
615.04 | succinyl-CoA synthetase beta subunit |
588.58 | succinate dehydrogenase subunit B |
553.90 | acetolactate synthase, small subunit |
518.04 | acetolactate synthase, large subunit |
517.77 | isocitrate dehydrogenase |
425.76 | cytochrome c oxidase cbb3-type subunit 3 |
424.15 | 2-isopropylmalate synthase |
420.08 | citrate synthase |
400.64 | acetyl-coenzyme A synthetase |
364.95 | succinate dehydrogenase subunit A |
309.10 | isocitrate dehydrogenase |
289.19 | dihydrolipoamide dehydrogenase |
288.81 | isocitrate lyase |
283.16 | glyceraldehyde-3-phosphate dehydrogenase |
222.93 | succinate dehydrogenase subunit C |
217.08 | Enolase |
214.48 | glutamate synthase (NADH) large subunit |
198.58 | 6-phosphogluconate dehydratase |
196.19 | respiratory nitrate reductase chaperone NarJ |
194.83 | pyruvate dehydrogenase E1 component |
167.72 | 2-oxoglutarate dehydrogenase E1 component |
167.20 | phosphoenolpyruvate synthase |
160.71 | NosR/NirI nitrous oxide reductase regulator |
160.36 | Transketolase |
145.43 | acetyl-CoA carboxylase carboxyltransferase alpha |
123.76 | pyruvate dehydrogenase E2 component |
116.03 | propionyl-CoA synthetase |
114.66 | glutamate synthase (NADH) small subunit |
111.75 | fructose-bisphosphate aldolase |
110.33 | succinate dehydrogenase subunit D |
107.42 | 2-oxoglutarate dehydrogenase E2 component |
105.95 | malate synthase |
Normalized Reads | Protein Annotation |
---|---|
8811.54 | preprotein translocase subunit SecE |
2575.34 | protein TonB |
2574.02 | outer membrane transport energization protein ExbB |
2170.64 | glyceraldehyde 3-phosphate dehydrogenase |
1962.49 | preprotein translocase subunit SecG |
1556.71 | biopolymer transport protein ExbD |
1468.84 | enolase |
1430.38 | gliding motility associated protien GldN |
1359.97 | pyruvate dehydrogenase E1 component beta subunit |
1303.32 | protein involved in gliding motility GldL |
1205.79 | fructose-bisphosphate aldolase |
1179.97 | citrate synthase |
1137.43 | phosphoenolpyruvate carboxykinase |
1072.83 | gliding motility-associated lipoprotein GldJ |
1058.14 | outer membrane transport energization protein ExbD |
1053.74 | protein involved in gliding motility GldK |
1028.16 | acetyl-CoA carboxylase carboxyl transferase beta |
956.30 | glycine cleavage system H protein |
849.13 | cytochrome c oxidase cbb3-type subunit I/II |
840.36 | malate dehydrogenase |
807.56 | triosephosphate isomerase |
717.63 | glycine hydroxymethyltransferase |
708.77 | dihydrolipoamide dehydrogenase |
682.67 | pyruvate dehydrogenase E1 component alpha subunit |
681.09 | succinate dehydrogenase iron-sulfur subunit |
673.95 | succinyl-CoA synthetase beta subunit |
660.97 | transaldolase |
625.88 | glutamine-fructose-6-phosphate transaminase |
580.02 | acetyl-CoA carboxylase biotin carboxyl carrier protein |
563.70 | acetyl-coenzyme A synthetase |
535.31 | starch-binding associating with outer membrane |
531.84 | succinyl-CoA synthetase alpha subunit |
525.95 | acetyl-CoA carboxylase carboxyl transferase alpha |
514.91 | aconitase |
509.61 | arabinose-5-phosphate isomerase |
508.92 | TonB-linked outer membrane protein, SusC/RagA |
507.51 | phosphoglycerate kinase |
473.35 | 2-oxoglutarate dehydrogenase E2 component |
472.65 | pyruvate dehydrogenase E2 component |
439.43 | acetyl-CoA carboxylase, biotin carboxylase subunit |
437.56 | 6-phosphofructokinase |
427.50 | ribose-phosphate pyrophosphokinase |
394.14 | biopolymer transport protein ExbD |
377.35 | transketolase |
370.57 | starch synthase |
363.35 | transketolase |
360.88 | 2-oxoglutarate dehydrogenase E1 component |
312.13 | 2-oxoglutarate dehydrogenase E2 component |
190.55 | Aconitase |
190.11 | triosephosphate isomerase |
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Zheng, Y.; Wang, H.; Yu, Z.; Haroon, F.; Hernández, M.E.; Chistoserdova, L. Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities. Microorganisms 2020, 8, 1614. https://doi.org/10.3390/microorganisms8101614
Zheng Y, Wang H, Yu Z, Haroon F, Hernández ME, Chistoserdova L. Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities. Microorganisms. 2020; 8(10):1614. https://doi.org/10.3390/microorganisms8101614
Chicago/Turabian StyleZheng, Yue, Huan Wang, Zheng Yu, Fauzi Haroon, Maria E. Hernández, and Ludmila Chistoserdova. 2020. "Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities" Microorganisms 8, no. 10: 1614. https://doi.org/10.3390/microorganisms8101614