Changes
On October 25, 2023 at 3:40:13 PM UTC,
-
Added resource readme.txt to Data for: Making Waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia
f | 1 | { | f | 1 | { |
2 | "author": "[\"Karakurt-Fischer, Sema\", \"Johnson, David R.\", | 2 | "author": "[\"Karakurt-Fischer, Sema\", \"Johnson, David R.\", | ||
3 | \"Fenner, Kathrin\", \"Hafner, Jasmin\"]", | 3 | \"Fenner, Kathrin\", \"Hafner, Jasmin\"]", | ||
4 | "author_email": null, | 4 | "author_email": null, | ||
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8 | "key": "citation_publication", | 8 | "key": "citation_publication", | ||
9 | "value": "Karakurt-Fischer, S., Johnson, D. R., Fenner, K., & | 9 | "value": "Karakurt-Fischer, S., Johnson, D. R., Fenner, K., & | ||
10 | Hafner, J. (2023). Making Waves: Enhancing pollutant biodegradation | 10 | Hafner, J. (2023). Making Waves: Enhancing pollutant biodegradation | ||
11 | via rational engineering of microbial consortia. Water Research, | 11 | via rational engineering of microbial consortia. Water Research, | ||
12 | 120756. https://doi.org/10.1016/j.watres.2023.120756\n" | 12 | 120756. https://doi.org/10.1016/j.watres.2023.120756\n" | ||
13 | }, | 13 | }, | ||
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38 | { | 38 | { | ||
39 | "key": "paper_doi", | 39 | "key": "paper_doi", | ||
40 | "value": "10.1016/j.watres.2023.120756" | 40 | "value": "10.1016/j.watres.2023.120756" | ||
41 | }, | 41 | }, | ||
42 | { | 42 | { | ||
43 | "key": "publicationlink", | 43 | "key": "publicationlink", | ||
44 | "value": "https://doi.org/10.1016/j.watres.2023.120756" | 44 | "value": "https://doi.org/10.1016/j.watres.2023.120756" | ||
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46 | { | 46 | { | ||
47 | "key": "review_level", | 47 | "key": "review_level", | ||
48 | "value": "none" | 48 | "value": "none" | ||
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50 | { | 50 | { | ||
51 | "key": "spatial", | 51 | "key": "spatial", | ||
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54 | { | 54 | { | ||
55 | "key": "status", | 55 | "key": "status", | ||
56 | "value": "complete" | 56 | "value": "complete" | ||
57 | }, | 57 | }, | ||
58 | { | 58 | { | ||
59 | "key": "substances", | 59 | "key": "substances", | ||
60 | "value": "[\"1) Atrazine | 60 | "value": "[\"1) Atrazine | ||
61 | 4-10-7-12-6(9)13-8(14-7)11-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14))\", | 61 | 4-10-7-12-6(9)13-8(14-7)11-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14))\", | ||
62 | \"2) Hydroxyatrazine | 62 | \"2) Hydroxyatrazine | ||
63 | 9-6-11-7(10-5(2)3)13-8(14)12-6/h5H,4H2,1-3H3,(H3,9,10,11,12,13,14))\", | 63 | 9-6-11-7(10-5(2)3)13-8(14)12-6/h5H,4H2,1-3H3,(H3,9,10,11,12,13,14))\", | ||
64 | \"3) N-isopropylammelide | 64 | \"3) N-isopropylammelide | ||
65 | 10N4O2/c1-3(2)7-4-8-5(11)10-6(12)9-4/h3H,1-2H3,(H3,7,8,9,10,11,12))\", | 65 | 10N4O2/c1-3(2)7-4-8-5(11)10-6(12)9-4/h3H,1-2H3,(H3,7,8,9,10,11,12))\", | ||
66 | \"4) Cyanuric acid | 66 | \"4) Cyanuric acid | ||
67 | (InChI=1S/C3H3N3O3/c7-1-4-2(8)6-3(9)5-1/h(H3,4,5,6,7,8,9))\", \"5) | 67 | (InChI=1S/C3H3N3O3/c7-1-4-2(8)6-3(9)5-1/h(H3,4,5,6,7,8,9))\", \"5) | ||
68 | 1-Carboxybiuret | 68 | 1-Carboxybiuret | ||
69 | (InChI=1S/C3H5N3O4/c4-1(7)5-2(8)6-3(9)10/h(H,9,10)(H4,4,5,6,7,8))\", | 69 | (InChI=1S/C3H5N3O4/c4-1(7)5-2(8)6-3(9)10/h(H,9,10)(H4,4,5,6,7,8))\", | ||
70 | \"6) Biuret (InChI=1S/C2H5N3O2/c3-1(6)5-2(4)7/h(H5,3,4,5,6,7))\", \"7) | 70 | \"6) Biuret (InChI=1S/C2H5N3O2/c3-1(6)5-2(4)7/h(H5,3,4,5,6,7))\", \"7) | ||
71 | Allophanate (InChI=1S/C2H4N2O3/c3-1(5)4-2(6)7/h(H,6,7)(H3,3,4,5))\", | 71 | Allophanate (InChI=1S/C2H4N2O3/c3-1(5)4-2(6)7/h(H,6,7)(H3,3,4,5))\", | ||
72 | \"8) Diuron | 72 | \"8) Diuron | ||
73 | 10Cl2N2O/c1-13(2)9(14)12-6-3-4-7(10)8(11)5-6/h3-5H,1-2H3,(H,12,14))\", | 73 | 10Cl2N2O/c1-13(2)9(14)12-6-3-4-7(10)8(11)5-6/h3-5H,1-2H3,(H,12,14))\", | ||
74 | \"9) 3,4-Dichloroaniline | 74 | \"9) 3,4-Dichloroaniline | ||
75 | (InChI=1S/C6H5Cl2N/c7-5-2-1-4(9)3-6(5)8/h1-3H,9H2)\", \"10) | 75 | (InChI=1S/C6H5Cl2N/c7-5-2-1-4(9)3-6(5)8/h1-3H,9H2)\", \"10) | ||
76 | Dimethylcarbamic acid | 76 | Dimethylcarbamic acid | ||
77 | (InChI=1S/C3H7NO2/c1-4(2)3(5)6/h1-2H3,(H,5,6))\", \"11) | 77 | (InChI=1S/C3H7NO2/c1-4(2)3(5)6/h1-2H3,(H,5,6))\", \"11) | ||
78 | 3,4-Dichlorocatechol | 78 | 3,4-Dichlorocatechol | ||
79 | (InChI=1S/C6H4Cl2O2/c7-3-1-2-4(9)6(10)5(3)8/h1-2,9-10H)\", \"12) | 79 | (InChI=1S/C6H4Cl2O2/c7-3-1-2-4(9)6(10)5(3)8/h1-2,9-10H)\", \"12) | ||
80 | 2,3-Dichloromuconic acid | 80 | 2,3-Dichloromuconic acid | ||
81 | InChI=1S/C6H4Cl2O4/c7-3(1-2-4(9)10)5(8)6(11)12/h1-2H,(H,9,10)(H,11,12) | 81 | InChI=1S/C6H4Cl2O4/c7-3(1-2-4(9)10)5(8)6(11)12/h1-2H,(H,9,10)(H,11,12) | ||
82 | )\", \"13) 2-Chlorodienelactone | 82 | )\", \"13) 2-Chlorodienelactone | ||
83 | ChI=1S/C6H3ClO4/c7-4-1-3(2-5(8)9)11-6(4)10/h1-2H,(H,8,9)/p-1/b3-2-)\", | 83 | ChI=1S/C6H3ClO4/c7-4-1-3(2-5(8)9)11-6(4)10/h1-2H,(H,8,9)/p-1/b3-2-)\", | ||
84 | \"14) 2-Chloromaleylacetic acid | 84 | \"14) 2-Chloromaleylacetic acid | ||
85 | O5/c7-4(6(11)12)1-3(8)2-5(9)10/h1H,2H2,(H,9,10)(H,11,12)/p-2/b4-1+)\", | 85 | O5/c7-4(6(11)12)1-3(8)2-5(9)10/h1H,2H2,(H,9,10)(H,11,12)/p-2/b4-1+)\", | ||
86 | \"15) Maleylacetic acid | 86 | \"15) Maleylacetic acid | ||
87 | /C6H6O5/c7-4(3-6(10)11)1-2-5(8)9/h1-2H,3H2,(H,8,9)(H,10,11)/b2-1-)\"]" | 87 | /C6H6O5/c7-4(3-6(10)11)1-2-5(8)9/h1-2H,3H2,(H,8,9)(H,10,11)/b2-1-)\"]" | ||
88 | }, | 88 | }, | ||
89 | { | 89 | { | ||
90 | "key": "substances_generic", | 90 | "key": "substances_generic", | ||
91 | "value": "[\"herbicide\", \"biotransformation products\"]" | 91 | "value": "[\"herbicide\", \"biotransformation products\"]" | ||
92 | }, | 92 | }, | ||
93 | { | 93 | { | ||
94 | "key": "systems", | 94 | "key": "systems", | ||
95 | "value": "[\"bioinformatics\"]" | 95 | "value": "[\"bioinformatics\"]" | ||
96 | }, | 96 | }, | ||
97 | { | 97 | { | ||
98 | "key": "tags_string", | 98 | "key": "tags_string", | ||
99 | "value": "bioaugmentation,environmental | 99 | "value": "bioaugmentation,environmental | ||
100 | bioinformatics,high-throughput community assembly,microbial community | 100 | bioinformatics,high-throughput community assembly,microbial community | ||
101 | engineering,pollutant biodegradation" | 101 | engineering,pollutant biodegradation" | ||
102 | }, | 102 | }, | ||
103 | { | 103 | { | ||
104 | "key": "taxa", | 104 | "key": "taxa", | ||
105 | "value": "[\"Achromobacter xylosoxidans\", \"Acinetobacter | 105 | "value": "[\"Achromobacter xylosoxidans\", \"Acinetobacter | ||
106 | baylyi\", \"Arthrobacter aurescens TC1\", \"Arthrobacter globiformis | 106 | baylyi\", \"Arthrobacter aurescens TC1\", \"Arthrobacter globiformis | ||
107 | D47\", \"Arthrobacter sp. AD1\", \"Arthrobacter sp. BS2\", | 107 | D47\", \"Arthrobacter sp. AD1\", \"Arthrobacter sp. BS2\", | ||
108 | \"Arthrobacter sp. DNS10\", \"Bacillus megaterium\", \"Comamonas | 108 | \"Arthrobacter sp. DNS10\", \"Bacillus megaterium\", \"Comamonas | ||
109 | testesteroni\", \"Delftia acidovorans\", \"Delftia tsuruhatensis\", | 109 | testesteroni\", \"Delftia acidovorans\", \"Delftia tsuruhatensis\", | ||
110 | \"Diaphorobacter sp. LR2014-1\", \"Hydrogenophaga sp. PBL-H3\", | 110 | \"Diaphorobacter sp. LR2014-1\", \"Hydrogenophaga sp. PBL-H3\", | ||
111 | \"Moorella thermoacetica ATCC 39073\", \"Mycobacterium brisbanense | 111 | \"Moorella thermoacetica ATCC 39073\", \"Mycobacterium brisbanense | ||
112 | JK1\", \"Pseudomonas fluorescens\", \"Pseudomonas putida\", | 112 | JK1\", \"Pseudomonas fluorescens\", \"Pseudomonas putida\", | ||
113 | \"Pseudomonas sp. ADP\", \"Rhizobium leguminosarum 3841\", | 113 | \"Pseudomonas sp. ADP\", \"Rhizobium leguminosarum 3841\", | ||
114 | \"Sphingomonas sp. SRS2\", \"Variovorax sp. 38R\", \"Variovorax sp. | 114 | \"Sphingomonas sp. SRS2\", \"Variovorax sp. 38R\", \"Variovorax sp. | ||
115 | PBL-H6\", \"Variovorax sp. SRS16\", \"Variovorax paradoxus PBL-E5\"]" | 115 | PBL-H6\", \"Variovorax sp. SRS16\", \"Variovorax paradoxus PBL-E5\"]" | ||
116 | }, | 116 | }, | ||
117 | { | 117 | { | ||
118 | "key": "taxa_generic", | 118 | "key": "taxa_generic", | ||
119 | "value": "[\"bacteria\"]" | 119 | "value": "[\"bacteria\"]" | ||
120 | }, | 120 | }, | ||
121 | { | 121 | { | ||
122 | "key": "timerange", | 122 | "key": "timerange", | ||
123 | "value": "[\"*\"]" | 123 | "value": "[\"*\"]" | ||
124 | }, | 124 | }, | ||
125 | { | 125 | { | ||
126 | "key": "variables", | 126 | "key": "variables", | ||
127 | "value": "[\"none\"]" | 127 | "value": "[\"none\"]" | ||
128 | } | 128 | } | ||
129 | ], | 129 | ], | ||
130 | "groups": [], | 130 | "groups": [], | ||
131 | "id": "3c327ba9-fea2-4ac4-9cb5-71bdd1254cab", | 131 | "id": "3c327ba9-fea2-4ac4-9cb5-71bdd1254cab", | ||
132 | "isopen": false, | 132 | "isopen": false, | ||
133 | "license_id": null, | 133 | "license_id": null, | ||
134 | "license_title": null, | 134 | "license_title": null, | ||
135 | "maintainer": "Karakurt-Fischer, Sema", | 135 | "maintainer": "Karakurt-Fischer, Sema", | ||
136 | "maintainer_email": "Johnson, David <David.Johnson@eawag.ch>", | 136 | "maintainer_email": "Johnson, David <David.Johnson@eawag.ch>", | ||
137 | "metadata_created": "2023-10-25T15:40:12.421565", | 137 | "metadata_created": "2023-10-25T15:40:12.421565", | ||
138 | "metadata_modified": "2023-10-25T15:40:12.421573", | 138 | "metadata_modified": "2023-10-25T15:40:12.421573", | ||
139 | "name": | 139 | "name": | ||
140 | utant-biodegradation-via-rational-engineering-of-microbial-consortia", | 140 | utant-biodegradation-via-rational-engineering-of-microbial-consortia", | ||
141 | "notes": "Biodegradation holds promise as an effective and | 141 | "notes": "Biodegradation holds promise as an effective and | ||
142 | sustainable process for the removal of synthetic chemical pollutants. | 142 | sustainable process for the removal of synthetic chemical pollutants. | ||
143 | Nevertheless, rational engineering of biodegradation for pollutant | 143 | Nevertheless, rational engineering of biodegradation for pollutant | ||
144 | remediation remains an unfulfilled goal, while chemical pollution of | 144 | remediation remains an unfulfilled goal, while chemical pollution of | ||
145 | waters and soils continues to advance. Efforts to (i) identify | 145 | waters and soils continues to advance. Efforts to (i) identify | ||
146 | functional bacteria from aquatic and soil microbiomes, (ii) assemble | 146 | functional bacteria from aquatic and soil microbiomes, (ii) assemble | ||
147 | them into biodegrading consortia, and (iii) identify maintenance and | 147 | them into biodegrading consortia, and (iii) identify maintenance and | ||
148 | performance determinants, are challenged by large number of pollutants | 148 | performance determinants, are challenged by large number of pollutants | ||
149 | and the complexity in the enzymology and ecology of pollutant | 149 | and the complexity in the enzymology and ecology of pollutant | ||
150 | biodegradation. To overcome these challenges, approaches that leverage | 150 | biodegradation. To overcome these challenges, approaches that leverage | ||
151 | knowledge from environmental bio-chem-informatics and metabolic | 151 | knowledge from environmental bio-chem-informatics and metabolic | ||
152 | engineering are crucial. Here, we propose a novel high-throughput | 152 | engineering are crucial. Here, we propose a novel high-throughput | ||
153 | bio-chem-informatics pipeline, to link chemicals and their predicted | 153 | bio-chem-informatics pipeline, to link chemicals and their predicted | ||
154 | biotransformation pathways with potential enzymes and bacterial | 154 | biotransformation pathways with potential enzymes and bacterial | ||
155 | strains. Our framework systematically selects the most promising | 155 | strains. Our framework systematically selects the most promising | ||
156 | candidates for the degradation of chemicals with unknown | 156 | candidates for the degradation of chemicals with unknown | ||
157 | biotransformation pathways and associated enzymes from the vast array | 157 | biotransformation pathways and associated enzymes from the vast array | ||
158 | of aquatic and soil bacteria. We substantiated our perspective by | 158 | of aquatic and soil bacteria. We substantiated our perspective by | ||
159 | validating the pipeline for two chemicals with known or predicted | 159 | validating the pipeline for two chemicals with known or predicted | ||
160 | pathways and show that our predicted strains are consistent with | 160 | pathways and show that our predicted strains are consistent with | ||
161 | strains known to biotransform those chemicals. Such pipelines can be | 161 | strains known to biotransform those chemicals. Such pipelines can be | ||
162 | integrated with metabolic network analysis built upon genome-scale | 162 | integrated with metabolic network analysis built upon genome-scale | ||
163 | models and ecological principles to rationally design fit-for-purpose | 163 | models and ecological principles to rationally design fit-for-purpose | ||
164 | bacterial communities for augmenting deficient biotransformation | 164 | bacterial communities for augmenting deficient biotransformation | ||
165 | functions and study operational and design parameters that influence | 165 | functions and study operational and design parameters that influence | ||
166 | their structure and function. We believe that research in this | 166 | their structure and function. We believe that research in this | ||
167 | direction can pave the way for achieving our long-term goal of | 167 | direction can pave the way for achieving our long-term goal of | ||
168 | enhancing pollutant biodegradation.", | 168 | enhancing pollutant biodegradation.", | ||
n | 169 | "num_resources": 0, | n | 169 | "num_resources": 1, |
170 | "num_tags": 5, | 170 | "num_tags": 5, | ||
171 | "organization": { | 171 | "organization": { | ||
172 | "approval_status": "approved", | 172 | "approval_status": "approved", | ||
173 | "created": "2019-09-18T14:11:46.562834", | 173 | "created": "2019-09-18T14:11:46.562834", | ||
174 | "description": "Our research is inspired by the extraordinary | 174 | "description": "Our research is inspired by the extraordinary | ||
175 | levels of biodiversity that are typically present within microbial | 175 | levels of biodiversity that are typically present within microbial | ||
176 | communities. For example, a single liter from a lake, a river, or the | 176 | communities. For example, a single liter from a lake, a river, or the | ||
177 | aeration basin of a wastewater treatment plant is estimated to contain | 177 | aeration basin of a wastewater treatment plant is estimated to contain | ||
178 | many thousands of microbial strains and express tremendous numbers of | 178 | many thousands of microbial strains and express tremendous numbers of | ||
179 | functional traits.", | 179 | functional traits.", | ||
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182 | n1/Abteilungen/umik/projekte/gemeinschaften/Project_Johnson_Pic2.jpg", | 182 | n1/Abteilungen/umik/projekte/gemeinschaften/Project_Johnson_Pic2.jpg", | ||
183 | "is_organization": true, | 183 | "is_organization": true, | ||
184 | "name": "microbial-community-assembly", | 184 | "name": "microbial-community-assembly", | ||
185 | "state": "active", | 185 | "state": "active", | ||
186 | "title": "Microbial Community Assembly", | 186 | "title": "Microbial Community Assembly", | ||
187 | "type": "organization" | 187 | "type": "organization" | ||
188 | }, | 188 | }, | ||
189 | "owner_org": "1f86dd29-9cf6-4ba0-b118-f20ba855d981", | 189 | "owner_org": "1f86dd29-9cf6-4ba0-b118-f20ba855d981", | ||
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196 | { | 223 | { | ||
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198 | "id": "db8df154-645b-45e4-a2c8-93506ded97aa", | 225 | "id": "db8df154-645b-45e4-a2c8-93506ded97aa", | ||
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216 | }, | 243 | }, | ||
217 | { | 244 | { | ||
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219 | "id": "15b90589-0ce5-4cd6-b85c-ac80ab98b80d", | 246 | "id": "15b90589-0ce5-4cd6-b85c-ac80ab98b80d", | ||
220 | "name": "microbial community engineering", | 247 | "name": "microbial community engineering", | ||
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222 | "vocabulary_id": null | 249 | "vocabulary_id": null | ||
223 | }, | 250 | }, | ||
224 | { | 251 | { | ||
225 | "display_name": "pollutant biodegradation", | 252 | "display_name": "pollutant biodegradation", | ||
226 | "id": "d2ecee1f-4a61-49a4-b041-68d61c22f43f", | 253 | "id": "d2ecee1f-4a61-49a4-b041-68d61c22f43f", | ||
227 | "name": "pollutant biodegradation", | 254 | "name": "pollutant biodegradation", | ||
228 | "state": "active", | 255 | "state": "active", | ||
229 | "vocabulary_id": null | 256 | "vocabulary_id": null | ||
230 | } | 257 | } | ||
231 | ], | 258 | ], | ||
232 | "title": "Data for: Making Waves: Enhancing pollutant biodegradation | 259 | "title": "Data for: Making Waves: Enhancing pollutant biodegradation | ||
233 | via rational engineering of microbial consortia", | 260 | via rational engineering of microbial consortia", | ||
234 | "type": "dataset", | 261 | "type": "dataset", | ||
235 | "url": "https://doi.org/10.25678/0008YV/", | 262 | "url": "https://doi.org/10.25678/0008YV/", | ||
236 | "version": null | 263 | "version": null | ||
237 | } | 264 | } |