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with valueDolinsek, J., Ramoneda, J., & Johnson, D. (2022). Data for: Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability (Version 1.0) [Data set]. Eawag: Swiss Federal Institute of Aquatic Science and Technology. https://doi.org/10.25678/0006RZ
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2 | "author": "[\"Dolinsek, Jan\", \"Ramoneda, Josep\", \"Johnson, | 2 | "author": "[\"Dolinsek, Jan\", \"Ramoneda, Josep\", \"Johnson, | ||
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10 | Data for: Initial community composition determines the long-term | ||||
11 | dynamics of a microbial cross-feeding interaction by modulating niche | ||||
12 | availability (Version 1.0) [Data set]. Eawag: Swiss Federal Institute | ||||
13 | of Aquatic Science and Technology. https://doi.org/10.25678/0006RZ" | ||||
14 | }, | ||||
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9 | "value": "Dolin\u0161ek, J., Ramoneda, J., & Johnson, D. R. | 17 | "value": "Dolin\u0161ek, J., Ramoneda, J., & Johnson, D. R. | ||
10 | (2022). Initial community composition determines the long-term | 18 | (2022). Initial community composition determines the long-term | ||
11 | dynamics of a microbial cross-feeding interaction by modulating niche | 19 | dynamics of a microbial cross-feeding interaction by modulating niche | ||
12 | availability. ISME Communications, 2(1). | 20 | availability. ISME Communications, 2(1). | ||
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63 | { | 71 | { | ||
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65 | "value": "[\"Nitrate (InChI=1S/NO3/c2-1(3)4/q-1)\", \"Nitrite | 73 | "value": "[\"Nitrate (InChI=1S/NO3/c2-1(3)4/q-1)\", \"Nitrite | ||
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76 | { | 84 | { | ||
77 | "key": "tags_string", | 85 | "key": "tags_string", | ||
78 | "value": "Cross-feeding,coexistence,microbial | 86 | "value": "Cross-feeding,coexistence,microbial | ||
79 | interactions,community dynamics,experimental evolution,synthetic | 87 | interactions,community dynamics,experimental evolution,synthetic | ||
80 | ecology,denitrification" | 88 | ecology,denitrification" | ||
81 | }, | 89 | }, | ||
82 | { | 90 | { | ||
83 | "key": "taxa", | 91 | "key": "taxa", | ||
84 | "value": "[\"Pseudomonas stutzeri\"]" | 92 | "value": "[\"Pseudomonas stutzeri\"]" | ||
85 | }, | 93 | }, | ||
86 | { | 94 | { | ||
87 | "key": "taxa_generic", | 95 | "key": "taxa_generic", | ||
88 | "value": "[\"bacteria\"]" | 96 | "value": "[\"bacteria\"]" | ||
89 | }, | 97 | }, | ||
90 | { | 98 | { | ||
91 | "key": "timerange", | 99 | "key": "timerange", | ||
92 | "value": "[\"[2014 TO 2018]\"]" | 100 | "value": "[\"[2014 TO 2018]\"]" | ||
93 | }, | 101 | }, | ||
94 | { | 102 | { | ||
95 | "key": "variables", | 103 | "key": "variables", | ||
96 | "value": "[\"concentration\", \"count\", | 104 | "value": "[\"concentration\", \"count\", | ||
97 | \"bacteria_abundance\"]" | 105 | \"bacteria_abundance\"]" | ||
98 | } | 106 | } | ||
99 | ], | 107 | ], | ||
100 | "groups": [], | 108 | "groups": [], | ||
101 | "id": "12348570-bf1b-4c30-a05a-849180f6744a", | 109 | "id": "12348570-bf1b-4c30-a05a-849180f6744a", | ||
102 | "isopen": false, | 110 | "isopen": false, | ||
103 | "license_id": null, | 111 | "license_id": null, | ||
104 | "license_title": null, | 112 | "license_title": null, | ||
105 | "maintainer": "Johnson, David", | 113 | "maintainer": "Johnson, David", | ||
106 | "maintainer_email": "Johnson, David <David.Johnson@eawag.ch>", | 114 | "maintainer_email": "Johnson, David <David.Johnson@eawag.ch>", | ||
107 | "metadata_created": "2022-12-13T14:53:22.193118", | 115 | "metadata_created": "2022-12-13T14:53:22.193118", | ||
108 | "metadata_modified": "2022-12-13T14:53:22.193128", | 116 | "metadata_modified": "2022-12-13T14:53:22.193128", | ||
109 | "name": "initial-community-composition", | 117 | "name": "initial-community-composition", | ||
110 | "notes": "Multi-step substrate consumption pathways can promote | 118 | "notes": "Multi-step substrate consumption pathways can promote | ||
111 | microbial biodiversity via cross-feeding. If one cell-type | 119 | microbial biodiversity via cross-feeding. If one cell-type | ||
112 | preferentially consumes a primary substrate rather than the | 120 | preferentially consumes a primary substrate rather than the | ||
113 | subsequently formed intermediates, then other cell-types can | 121 | subsequently formed intermediates, then other cell-types can | ||
114 | specialize at consuming the intermediates. While this mechanism for | 122 | specialize at consuming the intermediates. While this mechanism for | ||
115 | promoting biodiversity is established, predicting the long-term | 123 | promoting biodiversity is established, predicting the long-term | ||
116 | persistence of such cross-feeding interactions remains challenging. | 124 | persistence of such cross-feeding interactions remains challenging. | ||
117 | Under what conditions will the interaction (and thus biodiversity) | 125 | Under what conditions will the interaction (and thus biodiversity) | ||
118 | persist or disappear? To address this question, we propagated | 126 | persist or disappear? To address this question, we propagated | ||
119 | co-cultures of two isogenic strains of the bacterium Pseudomonas | 127 | co-cultures of two isogenic strains of the bacterium Pseudomonas | ||
120 | stutzeri. One completely reduces nitrate to nitrogen gas but | 128 | stutzeri. One completely reduces nitrate to nitrogen gas but | ||
121 | preferentially reduces nitrate rather than nitrite (referred to as the | 129 | preferentially reduces nitrate rather than nitrite (referred to as the | ||
122 | generalist) while the other only reduces nitrite to nitrogen gas | 130 | generalist) while the other only reduces nitrite to nitrogen gas | ||
123 | (referred to as the specialist). We found that the two strains coexist | 131 | (referred to as the specialist). We found that the two strains coexist | ||
124 | via nitrite cross-feeding when grown together, but the initial ratio | 132 | via nitrite cross-feeding when grown together, but the initial ratio | ||
125 | of specialist-to-generalist (rS/G) determines the long-term dynamics | 133 | of specialist-to-generalist (rS/G) determines the long-term dynamics | ||
126 | of the co-culture. Co-cultures with large initial rS/Gs converge to | 134 | of the co-culture. Co-cultures with large initial rS/Gs converge to | ||
127 | the same rS/G and persist thereafter. Co-cultures with small initial | 135 | the same rS/G and persist thereafter. Co-cultures with small initial | ||
128 | rS/Gs also converge to the same rS/G but then become increasingly | 136 | rS/Gs also converge to the same rS/G but then become increasingly | ||
129 | dominated by the generalist. The likely cause of these different | 137 | dominated by the generalist. The likely cause of these different | ||
130 | dynamics is that the initial rS/G determines the initial environment, | 138 | dynamics is that the initial rS/G determines the initial environment, | ||
131 | which in turn determines the initial selection pressures and | 139 | which in turn determines the initial selection pressures and | ||
132 | phenotypes acquired by the generalist. Our results demonstrate that | 140 | phenotypes acquired by the generalist. Our results demonstrate that | ||
133 | initial community composition controls the long-term dynamics and | 141 | initial community composition controls the long-term dynamics and | ||
134 | persistence of a cross-feeding interaction, and is therefore an | 142 | persistence of a cross-feeding interaction, and is therefore an | ||
135 | important factor for community development and for engineering | 143 | important factor for community development and for engineering | ||
136 | communities to achieve desired outcomes.", | 144 | communities to achieve desired outcomes.", | ||
137 | "num_resources": 3, | 145 | "num_resources": 3, | ||
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139 | "organization": { | 147 | "organization": { | ||
140 | "approval_status": "approved", | 148 | "approval_status": "approved", | ||
141 | "created": "2019-09-18T14:11:46.562834", | 149 | "created": "2019-09-18T14:11:46.562834", | ||
142 | "description": "Our research is inspired by the extraordinary | 150 | "description": "Our research is inspired by the extraordinary | ||
143 | levels of biodiversity that are typically present within microbial | 151 | levels of biodiversity that are typically present within microbial | ||
144 | communities. For example, a single liter from a lake, a river, or the | 152 | communities. For example, a single liter from a lake, a river, or the | ||
145 | aeration basin of a wastewater treatment plant is estimated to contain | 153 | aeration basin of a wastewater treatment plant is estimated to contain | ||
146 | many thousands of microbial strains and express tremendous numbers of | 154 | many thousands of microbial strains and express tremendous numbers of | ||
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276 | "name": "experimental evolution", | 285 | "name": "experimental evolution", | ||
277 | "state": "active", | 286 | "state": "active", | ||
278 | "vocabulary_id": null | 287 | "vocabulary_id": null | ||
279 | }, | 288 | }, | ||
280 | { | 289 | { | ||
281 | "display_name": "microbial interactions", | 290 | "display_name": "microbial interactions", | ||
282 | "id": "93ffe9e7-088c-41a7-a0a1-9261479d1f3c", | 291 | "id": "93ffe9e7-088c-41a7-a0a1-9261479d1f3c", | ||
283 | "name": "microbial interactions", | 292 | "name": "microbial interactions", | ||
284 | "state": "active", | 293 | "state": "active", | ||
285 | "vocabulary_id": null | 294 | "vocabulary_id": null | ||
286 | }, | 295 | }, | ||
287 | { | 296 | { | ||
288 | "display_name": "synthetic ecology", | 297 | "display_name": "synthetic ecology", | ||
289 | "id": "47a5fc7d-388f-4a1f-93f1-333ca9f1421f", | 298 | "id": "47a5fc7d-388f-4a1f-93f1-333ca9f1421f", | ||
290 | "name": "synthetic ecology", | 299 | "name": "synthetic ecology", | ||
291 | "state": "active", | 300 | "state": "active", | ||
292 | "vocabulary_id": null | 301 | "vocabulary_id": null | ||
293 | } | 302 | } | ||
294 | ], | 303 | ], | ||
295 | "title": "Data for: Initial community composition determines the | 304 | "title": "Data for: Initial community composition determines the | ||
296 | long-term dynamics of a microbial cross-feeding interaction by | 305 | long-term dynamics of a microbial cross-feeding interaction by | ||
297 | modulating niche availability", | 306 | modulating niche availability", | ||
298 | "type": "dataset", | 307 | "type": "dataset", | ||
299 | "url": "https://doi.org/10.25678/0006RZ/", | 308 | "url": "https://doi.org/10.25678/0006RZ/", | ||
300 | "version": null | 309 | "version": null | ||
301 | } | 310 | } |