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Each sample was concentrated onto a trap column (0.2 × 10 mm ID, 5 µm particle size, 120 Å pore size, C18 Reprosil-Gold, Dr. Maisch GmbH) and rinsed with 100 µL 0.1% formic acid, 2% acetonitrile (ACN), 97.9% water before gradient elution through a reverse phase C18 column (0.1 × 150 mm ID, 3 µm particle size, 120 Å pore size, C18 Reprosil-Gold, Dr. Maisch GmbH) at a flow rate of 500 nL/min. The chromatography consisted of a nonlinear 220 min gradient from 5% to 95% buffer B, where buffer A was 0.1% formic acid in water and buffer B was 0.1% formic acid in ACN (all solvents were Fisher Optima grade). The mass spectrometer monitored MS1 scans from 380 m/z to 1280 m/z at 70K resolution. MS2 scans were performed on the top 15 ions with an isolation window of 2.0 m/z and a 15 s exclusion time."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Mass spectra were searched against the translated genome using Proteome Discoverer’s SEQUEST HT algorithm (Thermo) with a fragment tolerance of 0.02 Da and parent tolerance of 10 ppm. Identification criteria consisted of a protein threshold of 1% False Discovery Rate (FDR), peptide threshold of 0.1% FDR, and two minimum peptides when analyzed with Scaffold version 5.1.2 (Proteome Software, Inc.)."],"omics_type":["Proteomics"],"labhead":["Mak Saito"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["Marine Chemistry and Geochemistry Woods Hole Oceanographic Institute"],"species":["Escherichia Coli","Bacteria"],"publication":["41671182 Lara-Gutiérrez J, Nguyen J, McIlvin MR, Sugiyama I, Landry ZC, Alcolombri U, Pontrelli S, Jiménez-Martínez J, Sauer U, Hwa T, Keegstra JM, Saito MA, Stocker R. Bacterial iron acquisition by &lt;i&gt;Escherichia coli&lt;/i&gt; is facilitated by amino acid complexation in a rapid-renewal environment. Proc Natl Acad Sci U S A. 2026 123(7):e2520431123 10.1073/pnas.2520431123"],"submitter_mail":["mmcilvin@whoi.edu"],"submitter_affiliation":["Woods Hole Oceanographic Inst."],"submitter_country":["United States"],"doi":["10.6019/PXD059988"],"pubmed_abstract":["In natural environments, bacteria often encounter low concentrations of nutrient mixtures that are continuously replenished by physical processes such as fluid flow. Studying bacterial physiology under such conditions is experimentally challenging because it is difficult to maintain steady, low nutrient concentrations with rapid renewal. Most studies on nutrient limitation have used approaches such as the chemostat, which rely on long renewal times to sustain low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD), inspired by microfluidics, that enables bacterial cultivation in nutrient mixtures at low micromolar concentrations with rapid renewal driven by fluid flow. Unlike microfluidic systems, the MCCD retains sufficient culture volume to support batch-scale 'omic analyses. Using the MCCD, we cultured <i>Escherichia coli</i> in a mixture of amino acids and nucleobases at three concentration ranges spanning a fivefold difference in growth rates. Surprisingly, at the lowest concentration range, cells exhibited proteomic signatures of iron limitation despite equal total ferrous iron across conditions. Uptake experiments with labeled iron-histidine and iron-cysteine complexes confirmed that amino acids facilitated ferrous iron acquisition. Under continuous flow, siderophores were washed out, rendering this pathway ineffective and revealing a previously unrecognized mechanism of iron acquisition via soluble ferrous iron-amino acid complexes. These findings highlight the importance of studying bacterial physiology at low nutrient concentrations and also suggest a broader role for other organic substrates capable of complexing iron as potential iron sources in environments with rapid renewal."],"pubmed_title":["Bacterial iron acquisition by &lt;i&gt;Escherichia coli&lt;/i&gt; is facilitated by amino acid complexation in a rapid-renewal environment."],"pubmed_authors":["Lara-Gutiérrez Juanita J, Nguyen Jen J, McIlvin Matthew R MR, Sugiyama Ichiko I, Landry Zachary C ZC, Alcolombri Uria U, Pontrelli Sammy S, Jiménez-Martínez Joaquín J, Sauer Uwe U, Hwa Terence T, Keegstra Johannes M JM, Saito Mak A MA, Stocker Roman R"],"additional_accession":[]},"is_claimable":false,"name":"Growth in Low Carbon Conditions Reveals Amino-Acid-Coupled Iron Uptake","description":"Bacteria in nature encounter substrates at widely varying concentrations, yet studies of bacterial physiology have focused more on nutrient type than concentration, partly due to challenges in maintaining low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD) to culture bacteria under precisely controlled nutrient conditions, including very low concentrations, in a manner suitable for proteomic analysis. Using the MCCD, we cultured 35 Escherichia coli with a mixture of amino acids as the sole carbon source at three concentrations supporting growth rates spanning a fivefold range. Surprisingly, at the lowest concentration, cells exhibited proteomic signatures of iron shortage despite constant iron levels across conditions. Uptake of labeled iron-histidine and iron-cysteine complexes demonstrated that amino-acidbound iron is bioavailable to E. coli. These findings reveal a previously unknown mechanism of 40 bacterial iron acquisition that emerged under the flow imposed by the MCCD, which diluted the siderophore pool and reduced their efficacy. This work highlights the importance of studying bacterial physiology under low nutrient concentrations and demonstrates how physical conditions, such as flow, shape microbial nutrient acquisition strategies.","dates":{"publication":"2026-09-09","submission":"2025-01-20"},"accession":"PXD059988","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:35795","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:57577","NEWT:247480","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:77173","NEWT:112509","NEWT:475174","NEWT:111205","NEWT:1599","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:12215","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NEWT:1748418","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:4615","NEWT:67352","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:3760","NEWT:1584","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:381198","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:3357","NEWT:111225","NEWT:7719","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:29064","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:273791","NEWT:3347","NEWT:49928","NEWT:3349","NEWT:160621","NEWT:2502409","NEWT:212790","NEWT:110368","NEWT:55350","NEWT:1916073","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:370038","NEWT:498211","NEWT:345076","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:200795","NEWT:37919","NEWT:2579791","NEWT:171719","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:260499","NEWT:410661","NEWT:329854","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:2649329","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:3715","NEWT:1538","NEWT:2065263","NEWT:177437","NEWT:717966","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:34878","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1608994","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:1122984","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:45972","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:2836","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:1945864","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:133894","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:1922344","NEWT:108458","NEWT:5936","NEWT:85692","NEWT:321967","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:279010","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:415978","NEWT:1255228","NEWT:410289","NEWT:191701","NEWT:373153","NEWT:1640278","NEWT:9054","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:41122","NEWT:5911","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166314","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:3726","NEWT:906914","NEWT:81231006","NEWT:30455","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:299467","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:542","NEWT:2903","NEWT:185579","NEWT:872227","NEWT:13076","NEWT:25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