Single-cell measurement of microbial growth rate with Raman microspectroscopy
Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope prob...
Saved in:
| Published in | FEMS microbiology ecology Vol. 100; no. 9 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
13.08.2024
|
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman–SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages. |
|---|---|
| AbstractList | Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman-SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman-SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages. Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman–SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages. Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable Isotope Probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman-SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, non-destructive technique, represents an important step towards application of single-cell analysis into complex sample matrices or cellular assemblages. Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium ( 2 H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2 H. Relative to Raman, we find that nanoSIMS measurements of 2 H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman–SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages. Evaluation of how Raman microspectroscopy can be used to measure biomass growth rates of individual microbial cells. |
| Author | Caro, Tristan A Templeton, Alexis S Kashyap, Srishti Kopf, Sebastian H Brown, George Chen, Claudia |
| Author_xml | – sequence: 1 givenname: Tristan A orcidid: 0000-0001-6177-7444 surname: Caro fullname: Caro, Tristan A – sequence: 2 givenname: Srishti surname: Kashyap fullname: Kashyap, Srishti – sequence: 3 givenname: George surname: Brown fullname: Brown, George – sequence: 4 givenname: Claudia surname: Chen fullname: Chen, Claudia – sequence: 5 givenname: Sebastian H surname: Kopf fullname: Kopf, Sebastian H – sequence: 6 givenname: Alexis S surname: Templeton fullname: Templeton, Alexis S |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/39113275$$D View this record in MEDLINE/PubMed |
| BookMark | eNp1UctKAzEUDaKorW5dyizdjCbNJG1WIuILKoKPdbiT3rSRmUlNppb-vRnaigqSxb2Q80jO6ZHdxjdIyAmj54wqfmGxjmgurANkjO6QQyaGRS5VwXZ_7AekF-M7pUzwgu6TA64Y44OhOCSPL66ZVpgbrKqsRoiLgDU2beZtVjsTfOmgyqbBL9tZFqDFbOnS9gw1NGtAnKNp0zB-vjoiexaqiMeb2Sdvtzev1_f5-Onu4fpqnJvk3OZCWi4tiHSUtQYnOGADECglVVbAQFHgfFKaorClVHKoRpSWODIToFyNJOd9crnWnS_KGicmPThApefB1RBW2oPTv28aN9NT_6nTt4uhKkRSONsoBP-xwNjq2sUuBGjQL6LmVFHJhaAd9PSn2bfLNsQEKNaALo0Y0GrjWmid77xdpRnVXVd63ZXedJVo539oW-V_CF8v_ZwA |
| CitedBy_id | crossref_primary_10_1038_s41559_024_02520_7 crossref_primary_10_3390_molecules29245956 |
| Cites_doi | 10.1128/AEM.02280-15 10.1002/prot.340170110 10.1016/j.ese.2022.100187 10.1039/C8AN02177E 10.1073/pnas.1504674112 10.1038/s43705-022-00134-3 10.1128/AEM.00924-20 10.1021/acs.analchem.6b04913 10.1002/jrs.2121 10.1039/9781782625025-00001 10.1021/acs.analchem.5b00673 10.1002/ecs2.2090 10.1073/pnas.1707525114 10.32942/X2M31M 10.3389/fmicb.2018.02342 10.1073/pnas.1818372116 10.1016/j.syapm.2007.12.002 10.1038/s41598-018-22392-9 10.1128/AEM.01460-21 10.1111/gbi.12391 10.1093/femsec/fiv106 10.1146/annurev-marine-122414-033938 10.1038/s41396-019-0373-4 10.1073/pnas.1107763108 10.1073/pnas.1208795109 10.1073/pnas.1420406112 10.1007/s00216-017-0303-0 10.1038/s41396-019-0422-z 10.1126/sciadv.abg0153 10.1039/C7FD00150A 10.1111/1462-2920.12752 10.1073/pnas.1512057112 10.1177/0003702818764672 10.1038/nrmicro1162 10.3389/fmicb.2019.02682 10.1016/j.cbpa.2016.05.010 10.1016/j.soilbio.2022.108807 10.1002/jbio.201000025 10.1146/annurev-earth-031920-081957 10.1128/AEM.69.6.3500-3509.2003 10.1073/pnas.1908512116 10.1038/s41579-022-00695-z 10.1038/nphoton.2015.60 10.1073/pnas.0903030106 10.1111/1462-2920.15264 10.1111/1462-2920.12518 10.1021/acs.jpcb.2c08270 10.1016/j.saa.2015.09.012 10.3390/bios7040051 10.1038/35036572 10.1073/pnas.2211625120 10.1038/s42003-020-0860-1 10.1038/ismej.2014.144 10.1016/S0959-440X(96)80090-X 10.1038/s41592-019-0538-0 10.1016/j.copbio.2016.04.022 10.1016/j.syapm.2014.02.002 10.1111/j.1749-6632.1960.tb39099.x 10.1007/978-1-4939-9721-3_8 10.1016/j.gca.2018.06.007 10.1111/1462-2920.15667 10.1038/s41579-020-0323-1 10.1073/pnas.1213344109 |
| ContentType | Journal Article |
| Copyright | The Author(s) 2024. Published by Oxford University Press on behalf of FEMS. The Author(s) 2024. Published by Oxford University Press on behalf of FEMS. 2024 |
| Copyright_xml | – notice: The Author(s) 2024. Published by Oxford University Press on behalf of FEMS. – notice: The Author(s) 2024. Published by Oxford University Press on behalf of FEMS. 2024 |
| DBID | AAYXX CITATION NPM 7X8 5PM |
| DOI | 10.1093/femsec/fiae110 |
| DatabaseName | CrossRef PubMed MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef PubMed MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic CrossRef PubMed |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology Environmental Sciences |
| EISSN | 1574-6941 |
| ExternalDocumentID | PMC11347945 39113275 10_1093_femsec_fiae110 |
| Genre | Journal Article |
| GrantInformation_xml | – fundername: ; – fundername: ; grantid: W911NF2120119/78484-LS – fundername: ; grantid: 80NSSC21K0489 – fundername: ; grantid: 1955109 |
| GroupedDBID | --- .3N .GA 0R~ 10A 1OC 29H 36B 4.4 48X 50Y 50Z 51W 51X 52M 52N 52O 52P 52S 52T 52W 52X 53G 5GY 5HH 5LA 66C 702 7PT 8-0 8-1 8-3 8-4 8-5 8UM 930 A03 AAHBH AAIMJ AAMDB AAMVS AAOGV AAPQZ AAPXW AARHZ AAVAP AAYXX ABCQN ABEJV ABEUO ABGNP ABIXL ABPTD ABQLI ABXVV ABXZS ACFRR ACGFO ACIWK ACPRK ACUFI ADBBV ADEZT ADGKP ADGZP ADHKW ADHZD ADPDF ADQBN ADRTK ADVEK ADYVW AEGPL AEJOX AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFZL AFGWE AFIYH AFOFC AFRAH AGINJ AGSYK AHGBF AHMBA AJEEA AKRWK AKWXX ALIPV ALMA_UNASSIGNED_HOLDINGS ALUQC ALXQX AMNDL APIBT APWMN ARIXL AVWKF AXUDD AYOIW AZBYB BAFTC BAYMD BENPR BEYMZ BHONS BHPHI BQDIO BSWAC BY8 CDBKE CITATION CS3 D-E D-F DAKXR DCZOG DILTD DR2 DU5 EBS EMB F00 F01 F04 F5P FDB FHSFR FLUFQ FOEOM G-S G.N GAUVT GJXCC GROUPED_DOAJ H.T H.X H13 HAR HCIFZ HZI HZ~ IAO IX1 J0M J21 JXSIZ K48 KAQDR KOP KSI KSN LC2 LC3 LP6 LP7 MK4 N04 N05 N9A NF~ NLBLG NOMLY O9- OAWHX ODMLO OIG OJQWA OK1 OVD OVEED P2P P2X P4D PAFKI PEELM Q.N Q11 Q5Y R.K ROL RPM RUSNO RX1 RXO SEW TEORI TLC TOX UB1 V8K W8V W99 WH7 WQJ XG1 YAYTL YKOAZ YXANX ~02 ~IA ~KM ~WT AACTN NPM 7X8 2XV 5PM 5VS 7X7 7XC 88E 8CJ 8FE 8FH 8FI 8FJ ABUWG AEUYN AFKRA ATCPS BBNVY BPHCQ BVXVI CCPQU D1J EDH FYUFA HMCUK I-F IHR LK8 M1P M7P PATMY PHGZM PHGZT PJZUB PPXIY PQGLB PQQKQ PSQYO PYCSY UKHRP ZCN |
| ID | FETCH-LOGICAL-c391t-56f36fa5a5a9ffcede212a5e6609f5a290a33dbc44fb69679800be8cda0398633 |
| ISSN | 1574-6941 0168-6496 |
| IngestDate | Thu Aug 21 18:32:13 EDT 2025 Tue Aug 05 11:12:53 EDT 2025 Thu Apr 03 07:01:45 EDT 2025 Thu Apr 24 23:09:48 EDT 2025 Tue Jul 01 00:56:16 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 9 |
| Keywords | Raman microspectroscopy growth rate Stable isotope probing deuterium nanoSIMS single-cell analysis |
| Language | English |
| License | https://creativecommons.org/licenses/by-nc/4.0 The Author(s) 2024. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c391t-56f36fa5a5a9ffcede212a5e6609f5a290a33dbc44fb69679800be8cda0398633 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ORCID | 0000-0001-6177-7444 |
| OpenAccessLink | http://dx.doi.org/10.1093/femsec/fiae110 |
| PMID | 39113275 |
| PQID | 3090635505 |
| PQPubID | 23479 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_11347945 proquest_miscellaneous_3090635505 pubmed_primary_39113275 crossref_citationtrail_10_1093_femsec_fiae110 crossref_primary_10_1093_femsec_fiae110 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 20240813 |
| PublicationDateYYYYMMDD | 2024-08-13 |
| PublicationDate_xml | – month: 08 year: 2024 text: 20240813 day: 13 |
| PublicationDecade | 2020 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | FEMS microbiology ecology |
| PublicationTitleAlternate | FEMS Microbiol Ecol |
| PublicationYear | 2024 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | Cui (2024091411095838700_bib15) 2019 Eichorst (2024091411095838700_bib20) 2015; 91 Trembath-Reichert (2024091411095838700_bib56) 2017; 114 Kopf (2024091411095838700_bib35) 2015; 17 Novelli-Rousseau (2024091411095838700_bib47) 2018; 8 Ebrahimi (2024091411095838700_bib18) 2019; 116 Kellermann (2024091411095838700_bib30) 2012; 109 Kirchman (2024091411095838700_bib32) 2016; 8 Cordero (2024091411095838700_bib11) 2012; 109 Li (2024091411095838700_bib39) 2019; 13 Bai (2024091411095838700_bib2) 1993; 17 Dekas (2024091411095838700_bib16) 2019; 10 Mosier-Boss (2024091411095838700_bib44) 2016; 153 Cui (2024091411095838700_bib13) 2022; 11 Ivleva (2024091411095838700_bib29) 2010; 3 Musat (2024091411095838700_bib46) 2014; 37 Templeton (2024091411095838700_bib54) 2023; 51 Wijker (2024091411095838700_bib63) 2019; 116 Coskun (2024091411095838700_bib12) 2019; 13 Meyer (2024091411095838700_bib41) 2021; 23 Koch (2024091411095838700_bib34) 2018; 9 Woebken (2024091411095838700_bib64) 2015; 9 Lester (2024091411095838700_bib38) 1960; 84 CAMECA (2024091411095838700_bib1) 2024 Chisanga (2024091411095838700_bib9) 2017; 205 Ivleva (2024091411095838700_bib28) 2017; 409 Englander (2024091411095838700_bib21) 1996; 6 Marlow (2024091411095838700_bib40) 2021; 23 Berry (2024091411095838700_bib3) 2015; 112 Weber (2024091411095838700_bib60) 2021; 87 Sokol (2024091411095838700_bib51) 2022; 20 Haouari (2024091411095838700_bib24) 2008; 31 Wang (2024091411095838700_bib59) 2020; 86 Kubryk (2024091411095838700_bib37) 2015; 87 Suzuki (2024091411095838700_bib53) 2020; 3 Védère (2024091411095838700_bib58) 2022; 174 Grossart (2024091411095838700_bib23) 2003; 69 Hu (2024091411095838700_bib26) 2019; 16 Hatzenpichler (2024091411095838700_bib25) 2020; 18 Klein (2024091411095838700_bib33) 2015; 112 Caro (2024091411095838700_bib6) 2023; 120 Schaible (2024091411095838700_bib49) 2024 Stryhanyuk (2024091411095838700_bib52) 2018; 9 Miller (2024091411095838700_bib42) 2018; 237 Schaible (2024091411095838700_bib50) 2022; 2 Zhang (2024091411095838700_bib65) 2009; 106 Casar (2024091411095838700_bib7) 2020; 18 Pernice (2024091411095838700_bib48) 2015; 17 Camp (2024091411095838700_bib5) 2015; 9 Efrima (2024091411095838700_bib19) 2009; 40 Kopf (2024091411095838700_bib36) 2016; 113 Kilburn (2024091411095838700_bib31) 2014 Cicerone (2024091411095838700_bib10) 2016; 33 Chisanga (2024091411095838700_bib8) 2018; 72 Weiss (2024091411095838700_bib62) 2019; 144 Wegener (2024091411095838700_bib61) 2016; 41 Cui (2024091411095838700_bib14) 2017; 89 Mosier-Boss (2024091411095838700_bib45) 2017; 7 Tempra (2024091411095838700_bib55) 2023; 127 Trembath-Reichert (2024091411095838700_bib57) 2021; 7 Dumont (2024091411095838700_bib17) 2005; 3 Hungate (2024091411095838700_bib27) 2015; 81 Foley (2024091411095838700_bib22) 2024 Morono (2024091411095838700_bib43) 2011; 108 Boetius (2024091411095838700_bib4) 2000; 407 |
| References_xml | – volume: 81 start-page: 7570 year: 2015 ident: 2024091411095838700_bib27 article-title: Quantitative microbial ecology through stable isotope probing publication-title: Appl Environ Microb doi: 10.1128/AEM.02280-15 – volume: 17 start-page: 75 year: 1993 ident: 2024091411095838700_bib2 article-title: Primary structure effects on peptide group hydrogen exchange publication-title: Proteins doi: 10.1002/prot.340170110 – volume: 11 start-page: 100187 year: 2022 ident: 2024091411095838700_bib13 article-title: In situ identification of environmental microorganisms with Raman spectroscopy publication-title: Environ Sci Ecotechnol doi: 10.1016/j.ese.2022.100187 – volume: 144 start-page: 943 year: 2019 ident: 2024091411095838700_bib62 article-title: Surface-enhanced Raman spectroscopy of microorganisms: limitations and applicability on the single-cell level publication-title: Analyst doi: 10.1039/C8AN02177E – volume: 112 start-page: 12036 year: 2015 ident: 2024091411095838700_bib33 article-title: Fluid mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1504674112 – volume: 2 start-page: 1 year: 2022 ident: 2024091411095838700_bib50 article-title: Correlative SIP–FISH–Raman–SEM–NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes publication-title: ISME Commun doi: 10.1038/s43705-022-00134-3 – volume: 86 start-page: e00924 year: 2020 ident: 2024091411095838700_bib59 article-title: Arcobacter identification and species determination using Raman spectroscopy combined with neural networks publication-title: Appl Environ Microb doi: 10.1128/AEM.00924-20 – volume: 89 start-page: 5793 year: 2017 ident: 2024091411095838700_bib14 article-title: Surface-enhanced Raman spectroscopy combined with stable isotope probing to monitor nitrogen assimilation at both bulk and single-cell level publication-title: Anal Chem doi: 10.1021/acs.analchem.6b04913 – volume: 40 start-page: 277 year: 2009 ident: 2024091411095838700_bib19 article-title: Understanding SERS of bacteria publication-title: J Raman Spectrosc doi: 10.1002/jrs.2121 – start-page: 1 volume-title: Principles and Practice of Analytical Techniques in Geosciences year: 2014 ident: 2024091411095838700_bib31 article-title: CHAPTER 1. Nanoscale secondary ion mass spectrometry (NanoSIMS) as an analytical tool in the geosciences doi: 10.1039/9781782625025-00001 – volume: 87 start-page: 6622 year: 2015 ident: 2024091411095838700_bib37 article-title: Exploring the potential of stable isotope (Resonance) Raman microspectroscopy and surface-enhanced Raman scattering for the analysis of microorganisms at single cell level publication-title: Anal Chem doi: 10.1021/acs.analchem.5b00673 – volume: 9 start-page: e02090 year: 2018 ident: 2024091411095838700_bib34 article-title: Estimating taxon-specific population dynamics in diverse microbial communities publication-title: Ecosphere doi: 10.1002/ecs2.2090 – volume: 114 start-page: E9206 year: 2017 ident: 2024091411095838700_bib56 article-title: Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1707525114 – volume-title: EcoEvoRxiv year: 2024 ident: 2024091411095838700_bib22 article-title: Microbial growth in soil doi: 10.32942/X2M31M – volume: 9 year: 2018 ident: 2024091411095838700_bib52 article-title: Calculation of single cell assimilation rates from SIP-NanoSIMS-derived isotope ratios: a comprehensive approach publication-title: Front Microbiol doi: 10.3389/fmicb.2018.02342 – volume: 116 start-page: 12173 year: 2019 ident: 2024091411095838700_bib63 article-title: 2H/1H variation in microbial lipids is controlled by NADPH metabolism publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1818372116 – volume: 31 start-page: 38 year: 2008 ident: 2024091411095838700_bib24 article-title: Thermodesulfovibrio hydrogeniphilus sp. nov., a new thermophilic sulphate-reducing bacterium isolated from a Tunisian hot spring publication-title: Syst Appl Microbiol doi: 10.1016/j.syapm.2007.12.002 – volume: 8 start-page: 3957 year: 2018 ident: 2024091411095838700_bib47 article-title: Culture-free antibiotic-susceptibility determination from single-bacterium Raman spectra publication-title: Sci Rep doi: 10.1038/s41598-018-22392-9 – volume: 87 start-page: e01460 year: 2021 ident: 2024091411095838700_bib60 article-title: Using stable isotope probing and Raman microspectroscopy to measure growth rates of heterotrophic bacteria publication-title: Appl Environ Microb doi: 10.1128/AEM.01460-21 – volume: 18 start-page: 508 year: 2020 ident: 2024091411095838700_bib7 article-title: Mineral-hosted biofilm communities in the continental deep subsurface, Deep Mine Microbial Observatory, SD, USA publication-title: Geobiology doi: 10.1111/gbi.12391 – volume: 91 start-page: fiv106 year: 2015 ident: 2024091411095838700_bib20 article-title: Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils publication-title: FEMS Microbiol Ecol doi: 10.1093/femsec/fiv106 – volume: 8 start-page: 285 year: 2016 ident: 2024091411095838700_bib32 article-title: Growth rates of microbes in the oceans publication-title: Annu Rev Mar Sci doi: 10.1146/annurev-marine-122414-033938 – volume: 13 start-page: 1546 year: 2019 ident: 2024091411095838700_bib12 article-title: Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O publication-title: ISME J doi: 10.1038/s41396-019-0373-4 – volume: 108 start-page: 18295 year: 2011 ident: 2024091411095838700_bib43 article-title: Carbon and nitrogen assimilation in deep subseafloor microbial cells publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1107763108 – volume: 109 start-page: 19321 year: 2012 ident: 2024091411095838700_bib30 article-title: Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1208795109 – volume: 112 start-page: E194 year: 2015 ident: 2024091411095838700_bib3 article-title: Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1420406112 – volume: 409 start-page: 4353 year: 2017 ident: 2024091411095838700_bib28 article-title: Raman microspectroscopy, surface-enhanced Raman scattering microspectroscopy, and stable-isotope Raman microspectroscopy for biofilm characterization publication-title: Anal Bioanal Chem doi: 10.1007/s00216-017-0303-0 – volume: 13 start-page: 2162 year: 2019 ident: 2024091411095838700_bib39 article-title: Predictive genomic traits for bacterial growth in culture versus actual growth in soil publication-title: ISME J doi: 10.1038/s41396-019-0422-z – volume: 7 start-page: eabg0153 year: 2021 ident: 2024091411095838700_bib57 article-title: Multiple carbon incorporation strategies support microbial survival in cold subseafloor crustal fluids publication-title: Sci Adv doi: 10.1126/sciadv.abg0153 – volume: 205 start-page: 331 year: 2017 ident: 2024091411095838700_bib9 article-title: Quantitative detection of isotopically enriched E. coli cells by SERS publication-title: Farad Discuss doi: 10.1039/C7FD00150A – volume: 17 start-page: 2542 year: 2015 ident: 2024091411095838700_bib35 article-title: Heavy water and 15 N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats publication-title: Environ Microbiol doi: 10.1111/1462-2920.12752 – volume: 113 start-page: E110 year: 2016 ident: 2024091411095838700_bib36 article-title: Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1512057112 – volume: 72 start-page: 987 year: 2018 ident: 2024091411095838700_bib8 article-title: Surface-enhanced raman scattering (SERS) in microbiology: illumination and enhancement of the microbial world publication-title: Appl Spectrosc doi: 10.1177/0003702818764672 – year: 2024 ident: 2024091411095838700_bib49 article-title: Comparing Raman and NanoSIMS for heavy water labeling of single cells [Internet] publication-title: BioRxiv – volume: 3 start-page: 499 year: 2005 ident: 2024091411095838700_bib17 article-title: Stable isotope probing—linking microbial identity to function publication-title: Nat Rev Micro doi: 10.1038/nrmicro1162 – volume: 10 year: 2019 ident: 2024091411095838700_bib16 article-title: Characterizing chemoautotrophy and heterotrophy in marine archaea and bacteria with single-cell multi-isotope NanoSIP publication-title: Front Microbiol doi: 10.3389/fmicb.2019.02682 – volume: 33 start-page: 179 year: 2016 ident: 2024091411095838700_bib10 article-title: Molecular imaging with CARS micro-spectroscopy publication-title: Curr Opin Chem Biol doi: 10.1016/j.cbpa.2016.05.010 – volume: 174 start-page: 108807 year: 2022 ident: 2024091411095838700_bib58 article-title: Opportunities and limits in imaging microorganisms and their activities in soil microhabitats publication-title: Soil Biol Biochem doi: 10.1016/j.soilbio.2022.108807 – volume: 3 start-page: 548 year: 2010 ident: 2024091411095838700_bib29 article-title: Raman microscopy and surface-enhanced Raman scattering (SERS) for in situ analysis of biofilms publication-title: J Biophotonics doi: 10.1002/jbio.201000025 – volume: 51 start-page: 493 year: 2023 ident: 2024091411095838700_bib54 article-title: The rock-hosted biosphere publication-title: Annu Rev Earth Planet Sci doi: 10.1146/annurev-earth-031920-081957 – volume: 69 start-page: 3500 year: 2003 ident: 2024091411095838700_bib23 article-title: Bacterial colonization of particles: growth and interactions publication-title: Appl Environ Microb doi: 10.1128/AEM.69.6.3500-3509.2003 – volume: 116 start-page: 23309 year: 2019 ident: 2024091411095838700_bib18 article-title: Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1908512116 – volume: 20 start-page: 1 year: 2022 ident: 2024091411095838700_bib51 article-title: Life and death in the soil microbiome: how ecological processes influence biogeochemistry publication-title: Nat Rev Micro doi: 10.1038/s41579-022-00695-z – volume: 9 start-page: 295 year: 2015 ident: 2024091411095838700_bib5 article-title: Chemically sensitive bioimaging with coherent Raman scattering publication-title: Nature Photon doi: 10.1038/nphoton.2015.60 – volume: 106 start-page: 12580 year: 2009 ident: 2024091411095838700_bib65 article-title: Large D/H variations in bacterial lipids reflect central metabolic pathways publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0903030106 – volume: 23 start-page: 81 year: 2021 ident: 2024091411095838700_bib41 article-title: NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity publication-title: Environ Microbiol doi: 10.1111/1462-2920.15264 – volume: 17 start-page: 3570 year: 2015 ident: 2024091411095838700_bib48 article-title: A nanoscale secondary ion mass spectrometry study of dinoflagellate functional diversity in reef-building corals publication-title: Environ Microbiol doi: 10.1111/1462-2920.12518 – volume: 127 start-page: 1138 year: 2023 ident: 2024091411095838700_bib55 article-title: Effects of water deuteration on thermodynamic and structural properties of proteins and biomembranes publication-title: J Phys Chem B doi: 10.1021/acs.jpcb.2c08270 – year: 2024 ident: 2024091411095838700_bib1 article-title: A selection of CAMECA NanoSIMS users – volume: 153 start-page: 591 year: 2016 ident: 2024091411095838700_bib44 article-title: SERS substrates fabricated using ceramic filters for the detection of bacteria publication-title: Spectrochim Acta Part A doi: 10.1016/j.saa.2015.09.012 – volume: 7 start-page: 51 year: 2017 ident: 2024091411095838700_bib45 article-title: Review on SERS of bacteria publication-title: Biosensors doi: 10.3390/bios7040051 – volume: 407 start-page: 623 year: 2000 ident: 2024091411095838700_bib4 article-title: A marine microbial consortium apparently mediating anaerobic oxidation of methane publication-title: Nature doi: 10.1038/35036572 – volume: 120 start-page: e2211625120 year: 2023 ident: 2024091411095838700_bib6 article-title: Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.2211625120 – volume: 3 start-page: 1 year: 2020 ident: 2024091411095838700_bib53 article-title: Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust publication-title: Commun Biol doi: 10.1038/s42003-020-0860-1 – volume: 9 start-page: 485 year: 2015 ident: 2024091411095838700_bib64 article-title: Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach publication-title: ISME J doi: 10.1038/ismej.2014.144 – volume: 6 start-page: 18 year: 1996 ident: 2024091411095838700_bib21 article-title: Mechanisms and uses of hydrogen exchange publication-title: Curr Opin Struct Biol doi: 10.1016/S0959-440X(96)80090-X – volume: 16 start-page: 830 year: 2019 ident: 2024091411095838700_bib26 article-title: Biological imaging of chemical bonds by stimulated Raman scattering microscopy publication-title: Nat Methods doi: 10.1038/s41592-019-0538-0 – volume: 41 start-page: 43 year: 2016 ident: 2024091411095838700_bib61 article-title: Tracking activity and function of microorganisms by stable isotope probing of membrane lipids publication-title: Curr Opin Biotechnol doi: 10.1016/j.copbio.2016.04.022 – volume: 37 start-page: 267 year: 2014 ident: 2024091411095838700_bib46 article-title: The effect of FISH and CARD-FISH on the isotopic composition of 13C- and 15N-labeled Pseudomonas putida cells measured by nanoSIMS publication-title: Syst Appl Microbiol doi: 10.1016/j.syapm.2014.02.002 – volume: 84 start-page: 667 year: 1960 ident: 2024091411095838700_bib38 article-title: Observations on the influence of deuterium on bacterial growth publication-title: Ann NY Acad Sci doi: 10.1111/j.1749-6632.1960.tb39099.x – start-page: 95 volume-title: Stable Isotope Probing: Methods and Protocols year: 2019 ident: 2024091411095838700_bib15 article-title: Stable isotope-labeled single-cell Raman spectroscopy revealing function and activity of environmental microbes doi: 10.1007/978-1-4939-9721-3_8 – volume: 237 start-page: 18 year: 2018 ident: 2024091411095838700_bib42 article-title: Large carbon isotope variability during methanogenesis under alkaline conditions publication-title: Geochim Cosmochim Acta doi: 10.1016/j.gca.2018.06.007 – volume: 23 start-page: 4756 year: 2021 ident: 2024091411095838700_bib40 article-title: Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment publication-title: Environ Microbiol doi: 10.1111/1462-2920.15667 – volume: 18 start-page: 241 year: 2020 ident: 2024091411095838700_bib25 article-title: Next-generation physiology approaches to study microbiome function at single cell level publication-title: Nat Rev Micro doi: 10.1038/s41579-020-0323-1 – volume: 109 start-page: 20059 year: 2012 ident: 2024091411095838700_bib11 article-title: Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1213344109 |
| SSID | ssj0015340 |
| Score | 2.453975 |
| Snippet | Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity... |
| SourceID | pubmedcentral proquest pubmed crossref |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source |
| Title | Single-cell measurement of microbial growth rate with Raman microspectroscopy |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/39113275 https://www.proquest.com/docview/3090635505 https://pubmed.ncbi.nlm.nih.gov/PMC11347945 |
| Volume | 100 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3da9swEBdry2AvY-vWNesWNBjsoWiVrQ9bj1tJKYOW0Q_om5FteTGkSVmch-6v70nyZ5NBNwLCyJKw_bucdHe6nxD6HOqASR0IIkUuCRcqIynngiiTS5amKlAugn92Lk-v-Y8b0Qu0u-ySKv2a_dmYV_I_qEId4GqzZP8B2XZQqIBrwBdKQBjKJ2F8CfPOzBDrfD-87Zx9LmZeOoYlAOAXGNrV9NBSQniv64W2fnvXwOVZWj7Lxd0gvHsyAfu-HsKTNJls4H-3-0Qc1FZHwGid4tbL6b12h95d2sPrq3LN4Pdu-G5fgVd8xzO9ykvd90KE3LpVfRJpozgjTmxSrJ9XNtQ12pbSnlipjVrcM1wV5nZpMntRahPUm18HhNmPJrJ2e6EPrLPEj5DU_bfQTgi2RNjY3XWoSTCfNds8bMvsyY58_6O6_3DlsmaOPN5V21umXL1CL2v7An_zwvIaPTPzXfTcnzh6v4v2Jl1iIzSrNfvyDTrryRLuyRJeFLiVJexlCVtZwlaWsJMlvCZLb9H1yeTq-JTUR22QjKmgIkIWTBZawE8VRWZyA0saLYyUVBVCh4pqxvI047xIpbKRO0pTE2e5pkzFkrE9tD1fzM0-wjpmrBA8UgZKLo2WUQA2hJa5khlj8QiR5jMmWc1Db49DmSWbYRuhL237O8_A8teWnxpUElCS9oPpuVmslgmjitqVNRUj9M6j1I4F7x-wMII78QC_toElYB_emZdTR8QeuDxsLt4_-REP0Ivu3_MBbVe_V-YjrGqrdIy2optojHa-T85_XoydjD4ArxiuKA |
| linkProvider | Directory of Open Access Journals |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Single-cell+measurement+of+microbial+growth+rate+with+Raman+microspectroscopy&rft.jtitle=FEMS+microbiology+ecology&rft.au=Caro%2C+Tristan+A&rft.au=Kashyap%2C+Srishti&rft.au=Brown%2C+George&rft.au=Chen%2C+Claudia&rft.date=2024-08-13&rft.issn=1574-6941&rft.eissn=1574-6941&rft.volume=100&rft.issue=9&rft_id=info:doi/10.1093%2Ffemsec%2Ffiae110&rft.externalDBID=n%2Fa&rft.externalDocID=10_1093_femsec_fiae110 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1574-6941&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1574-6941&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1574-6941&client=summon |