High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

Mayali, Xavier; Weber, Peter K.; Brodie, Eoin L.; Mabery, Shalini; Hoeprich, Paul D.; Pett‐Ridge, Jennifer

doi:10.1038/ismej.2011.175

Cited by 61 publications

(80 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The limited phylogenetic coverage of nanoSIMS might be overcome in the future by the steadily growing databases on species or phylum-specific probes [Cole et al, 2014;Jaziri et al, 2014] or by coupling nanoSIMS with microarrays (CHIP-SIP) [Mayali et al, 2012].…”

Section: Methods Developments In Sip Techniquesmentioning

confidence: 99%

“…Another method development was described as CHIP-SIP where RNA-SIP, phylogenetic microarrays and nanoSIMS were combined to increase the sensitivity of 13 C and 15 N incorporation and to determine the phylogenetic identity of the 'heavy' cells. The method requires a sample-specific microarray and nanoSIMS equipment [Mayali et al, 2012]. However, so far, no other application was described for CHIP-SIP.…”

Section: Methods Developments In Sip Techniquesmentioning

confidence: 99%

See 1 more Smart Citation

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

et al. 2016

View full text Add to dashboard Cite

Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using ¹³C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.

show abstract

Section: Methods Developments In Sip Techniquesmentioning

confidence: 99%

Section: Methods Developments In Sip Techniquesmentioning

confidence: 99%

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

et al. 2016

View full text Add to dashboard Cite

show abstract

“…These bacteria are generally heterotrophs, able to metabolize a variety of labile and recalcitrant organic substrates, including monocyclic and polycyclic aromatic hydrocarbons as well as various algal osmolytes and other metabolites (173,175,272,594,(762)(763)(764)(765)(766)(767). They usually react to and grow quickly after small increases in levels of labile organic substrates, such as amino acids, simple sugars, and DMSP, especially during the initial phase of algal blooms (8,13,252,265,272,(768)(769)(770)(771)(772).…”

Section: The Marine Roseobacter Cladementioning

confidence: 99%

Microbial Surface Colonization and Biofilm Development in Marine Environments

Dang

Lovell

2016

Microbiol Mol Biol Rev

799

636

View full text Add to dashboard Cite

SUMMARYBiotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

show abstract

“…The in situ study of microbial activity in natural and engineered ecosystems is therefore of great interest. For this purpose, several elegant methods have been established that use either transcriptional or translational activity of community members (i.e., metatranscriptomics, metaproteomics) (1)(2)(3) or the incorporation of isotopically labeled substrates into biomolecules (4)(5)(6)(7)(8)(9)(10) to infer the ecophysiology of microbes in such systems. However, these bulk techniques do not offer sufficient spatial resolution to study microbial activities at the micrometer scale.…”

mentioning

confidence: 99%

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells

Berry

Mader

Lee

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

352

512

View full text Add to dashboard Cite

Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D 2 O) combined with Raman microspectroscopy. Incorporation of D 2 O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscaleresolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D 2 O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Ramanbased cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/ or glucosamine were identified, demonstrating the potential of the nondestructive D 2 O-Raman approach for targeted sorting of microbial cells with defined functional properties for singlecell genomics.ecophysiology | single-cell microbiology | carbohydrate utilization | nitrifier | Raman microspectroscopy M icroorganisms play a vital role in many environments. They mediate global biogeochemical cycles, catalyze biotechnological processes, and contribute to health and disease in the human body. The in situ study of microbial activity in natural and engineered ecosystems is therefore of great interest. For this purpose, several elegant methods have been established that use either transcriptional or translational activity of community members (i.e., metatranscriptomics, metaproteomics) (1-3) or the incorporation of isotopically labeled substrates into biomolecules (4-10) to infer the ecophysiology of microbes in such systems. However, these bulk techniques do not offer sufficient spatial resolution to study microbial activities at the micrometer scale. Therefore, important information can be overlooked because microbial communities are frequently spatially structured (e.g., biofilms) (11) and contain populations with life cycles (12,13). Furthermore, even apparently identical cells in clonal populations can have strongly divergent activities (14).Consequently, microbial ecophysiology is ideally studied also at the level of the single cell, but only a restricted number of approaches exist for determining physiological properties of individual cells in a microbial community. For exa...

show abstract

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

Cited by 61 publications

References 41 publications

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Microbial Surface Colonization and Biofilm Development in Marine Environments

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells

Contact Info

Product

Resources

About

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

Cited by 61 publications

References 41 publications

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Microbial Surface Colonization and Biofilm Development in Marine Environments

Tracking heavy water (D 2 O) incorporation for identifying and sorting active microbial cells

Contact Info

Product

Resources

About

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells