Experimental improvements in combining CARD-FISH and flow cytometry for bacterial cell quantification

Manti, Anita; Boi, Paola; Amalfitano, Stefano; Puddu, A.; Papa, Stefano

doi:10.1016/j.mimet.2011.09.003

Cited by 24 publications

(15 citation statements)

References 38 publications

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“…These two methods, when used in soil studies, give access to different information concerning the microbial community and should be considered as complementary. The FCM method has the advantage of counting both culturable and non-culturable bacteria, with the possibility of preferential labeling: species or group distinction by FISH (Manti et al, 2011) and the evaluation of viability with Live/Dead markers. The culture method, on the other hand, informs about organisms' physiology.…”

Section: Comparison With Viable Plate Resultsmentioning

confidence: 99%

A rapid flow cytometry method to assess bacterial abundance in agricultural soil

Bressan¹,

Gattin²,

Desaire³

et al. 2015

Applied Soil Ecology

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Section: Comparison With Viable Plate Resultsmentioning

confidence: 99%

A rapid flow cytometry method to assess bacterial abundance in agricultural soil

Bressan¹,

Gattin²,

Desaire³

et al. 2015

Applied Soil Ecology

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“…The recent introduction and development of new molecular methods permit natural assemblages of bacterioplankton to be explored, allowing the direct quantification of total, viable and potentially active cells (Sgorbati et al ., ; Manti et al ., ). Observed changes in redox conditions and nutrient availability can rapidly affect the riverine microbial community structure, with direct consequences for overall ecological functioning (Wu and Hahn, ; Lymer et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Strategies for Water Quality Assessment: A Multiparametric Analysis of Microbiological Changes in River Waters

Boi

Amalfitano

Manti

et al. 2015

River Research & Apps

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River waters are classified worldwide in relation to their chemical quality status, which is assessed by the presence of inorganic and organic\ud pollutants. Meanwhile, microbiological quality evaluations are based mainly on the occurrence of pathogens and faecal contaminants, which\ud are indirectly retrieved by standard cultivation methods. In this study, the structural dynamics of a riverine bacterioplankton community were\ud investigated through a quantitative single-cell approach with the use of flow cytometry for the quantification of total, viable and active cells.\ud Furthermore, catalyzed reporter deposition (CARD)-FISH was used for the evaluation of Proteobacteria and Cytophaga–Flavobacteria bacterial\ud classes. The aim was to identify the major cytometric and phylogenetic cell groups that most representatively reflect the physical and\ud chemical changes occurring in an upland-to-lowland transect along a human-impacted river (the Foglia River, Italy). The use of CARD-FISH\ud to obtain cell abundance measurements of specific taxonomic clusters enabled different microbial propagation dynamics along the river transects\ud to be identified. Furthermore, our results highlighted that the multiparametric approach with flow cytometry produces basic microbiological\ud parameters in a reasonable time span that is consistent with the requirements for an early warning monitoring strategy with respect to\ud integrated riverine water quality assessments

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“…One more specific challenge is the lack of phylogenetic resolution. Despite the enumeration of targeted taxa may rely on specific fluorescence staining procedures (Couradeau et al, 2019;Manti et al, 2011;Neuenschwander et al, 2015), the cytometric information characterizing different subpopulations of microbial cells is generally ataxonomic. A direct link between cytometric fingerprinting and microbial diversity, assessed by 16S rRNA gene amplicon sequencing, was demonstrated in recent studies (Props et al, 2017(Props et al, , 2016.…”

Section: Flow Cytometrymentioning

confidence: 99%

Water and Microbial Monitoring Technologies towards the Near Future Space Exploration

Amalfitano¹,

Levantesi²,

Copetti³

et al. 2019

Preprint

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Space exploration is demanding longer lasting human missions and water resupply from Earth will become increasingly unrealistic. In a near future, the spacecraft water monitoring systems will require technological advances to promptly identify and counteract contingent events of waterborne microbial contamination, posing health risks to astronauts with lowered immune responsiveness. The search for bio-analytical approaches, alternative to those applied on Earth by cultivation-dependent methods, is pushed by the compelling need to limit waste disposal and avoid microbial regrowth from analytical carryovers. Prospective technologies will be selected only if first validated in a flight-like environment, by following basic principles, advantages, and limitations beyond their current applications on Earth. Starting from the water monitoring activities applied on the International Space Station, we provide a critical overview of the nucleic acid amplification-based approaches (i.e., loop-mediated isothermal amplification, quantitative PCR, and high-throughput sequencing) and early-warning methods for total microbial load assessments (i.e., ATP-metry, flow cytometry), already used at a high readiness level aboard crewed space vehicles. Our findings suggest that the forthcoming space applications of mature technologies will be necessarily bounded by a compromise between analytical performances (e.g., speed to results, identification depth, reproducibility, multiparametricity) and detrimental technical requirements (e.g., reagent usage, waste production, operator skills, crew time). As space exploration progresses toward extended missions to Moon and Mars, miniaturized systems that also minimize crew involvement in their end-to-end operation are likely applicable on the long-term and suitable for the in-flight water and microbiological research.

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Experimental improvements in combining CARD-FISH and flow cytometry for bacterial cell quantification

Cited by 24 publications

References 38 publications

A rapid flow cytometry method to assess bacterial abundance in agricultural soil

A rapid flow cytometry method to assess bacterial abundance in agricultural soil

Strategies for Water Quality Assessment: A Multiparametric Analysis of Microbiological Changes in River Waters

Water and Microbial Monitoring Technologies towards the Near Future Space Exploration

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