Application of molecular tools for <i>in situ</i> monitoring of bacterial growth activity

Molin, Søren; Givskov, Michael

doi:10.1046/j.1462-2920.1999.00056.x

Cited by 89 publications

(55 citation statements)

References 68 publications

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“…SJ Blazewicz et al methodological reviews (for example, Molin and Givskov, 1999). However, while most of these limitations are also pertinent when attempting to identify which microbes are currently active in a community, these limitations are frequently overlooked or ignored in practice.…”

Section: Rrna and Its Use In Microbial Ecologymentioning

confidence: 99%

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

et al. 2013

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Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the 'active' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population's growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.

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Section: Rrna and Its Use In Microbial Ecologymentioning

confidence: 99%

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

et al. 2013

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“…However, examining the transcriptionally active community revealed a more dynamic and complicated response to straw and/or nitrate addition. This probably resulted from that the transcription level analysis is much more sensitive than the gene level, as activity of cells is directly associated with turnover and synthesis of rRNA (Molin and Givskov 1999).…”

Section: Responses Of the Methanogenic Communities To Treatmentsmentioning

confidence: 99%

Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil

Bao

Huang

Wang

et al. 2016

Appl Microbiol Biotechnol

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Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH 4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH 4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH 4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.

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“…For instance, lineage-specific PCR (e.g., [54]), combined or not with enrichment steps when population abundance in the samples is thought to be low (e.g., [56]), may be used to validate the presence (or absence) of rare genotypes. Alternatively, direct microscopic observations of the samples (e.g., using fluorescent in situ hybridization with taxon-specific probes) or the utilization of various physiological methods to identify prokaryotic activity (e.g., [2,46,65]) may be used.…”

Section: Sampling Issue and Spatial Scalementioning

confidence: 99%

Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution

2006

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New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.

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Application of molecular tools for in situ monitoring of bacterial growth activity

Cited by 89 publications

References 68 publications

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil

Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution

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