Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP)

Prakash, Om; Pandey, Prashant; Kulkarni, Girish; Mahale, Kiran N.; Shouche, Yogesh S.

doi:10.1007/s12088-014-0461-0

Cited by 37 publications

(21 citation statements)

References 51 publications

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“…However, similar as in other fields of microbiome research, 'omic' techniques only display snapshots of the microbial diversity at a certain time under certain conditions and provide limited information about community dynamics or ecological behavior [114], especially on the response of single species, groups of microorganisms or entire microbiomes to varying environmental factors over time. Hence, established techniques, such as the terminal restriction fragment length polymorphism (TRFLP), are still valuable for microbiome screening in full-scale biogas plants, in particular with respect to microbial process monitoring [64,80,[115][116][117][118]. The disadvantage of this method, however, is a low phylogenetic resolution, so that the identification of indicator species is not completely possible.…”

Section: Indicator Direct or Indirect Information On Measuring Effortmentioning

confidence: 99%

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

2019

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Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H2), ammonium/ammonia (NH4+/NH3) or hydrogen sulphide (H2S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided.

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Section: Indicator Direct or Indirect Information On Measuring Effortmentioning

confidence: 99%

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

2019

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“…Although there is extensive research on soil microbial diversity, relatively few studies have been undertaken to evaluate the lasting impact of crop rotation on bacterial diversity and community structure by means of terminal restriction fragment length polymorphism (T-RFLP) [15,16]. Despite the limitations of this technique, it provides a high-throughput, cultivation-independent, reproducible approach to rapidly describe and compare bacterial communities from a large number of samples [17,18]. In addition, data collection from a 54-year field experiment enables us to evaluate the long-term effect of crop rotation practices on soil bacterial communities.…”

Section: Introductionmentioning

confidence: 99%

Effect of Long-Term Cropping Systems on the Diversity of the Soil Bacterial Communities

et al. 2019

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Soil microbial communities are involved in the maintenance of productivity and health of agricultural systems; therefore an adequate understanding of soil biodiversity plays a key role in ensuring sustainable use of soil. In the present study, we evaluated the influence of different cropping systems on the biodiversity of the soil bacterial communities, based on a 54-year field experiment established in Martonvásár, Hungary. Terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique was used to assess soil bacterial diversity and community structure in maize monoculture and three different crop rotations (maize-alfalfa, maize-wheat and the maize-barley-peas-wheat Norfolk type). No differences in richness and diversity were detected between maize monoculture and crop rotations except for the most intense rotation system (Norfolk-type). Although the principal component analysis did not reveal a clear separation between maize monoculture and the other rotation systems, the pairwise tests of analysis of similarity (ANOSIM) revealed that there are significant differences in the composition of bacterial communities between the maize monoculture and maize-alfalfa rotation as well as between wheat-maize and Norfolk-type rotation.

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“…And perhaps the best part of this study is its potential to be extended to any gene and organism of interest. A few studies have in fact been conducted, where RE digestion patterns of functional genes have been used as markers [8,10,[13][14][15][16][17].…”

Section: Discussionmentioning

confidence: 99%

Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains

et al. 2015

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Microbial classification is based largely on the 16S rRNA (rrs) gene sequence, which is conserved throughout the prokaryotic domain. The Ribosomal Database Project (RDP) has become a reference point for almost all practical purposes. The use of this gene is limited by the fact that it can be used to identify only to the extent to what has been known and is available in the RDP. In order to identify an organism whose rrs is not present in the RDP database, we need to generate novel markers to place the unknown on the evolutionary map. Here, sequenced genomes of 27 Clostridium strains belonging to 9 species have been used to identify two sets of genes: (1) common to most of the species, and (2) unique to a species. Combinations of genes (recN, dnaJ, secA, mutS, and/or grpE) and their unique restriction endonuclease digestion (AluI, BfaI and/or Tru9I) patterns have been established to rapidly identify Clostridium species. This strategy for identifying novel markers can be extended to all other organisms and diagnostic applications.

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Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP)

Cited by 37 publications

References 51 publications

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

Effect of Long-Term Cropping Systems on the Diversity of the Soil Bacterial Communities

Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains

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