Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology

Mocali, Stefano; Benedetti, Antonio

doi:10.1016/j.resmic.2010.04.010

Cited by 111 publications

(76 citation statements)

References 79 publications

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“…The disadvantage of traditional cultivation techniques is that they are unable to identify the majority of microorganisms in environmental samples, due to the inability of many organisms to grow on laboratory media (Mocali and Benedetti 2010). For slowgrowing microorganisms, traditional phenotypic identification is difficult and timeconsuming, besides, the interpretation of test results involves substantial subjective judgment (Stager and Davis 1992).…”

Section: Identification By Enzyme Activitiesmentioning

confidence: 99%

Review of Molecular Techniques for the Identification of Bacterial Communities in Biological Effluent Treatment Facilities at Pulp and Paper Mills

et al. 2017

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One of the processes most used in biotechnology today for handling industrial liquid wastes is biological wastewater treatment. The efficiency and quality of its operation depends on the composition and activity of the microbial community that is present. The application of traditional and molecular techniques has provided a glimpse into the "black box" and has given information to improve the wastewater treatment process. However, bleach pulp and paper mill effluents require a better understanding of the active bacterial population. For the study of these microorganisms, molecular techniques have been used for more than 15 years. However, there has been a lack of knowledge of the physiological requirements and relations with the environment, which seems to be very difficult to obtain involving profile on the diversity. Nowadays, highthroughput sequencing technology is a promising method that makes it possible to identify the entire profile of microbial communities. In combination with fingerprint methods, this approach allows the identification and analysis of the whole biodiversity of microbial communities. In this review, several identification techniques will be discussed.

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Section: Identification By Enzyme Activitiesmentioning

confidence: 99%

Review of Molecular Techniques for the Identification of Bacterial Communities in Biological Effluent Treatment Facilities at Pulp and Paper Mills

et al. 2017

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“…Preliminary results revealed different amounts of Actinobacteria and Proteobacteria among the two sites and an overrepresentation of sulfur-oxidation genes in samples where both the increased level of sulfates and the abundance of Firmicutes such as Sulfobacillus thermosulfidooxidans occurred. A further step might be to sequence the entire genomic DNA present in a vineyard soil sample and referred to as the "metagenome", which could provide a cultivation-independent assessment of the largely unexplored genetic reservoir of soil microbial communities and their functions (Daniel, 2005;Mocali and Benedetti, 2010). The importance of this approach has led to the establishment of "Terragenome", an international consortium for the exploitation of the soil metagenome (Vogel et al, 2009).…”

Section: Biological Fingerprinting Through Molecular and "Omics" Apprmentioning

confidence: 99%

An overview of the recent approaches to terroir functional modelling, footprinting and zoning

Vaudour

Costantini²,

Jones

et al. 2015

SOIL

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Abstract. Notions of terroir and their conceptualization through agro-environmental sciences have become popular in many parts of world. Originally developed for wine, terroir now encompasses many other crops including fruits, vegetables, cheese, olive oil, coffee, cacao and other crops, linking the uniqueness and quality of both beverages and foods to the environment where they are produced, giving the consumer a sense of place. Climate, geology, geomorphology and soil are the main environmental factors which make up the terroir effect on different scales. Often considered immutable culturally, the natural components of terroir are actually a set of processes, which together create a delicate equilibrium and regulation of its effect on products in both space and time. Due to both a greater need to better understand regional-to-site variations in crop production and the growth in spatial analytic technologies, the study of terroir has shifted from a largely descriptive regional science to a more applied, technical research field. Furthermore, the explosion of spatial data availability and sensing technologies has made the within-field scale of study more valuable to the individual grower. The result has been greater adoption of these technologies but also issues associated with both the spatial and temporal scales required for practical applications, as well as the relevant approaches for data synthesis. Moreover, as soil microbial communities are known to be of vital importance for terrestrial processes by driving the major soil geochemical cycles and supporting healthy plant growth, an intensive investigation of the microbial organization and their function is also required. Our objective is to present an overview of existing data and modelling approaches for terroir functional modelling, footprinting and zoning on local and regional scales. This review will focus on two main areas of recent terroir research: (1) using new tools to unravel the biogeochemical cycles of both macro-and micronutrients, the biological and chemical signatures of terroirs (i.e. the metagenomic approach and regional fingerprinting); (2) terroir zoning on different scales: mapping terroirs and using remoteand proxy-sensing technologies to monitor soil quality and manage the crop system for better food quality.

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“…However, the number of strains that have been isolated till date is negligible compared to the estimated number of existing bacterial taxa, which are estimated at between 10 7 and 10 9 (Schloss and Handelsman, 2004;Mocali and Benedetti;. This situation has been explained through several molecular ecology studies, which have demonstrated that more than 99% of environmental bacteria are not readily cultivated with classically used culture methods.…”

Section: Cultivation-dependent Approaches For Drug Discoverymentioning

confidence: 99%

“…This situation has been explained through several molecular ecology studies, which have demonstrated that more than 99% of environmental bacteria are not readily cultivated with classically used culture methods. It has been estimated that less than 0.3% of soil bacteria can be cultured in the laboratory using a single medium type, and this fraction reduces to 0.00001% for water associated microorganisms (Amann et al 1995;Oren, 2004;Abulencia et al, 2006;Schloss and Handelsman, 2004;Mocali and Benedetti;. This huge reservoir of previously uncultured microorganisms had remained unknown and untapped until the recent development and combination of molecular ecology and molecular biology, which gave rise to a new approach called ''metagenomics'' (Gillespie et al, 2002;Rouhi, 2003, Schloss andHandelsman, 2004;Gullo et al, 2005;Hirsch et al, 2010;Monier et al, 2011).…”

Section: Cultivation-dependent Approaches For Drug Discoverymentioning

confidence: 99%

“…These environmental DNAbased methods do not rely on isolation and cultivation of single microorganisms and thus reduce the cultivation bias (Daniel, 2004). A metagenomic library can then be used to study the structural and functional diversity of a microbial assemblage by DNA sequencing or to search for new products based on sequence mining or functional expression (Figure 3), (Daniel, 2004;Singh and Macdonald 2010;Mocali and Benedetti, 2010). Environmental DNA is extracted by direct or indirect lysis of cells from soil particles.…”

Section: Metagenomics Versus Drug Discoverymentioning

confidence: 99%

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Tapping uncultured microorganisms through metagenomics for drug discovery

Ibrahim¹,

Al-Salamah²,

Hatamleh³

et al. 2012

Afr. J. Biotechnol.

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Natural products have been an important historical source of therapeutic agents. Microorganisms are major source of bioactive natural products, and several microbial products including antibiotics, antiinflammatory, anti-tumour, immunosuppressants and others are currently used as therapeutic agents for human and domestic animals. Most of these products were obtained from cultured environmental microorganisms. However, it is widely accepted that a very large majority of the microorganisms present in natural environments are not readily cultured under laboratory conditions, and therefore are not accessible for drug discovery. Metagenomics is a recent culture-independent approach that has been developed to access the collective genomes of natural bacterial populations. It enables discovery of the diverse biosynthetic pathways encoded by diverse microbial assemblages that are known to be present in the environment but not-yet cultured. Recently, several new bioactive molecules and proteins have been discovered using a metagenomic approach. This review highlights the recent methodologies, limitations, and applications of metagenomics for the discovery of new drugs. Moreover, it shows how a multidisciplinary approach combining metagenomics with other technologies can expedite and revolutionize drug discovery from diverse environmental microorganisms.

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Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology

Cited by 111 publications

References 79 publications

Review of Molecular Techniques for the Identification of Bacterial Communities in Biological Effluent Treatment Facilities at Pulp and Paper Mills

Review of Molecular Techniques for the Identification of Bacterial Communities in Biological Effluent Treatment Facilities at Pulp and Paper Mills

An overview of the recent approaches to terroir functional modelling, footprinting and zoning

Tapping uncultured microorganisms through metagenomics for drug discovery

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