Environmental proteomics: A long march in the pedosphere

Renella, Giancarlo; Ogunseitan, Oladele A.; Arenella, Mariarita

doi:10.1016/j.soilbio.2013.10.035

Cited by 18 publications

(8 citation statements)

References 32 publications

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“…Similar to metagenomics and transcriptomics, the method of extracting proteins from a sample requires due consideration (Keiblinger et al 2012; Wang et al 2006). One of the main issues is to successfully recover a representative profile from samples with various characteristics, the challenges of soil proteomics is reviewed by Renella et al (2014). The purified protein samples are then run on a mass spectrophotometer to determine the sequences of proteins present (Armengaud 2013).…”

Section: Efficient Strategies For Ngs Technologiesmentioning

confidence: 99%

Microbial Ecology: Where are we now?

Boughner¹,

Singh²

2016

PDJ

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Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages.

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Section: Efficient Strategies For Ngs Technologiesmentioning

confidence: 99%

Microbial Ecology: Where are we now?

Boughner¹,

Singh²

2016

PDJ

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“…Currently, this information cannot be obtained by soil chemical analyses, and can only be indirectly inferred by studies on the genomic and proteomic responses of soil organisms [108]; in fact effects of nutrient or pollutant availability to soil microbial communities can be estimated from the induced permanent changes in the structure and diversity of the soil microbial communities.…”

Section: Indication Of Bioavailability: the Edge Over Soil Chemical Amentioning

confidence: 99%

Light dazzles from the black box: whole-cell biosensors are ready to inform on fundamental soil biological processes

Renella

2016

Chem. Biol. Technol. Agric.

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Whole-cell biosensors are natural or engineered microorganisms producing signals in response to specific stimuli. This review introduces the use of whole-cell biosensors for the study of the soil system, discuss the recent developments and some current limitations and draws future prospects of the whole-cell biosensors for application to the study of the agro-ecosystems. The review focuses mainly on the lux-and gfp-inserted whole-cell biosensors producing bioluminescence and multicoloured fluorescent proteins, which allow an easy and reproducible detection of the signals from a large number of prokaryotic and eukaryotic soil-borne microorganisms. This review also points out how the whole-cell biosensors indicate the bioavailability of selected analyte, an information that cannot be straight forwardly extrapolated using the chemical methods of soil analysis. However, regardless of the immense progress in biotechnology and genetics that allows to construct whole-cell biosensors for virtually detecting any chemical at ultra low concentrations, the soil still remains the most extreme natural system to be studied with these biotechnological analytical tools. Although a lack of standardization for most of the constructed whole-cell biosensors along with the scarce knowledge of their performance concur to prevent their use in the official methods of soil and environmental analysis, owing to their stability and selectivity we restate that the whole-cell biosensors are ready to provide information on the main processes occurring in soil, and represent unprecedented sensitive tools for improving agriculture and for soil monitoring.

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“…Beyond the genome and metagenome (the whole genetic material from an environmental sample), analysis of the proteome and metaproteome contributes to our understanding of the microbial biodiversity in the soil/rhizosphere and their functions in aspects related to plantmicroorganism molecular dialog, plant nutrition and nutrient recycling (Badri et al 2009;Xiong et al 2013;Renella et al 2014).…”

Section: Molecular Techniques For the Study Of Functional Groups Of Smentioning

confidence: 99%

Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach

2015

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Classical soil science approaches have enabled us to establish basic principles of how the soil system functions and have answered numerous practical agricultural application questions. In recent years, efforts have been refocused on better understanding, managing and benefiting from this system that contains one of the most complex biological communities of the planet. Soil biology is seen as being at the center of scientific research of this century, with novel research objectives and goals being set. In addition, plant nutrition has enabled us to understand nutrient uptake, transport and mobilization mechanisms in plants, and both disciplines have converged on the area of microorganism-mediated plant nutrition. The challenge for these scientific areas is to identify microorganism communities and the roles they play in their habitats, as well as the mechanisms that plants have to make better use of nutrients. Genomics and metagenomics, along with microbiological techniques, are contributing greatly to advances in our understanding of living systems that exist in the soil and their interaction with plants. For its part, molecular plant nutrition has made significant progress in understanding the use of nutrients by plant cells, and has identified molecular mechanisms that can improve nutrient use efficiency. Together, molecular soil microbiology and molecular plant nutrition are projected to be a driving force in agriculture and sustainable food production in the coming years. Herewith, we aim to integrate recent literature on basic and applied research concerning plant and microbe genomics in terms of their potential for developing a novel molecular plant nutrition approach, with special emphasis on nitrogen, potassium and phosphorous as the major macronutrients for crop plants.

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Environmental proteomics: A long march in the pedosphere

Cited by 18 publications

References 32 publications

Microbial Ecology: Where are we now?

Microbial Ecology: Where are we now?

Light dazzles from the black box: whole-cell biosensors are ready to inform on fundamental soil biological processes

Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach

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