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Principal component analysis and kinetic model adjustment to describe the community-level physiological profiles (CLPP) in the sediments of the river Minho estuary (Northern Portugal)

Julio C. Lopes1*, Virgílio Peixoto1, Cláudia Mota1, Sara Fernandes1 and Ana Coutinho1
  • 1 Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Portugal

The CLPP is a rapid screening method used to characterize microbial communities of different habitats, ranging between sediments to seawater and between oligotrophic groundwater to soil and fertilizers. This method involves the direct inoculation of environmental samples in microtiter plates containing different carbon sources, nutrients and a redox dye, incubation and detection by mass spectrometry of heterotrophic microbial activity. It has the advantage that it is a simple and fast technique to analyse but as the disadvantages that require careful with the data acquisition and the interpretation analysis. CLPP has advantages over both classic cell culturing techniques and molecular level RNA amplification as these other techniques are time consuming and require specialized expertise. BIOLOG EcoPlates™, consisting of 96 well plates containing 31 different carbon sources and a blank in triplicate, have been developed specifically for ecological studies (other BIOLOG plates were originally designed for species identification). Coastal regions in recent decades have been characterized by a high population and urban growth that was aided by the rapid industrial development, which translates into a reduction of the environmental quality of coastal areas. In Portugal, more than 40% of the population is concentrated in the coastal strip, which corresponds to 4 million inhabitants and thus there is a high human pressure on the coastal zone and there are currently 13 estuaries and lagoons: north Tagus (Minho, Cávado, Lima, Ave, Douro, Ria de Aveiro, Mondego, Tagus) and south lies the Sado, Mira, Arade, Ria Formosa and Guadiana. The samples analyzed were collected at 5 sampling points in the estuarine area of the river Minho, in the Portuguese bank. Each well of the BIOLOG Eco-Plate™ (Biolog Inc., Hayward CA., USA) was inoculated with 150 μL of inoculum and incubated at 20°C. Absorbance readings were taken periodically (0, 12, 24, 36, 60, 84, 108, 132, 156, 180, 220, 268, 336 and 456 h) at 592 nm with an automatic plate reader. The collected data where used to determine average well colour development (AWCD) and the different AWCD value is used to determine the carbon source utilization and the adjust kinetic parameters (K, r and s) using a model proposing by Lindstrom (1998), where K is the asymptote (or carrying capacity) that the test well OD curve approaches, r determines the exponential rate of OD change, t is the time following inoculation of the microplates, and s is the time when the midpoint of the exponential portion of the curve (i.e., when y = K/2) is reached. The principal component analysis (PCA) is used to determine the effect of different class of carbon sources in the variation of CLPP. The estimation of the kinetic parameters results in values between 0,104 (Carboxylic acids) and 0,265 (Polymers) to K, -5,041 (Carboxylic acids) and -24,018 (Amines) to r and 7,041 (Carboxylic acids) and 26,018 (Amines) to s. No significant differences are found between carbon sources classes parameters and between year of sampling. The PCA demonstrates the importance of Polymers and Carbohydrates (explain 83,1% of the observed variance) on the AWCD development.

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Keywords: CLPP, Microbial Diversity, microbial development, Estuaries/Coastal Systems, Estuarine ecology

Conference: IMMR | International Meeting on Marine Research 2016, Peniche, Portugal, 14 Jul - 15 Jul, 2016.

Presentation Type: Poster presentation

Topic: Biodiversity, Conservation and Coastal Management

Citation: Lopes JC, Peixoto V, Mota C, Fernandes S and Coutinho A (2016). Principal component analysis and kinetic model adjustment to describe the community-level physiological profiles (CLPP) in the sediments of the river Minho estuary (Northern Portugal). Front. Mar. Sci. Conference Abstract: IMMR | International Meeting on Marine Research 2016. doi: 10.3389/conf.FMARS.2016.04.00091

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Received: 18 May 2016; Published Online: 13 Jul 2016.

* Correspondence: Prof. Julio C Lopes, Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Ponte de Lima, Portugal, juliocesar@esa.ipvc.pt