Summary
Phytobenthic communities inhabiting intertidal mud and sand flats of estuaries and shallow coastal zones have been identified as one of the most important primary producers in these ecosystems [1,2]. One of the best remote sensing, non-destructive methods for studying plant communities is the analysis of fluorescence spectra of vegetation induced by laser [3]. Slow implementation of this method is a consequence of the fact that till now portable laser-induced-fluorescence LIght Detection And Ranging sensors (LIF-LIDAR) are virtually absent in the market.
The objective of the Project is to couple the vast innovative experience in active optical remote sensing of various objects (smoke particles, oil spills, etc.) of INOV Group [T1, T2] with significant know-how of CO FCUL Group in the in situ investigation of intertidal estuarine microphytobenthos using both spectral reflectance and pulse-amplitude-modulated (PAM) fluorescence [T3-T5].
A portable LIF-LIDAR sensor will be developed on the basis of available CCD spectrometer and a compact and reliable frequency-doubled Nd:YAG laser, offering short intense radiation pulses comprising sufficiently energetic photons. The spectral data provided by LIF-LIDAR, containing the chlorophyll fluorescence component, will yield information about algal physiological status.
Portable LIF-LIDAR sensor will allow estimating the microphytobenthos biomass of muddy and sandy sediments in the Tagus estuary and, in the case of epipelic (motile, fine sediment-inhabiting) diatom communities, tracking microalgae migration caused by diurnal/tidal cycles and changes in irradiance levels. The LIF-LIDAR sensor will be tested in the field conditions during several tidal cycles. The MPB biomass distribution will be mapped in different intertidal areas of the Tagus estuary.
The LIF-LIDAR instrument will also be used to study sediments colonised by different macroalgae. Here the analysis of fluorescence emission will enable the major groups of macroalgae (green, brown, and red) to be discriminated due to their different pigment composition and light energy transfer processes from accessory pigments to chlorophyll a. The LIF-LIDAR sensor will then be used for investigating different types of substrate (e.g. mud, sand, oyster shells) colonised by macroalgae. As in the previous study, the macroalgae distribution will be mapped in different intertidal areas of the Tagus estuary.
The final expected results of the Project comprises:
1. Designing, building and testing a portable, lightweight, and low power consumption LIF-LIDAR sensor for investigation of micro- and macroalgal fluorescence. Developing software for computer-controlled operation of the instrument and preliminary signal processing.
2. Studying and mapping the MPB biomass distribution over muddy and sandy sediments of the Tagus estuary.
3. Studying and mapping sediments colonized by different macroalgae for different types of substrate (e.g., mud, sand, and oyster shells).
4. Creating a phenomenological model for estimation the LIF-LIDAR range in the process of capturing microalgae and macroalgae fluorescence spectra. The forecast of the LIF-LIDAR range will be based on the experimental data obtained previously for microalgae, and green, brown, and red macroalgae.
Brief Technical Description
During last several years INOV gained significant experience in the area of investigation of environment on the basis of modern optoelectronic equipment. In particular, the methods of remote detection of various smokes in the atmosphere using LIDAR (Light Detection And Ranging) were developed. The results achieved by the INOV Group in this area using direct detection LIDAR were published in 15 papers in SCI journals (see, for example, [T6-T10]) and a book chapter [T11]. Key methods of the developed LIDAR surveillance technique, including application of the artificial intelligence methods for automatic recognition of the smoke signatures, are protected by a patent [T12]. During joint activity of INOV and FCUL Groups, this approach was recently extended to investigation of leaves, needles, and microalgae physiological status and evaluation of oil spills on the water surface using laser induced fluorescence (LIF) LIDAR. More detailed technical description, literature review and discussion of the results obtained up to now with the LIF-LIDAR technique can be found in [T13-T20].
Methodology
This project will assess the prospects of LIF-LIDAR technique for non-destructive remote sensing of the biomass and physiological status of micro- and macroalgae. The assessment will be carried out in the field conditions in the intertidal areas of the Tagus estuary using a specially developed portable LIF-LIDAR sensor, joining the experts in developing modern opto-electronic equipment for remote sensing of environment from INOV and experts in investigation of microalgae and macroalgae (FCUL). To the best of our knowledge, LIF-LIDAR has never been applied to microphytobenthos (MPB), which compose dense micro-algal, diatom-dominated biofilms with large spatio-temporal variability in the areas of difficult access in estuarine and coastal ecosystems. This makes the use of remote sensing techniques particularly useful in assessing MPB distribution.
At the initial stage of the Project the market survey and specifications of the LIF LIDAR sensor configuration will be made. Then a portable LIF LIDAR sensor will be designed and constructed according to these specifications, providing to the applicants an efficient in situ non-contact method for analysing the stress physiology of MPB and will deepen significantly the general knowledge related to the intertidal macroalgae.
The LIF-LIDAR instrument will first be used to study MPB biomass of muddy and sandy sediments of the Tagus estuary, to estimate MPB biomass and - in the case of epipelic (motile, fine sediment-inhabiting) diatom communities - to track microalgae migration caused by diurnal/tidal cycles and changes in the irradiance levels. Latrunculin A, a diatom motility inhibitor, will be used to compare migratory and non-migratory benthic biofilms. This will be done first in the controlled laboratory conditions using sediment samples differing in the grain size (from fine silt to coarse sand). The field testing will be carried out along different tidal cycles, and the MPB biomass will be mapped in different intertidal areas of the Tagus estuary.
Then the developed LIF-LIDAR sensor will be used for the laboratory testing and in situ study and mapping (as well, in different intertidal areas of the Tagus estuary) of sediments colonized by different macroalgae.
In the final stage of the BenthicLIF project, the phenomenological model of the LIF-LIDAR detection of algae activity will be developed, allowing estimation of LIF-LIDAR range in the process of capturing microalgae and macroalgae fluorescence spectra. The input parameters of the model will be: laser pulse energy and repetition rate, receiver's telescope diameter, and the type of the CCD (non-intensified or intensified) spectrometer used. The forecast of the LIF-LIDAR detection range will be based on the experimental data obtained previously in Tasks 3 and 4 for microalgae, and green, brown, and red macroalgae.
The subsequent cooperative use of this model by INOV and FCUL Groups will be two-fold, comprising (within the framework of R&D projects with Industry) the development of novel optoelectronic equipment for monitoring the health & activity of plants and carrying out a series of new fundamental biological researches involving the LIF LIDAR technique as a primary source of information.
Consortium
INOV INESC Inovação - Istituto de Novas Tecnologias
Fundação da Faculdade de Ciências (FFC/FC/UL)
Centro de Oceanografia (CO/FC/UL)
References: Team publications
[T1] A.B. Utkin, A. Lavrov, L. Costa, F. Simões, R. Vilar. Detection of small forest fires by lidar. Appl. Phys. B74, 77-83 (2002).
[T2] A. Lavrov, A.B. Utkin, R. Vilar, A. Fernandes. Application of lidar in ultraviolet, visible and infrared ranges for early forest fire detection. Appl. Phys. B76, 87-95 (2003).
[T3] R.G. Perkins, J. Lavaud, L Serôdio, P. Mouget, P. Cartaxana, R. Rosa, L. Barille, V. Brotas, B.M. Jesus. Vertical cell movement is a primary response of intertidal benthic biofilms to increasing light dose. Marine Ecology Progress Series 416, 93-103 (2010).
[T4] J. Serôdio, P. Cartaxana, H. Coelho, S. Vieira. Effects of chlorophyll fluorescence on the estimation of microphytobenthos biomass using spectral reflectance indices. Remote Sensing of Environment 113, 1760-1768 (2009).
[T5] P. Cartaxana, J. Serôdio. Inhibiting diatom motility: a new tool for the study of the photophysiology of intertidal microphytobenthic biofilms. Limnology and Oceanography Methods 6, 466-476 (2008).
[T6] A.B. Utkin, A. Fernandes, F. Simoes, A. Lavrov, R. Vilar. Feasibility of forest-fire smoke detection using lidar. Int. J. Wildland Fire 12, 159-166 (2003).
[T7] A. Lavrov, A.B. Utkin, R. Vilar, A. Fernandes. Evaluation of smoke dispersion from forest fire plumes using lidar experiments and modelling. International Journal of Thermal Sciences 45, 848-859 (2006).
[T8] A.Fernandes, A.B. Utkin, A. Lavrov, R.Vilar. Optimisation of location and number of lidar apparatuses for early forest fire detection in hilly terrain, Fire Safety Journal 41 (2), 144-154 (2006).
[T9] A.B. Utkin, A. Lavrov, R. Vilar. Laser rangefinder architecture as a cost-effective platform for lidar fire surveillance. Optics & Laser Technology 41, 862-870 (2009).
[T10] A. Lavrov, A.B. Utkin, R. Vilar. Simple eye-safe lidar for cloud height measurement and small forest fire detection. Optics and Spectroscopy 109, 144-150 (2010).
[T11] A.B. Utkin, A. Lavrov, R. Vilar. Fire Surveillance and Evaluation by Means of Lidar Technique. In: Fire Detection. Ed. Roger P. Bennett, Nova Science Publishers: New York, ISBN 978-1-61122-369-9 (eBook) & 978-1-61122-025-4 (hardcover), p. 41-78 (2011).
[T12] R. Vilar, F.S. Simões, J.L.V. Costa, A.B. Utkin, A. Lavrov. Lidar system controlled by computer for smoke identification applied, in particular, to early stage forest fire detection. International Patent WO 03/073128 A1 (04.09.2003).
[T13] A.B. Utkin, A. Lavrov, R. Vilar. Evaluation of oil spills by laser induced fluorescence spectra. Program of International Conference "ICONO/LAT - 2010", 23-27 August 2010, Kazan, Russia, presentation LTuN11.
[T14] A.B. Utkin, A. Lavrov, R. Vilar. Evaluation of oil spills by laser induced fluorescence spectra. Proc. SPIE 7994, 799415, (2011).
[T15] A.B. Utkin, A. Lavrov, R. Vilar. Optical methods for remote water pollution monitoring. Book of Abstracts of the KIMERAA 2nd Transnational Seminar "Competencies and Services in Marine Sciences and Clusters in Atlantic Sea", Faro, Portugal, 4 July 2011, p. 22.
[T16] A.B. Utkin, A. Lavrov, R. Vilar. Evaluation of water pollution by LIF LIDAR. Proc. of 5th EARSeL Workshop on Coastal Zones (a part of the 31st EARSeL Symposium), Prague, Czech Republic, 30 May - 2 June 2011, paper C28-A2589 (2011).
[T17] A.B. Utkin, A.V. Lavrov, R. Vilar, S. Babichenko, S. Shchemelyov, I. Sobolev, L. Bastos, R.A. Deurloo, J. Torres Palenzuela, N.V. Yarovenko, I. Cruz. Optical methods for water pollution monitoring. In: Spatial and Organizational Dynamics: Discussion Papers, Nº 8 (Special Issue on Marine Clusters), ISSN 1647-3188, University of Algarve, Faro, 129-146 (2011).
[T18] S. Vieira, A.B. Utkin, A. Lavrov, N.M. Santos, R. Vilar, J. Marques da Silva, P. Cartaxana. Effects of intertidal microphytobenthos migration on biomass determination via laser-induced fluorescence. Marine Ecology Progress Series 432, 45-52 (2011).
[T19] A. Lavrov, A.B. Utkin, J. Marques da Silva, R. Vilar, N.M. Santos, B. Alves. Water stress assessment of cork oak leaves and maritime pine needles based on LIF spectra. Optics and Spectroscopy 112(2), 271-279 (2012).
[T20] A.B. Utkin, S. Vieira, J. Marques da Silva, A. Lavrov, E. Leite, P. Cartaxana. Compact low-cost detector for in vivo assessment of microphytobenthos using laser induced fluorescence. Optics and Spectroscopy 114(3), 471-477, (2013).
References: Other publications
[1] G.J.C. Underwood, J.Kromkamp. Primary production by phytoplankton and microphytobenthos in estuaries. Adv. Ecol. Res. 29, 93-153 (1999).
[2] J. Serôdio, J. Marques da Silva, F. Catarino. Nondestructive tracing of migratory rhythms of intertidal benthic microalgae using in vivo chlorophyll a fluorescence. J. Phycol. 33, 542-553 (1989).
[3] C. Buschmann. Variability and application of the chlorophyll fluorescence emission ratio red/far-red of leaves. Photosynth. Res. 92, 261-271 (2007).