ISSN 1239-6095 (print),   ISSN 1797-2469 (online)
© Boreal Environment Research 2011

Contents of Volume 16 Supplement A

Preface. Boreal Env. Res. 16 (suppl. A): 1–2.
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Olli, K., Klais, R., Tamminen, T., Ptacnik, R. & Andersen, T. 2011: Long term changes in the Baltic Sea phytoplankton community. Boreal Env. Res. 16 (suppl. A): 3–14.
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Laanemets, J., Väli, G., Zhurbas, V., Elken, J., Lips, I. & Lips, U. 2011: Simulation of mesoscale structures and nutrient transport during summer upwelling events in the Gulf of Finland in 2006. Boreal Env. Res. 16 (suppl. A): 15–26.
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Kowalewski, M. & Kowalewska-Kalkowska, H. 2011: Performance of operationally calculated hydrodynamic forecasts during storm surges in the Pomeranian Bay and the Szczecin Lagoon. Boreal Env. Res. 16 (suppl. A): 27–41.
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Sipelgas, L. 2011: Monitoring the concentration, distribution, origin and size of suspended particles in the water column during harbour dredging in Pakri Bay, the Gulf of Finland. Boreal Env. Res. 16 (suppl. A): 42–48.
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Soomere, T., Delpeche, N., Viikmäe, B., Quak, E., Meier, H. E. M. & Döös, K. 2011: Patterns of current-induced transport in the surface layer of the Gulf of Finland. Boreal Env. Res. 16 (suppl. A): 49–63.
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Kotta, J., Orav-Kotta, H., Herkül, K. & Kotta, I. 2011: Habitat choice of the invasive Gammarus tigrinus and the native Gammarus salinus indicates weak interspecific competition. Boreal Env. Res. 16 (suppl. A): 64–72.
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Liblik, T. & Lips, U. 2011: Characteristics and variability of the vertical thermohaline structure in the Gulf of Finland in summer. Boreal Env. Res. 16 (suppl. A): 73–83.
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Elken, J., Nõmm, M. & Lagemaa, P. 2011: Circulation patterns in the Gulf of Finland derived from the EOF analysis of model results. Boreal Env. Res. 16 (suppl. A): 84–102.
Abstract
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Lilover, M.-J. & Stips, A. K. 2011: An alternative parameterization of eddy diffusivity in the Gulf of Finland based on the kinetic energy of high frequency internal wave band. Boreal Env. Res. 16 (suppl. A): 103–116.
Abstract
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Ryabchuk, D., Kolesov, A., Chubarenko, B., Spiridonov, M., Kurennoy, D. & Soomere, T. 2011: Coastal erosion processes in the eastern Gulf of Finland and their links with geological and hydrometeorological factors. Boreal Env. Res. 16 (suppl. A): 117–137.
Abstract
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Didenkulova, I. 2011: Shapes of freak waves in the coastal zone of the Baltic Sea (Tallinn Bay). Boreal Env. Res. 16 (suppl. A): 138–148.
Abstract
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Erm, A., Alari, V., Lips, I. & Kask, J. 2011: Resuspension of sediment in a semi-sheltered bay due to wind waves and fast ferry wakes. Boreal Env. Res. 16 (suppl. A): 149–163.
Abstract
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Lilover, M.-J., Pavelson, J. & Kõuts, T. 2011: Wind forced currents over the shallow Naissaar Bank in the Gulf of Finland. Boreal Env. Res. 16 (suppl. A): 164–174.
Abstract
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Soomere, T., Zaitseva-Pärnaste, I. & Räämet, A. 2011: Variations in wave conditions in Estonian coastal waters from weekly to decadal scales. Boreal Env. Res. 16 (suppl. A): 175–190.
Abstract
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Jaanus, A., Andersson, A., Olenina, I., Toming, K. & Kaljurand, K. 2011: Changes in phytoplankton communities along a north–south gradient in the Baltic Sea between 1990 and 2008. Boreal Env. Res. 16 (suppl. A): 191–208.
Abstract
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Herkül, K., Kotta, J. & Pärnoja, M. 2011: Effect of physical disturbance on the soft sediment benthic macrophyte and invertebrate community in the northern Baltic Sea. Boreal Env. Res. 16 (suppl. A): 209–219.
Abstract
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Kelpšaitė, L., Dailidienė, I. & Soomere, T. 2011: Changes in wave dynamics at the south-eastern coast of the Baltic Proper during 1993–2008. Boreal Env. Res. 16 (suppl. A): 220–232.
Abstract
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Olli, K., Klais, R., Tamminen, T., Ptacnik, R. & Andersen, T. 2011: Long term changes in the Baltic Sea phytoplankton community. Boreal Env. Res. 16 (suppl. A): 3–14.

During the last four decades the Baltic Sea phytoplankton went through a significant and gradual change in community composition. An analysis of several thousand quantitative samples from 1966 to 2008 reveals significant changes in the phytoplankton summer community in most parts of the Baltic Sea. By using community gradient analysis methods (NMDS, DCA), we found a strong correspondence between sample ordination scores and sampling year (R2 > 0.5). The association was stronger when the samples were geographically more confined and the temporal range sufficiently large (R2 > 0.8). Only in the southern Baltic Sea and the Kattegat had the salinity gradient stronger associations with the phytoplankton community composition as compared with the time effect over four decades. Eutrophication-related parameters (total and mineral nutrients) revealed low association with the phytoplankton community composition in all Baltic Sea sub-basins (R2 < 0.2). Also, known eutrophication gradients in the Baltic Sea had low association with phytoplankton community. The phytoplankton community in the Baltic Sea is not in a steady state or equilibrium, and is not the same today as it was decades ago.
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Laanemets, J., Väli, G., Zhurbas, V., Elken, J., Lips, I. & Lips, U. 2011: Simulation of mesoscale structures and nutrient transport during summer upwelling events in the Gulf of Finland in 2006. Boreal Env. Res. 16 (suppl. A): 15–26.

A high resolution numerical study was carried out to simulate a series of upwelling events and related nutrient transport in the Gulf of Finland. In order to characterize the intensity of water motions of different nature in the surface layer, simulated velocity components were decomposed into mesoscale fluctuations, inertial oscillations and mean currents. Mean currents contained 14%, inertial oscillations 20% and mesoscale fluctuations 66% of the total kinetic energy. High values of kinetic energy of mesoscale fluctuations were in the coastal zones (up to 0.03 m2 s–2) due to along-shore baroclinic upwelling/downwelling jets and in the narrowest western-central part (0.01–0.02 m2 s–2) of the Gulf, where intensive squirts and eddies were formed. In this region also the most intensive coastal offshore exchange of upwelled nutrients occurred. The total content of phosphorus and nitrogen in the upper 10-m layer introduced by the upwelling events was estimated at 1100 tonnes, with a clear excess of phosphorus.
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Kowalewski, M. & Kowalewska-Kalkowska, H. 2011: Performance of operationally calculated hydrodynamic forecasts during storm surges in the Pomeranian Bay and the Szczecin Lagoon. Boreal Env. Res. 16 (suppl. A): 27–41.

The modified hydrodynamic model of the Baltic Sea, developed at the Institute of Oceanography, University of Gdańsk was validated using storm-related sea level fluctuations as well as water temperature and salinity variations in the Pomeranian Bay and the Szczecin Lagoon (southern Baltic). The high resolution (about 300 m) applied to the model for the Szczecin Lagoon area resulted in a much better description of the area's bathymetry, and in an improved fit between the modelled and the observed distributions of the data sets both in the Bay and in the Lagoon. Model quality tests involving 2002–2007 storm surge events showed a better representation of events characterised by rapid water level fluctuations and fast changes of physical water properties. The numerical model's high quality of simulations allows for applying the higher resolution of spatial spacing to the Szczecin Lagoon area also in the operational version of the model.
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Sipelgas, L. 2011: Monitoring the concentration, distribution, origin and size of suspended particles in the water column during harbour dredging in Pakri Bay, the Gulf of Finland. Boreal Env. Res. 16 (suppl. A): 42–48.

Dredging activities can influence ecological balance in the vicinity of developing ports. In the current study, monitoring of suspended matter load in the water column during dredging operations was performed using WetLabs AC-spectra instrument which allows for direct measurements of absorption and attenuation coefficients. The corresponding spectral scattering coefficients were calculated and used for the description of the concentration and composition of suspended matter. Also, concentrations of suspended matter (SPM) and chlorophyll a (Chl a) were determined from the water samples. The analysis showed that the particles were mainly of mineral origin in the south-eastern part of the bay near the harbour dredging area and mainly of organic origin in the central and open part of the bay. The current study also showed that the calculation of the Chl-a concentration from the absorption coefficient using the empirical regression method can sometimes produce questionable results.
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Soomere, T., Delpeche, N., Viikmäe, B., Quak, E., Meier, H. E. M. & Döös, K. 2011: Patterns of current-induced transport in the surface layer of the Gulf of Finland. Boreal Env. Res. 16 (suppl. A): 49–63.

The Lagrangian trajectory model TRACMASS based on an Eulerian field of velocities (calculated using the Rossby Centre Ocean Model), combined with relevant statistical analysis, is used for the identification of transport patterns in the surface layer of the Gulf of Finland from 1987–1991. The analysis of velocity fields and properties of net and bulk transport (the distance between the start and end positions of a trajectory, and the total length of the trajectory, respectively) shows the presence of semi-persistent (with a typical lifetime from a week to a few months) features of the surface-layer dynamics, a part of which evidently cannot be extracted directly from the velocity fields. The modelled surface dynamics mostly hosts an Ekman-type drift and, in yearly average, contains an anticyclonic gyre occupying the western part of the gulf. The prevailing transport directions to the east and slightly to the south match the direction of the Ekman surface drift created by predominant south-western winds. The spatial patterns of the net transport substantially vary over different seasons. The most intense net transport along the coasts occurs in the western and central parts of the gulf but contains relatively intense largely meridional transport pathways in some seasons.
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Kotta, J., Orav-Kotta, H., Herkül, K. & Kotta, I. 2011: Habitat choice of the invasive Gammarus tigrinus and the native Gammarus salinus indicates weak interspecific competition. Boreal Env. Res. 16 (suppl. A): 64–72.

Following the establishment of the invasive gammarid amphipod Gammarus tigrinus the native gammarids almost disappeared from some habitats of the northeastern Baltic Sea. The aims of the current work were to experimentally study whether the habitat choice of G. tigrinus and G. salinus was similar and whether G. tigrinus modified the habitat selection of G. salinus, providing thus evidence that competition for space between the two species might explain the disappearance of the native gammarids from the study area. In general, the gammarid amphipods had a significant overlap in habitat selection. Gammarids modified the habitat choices of co-occurring species but impacts were disproportional among species. The effects of G. tigrinus on G. salinus were stronger than vice versa. However, the effects varied among months, and the negative responses were not observed in all habitats. Thus, competition for space alone cannot explain the mass disappearance of the native G. salinus.
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Liblik, T. & Lips, U. 2011: Characteristics and variability of the vertical thermohaline structure in the Gulf of Finland in summer. Boreal Env. Res. 16 (suppl. A): 73–83.

Vertical profiles of temperature and salinity collected in the summers of 1987–2008 were analyzed in order to describe the mean characteristics and variability of the vertical termohaline structure in the Gulf of Finland. Quantitative estimates of the mean characteristics of the upper mixed layer, seasonal thermocline, cold intermediate layer, halocline and deep layer as well as their along-gulf changes were obtained. Both the long-term (inter-annual) and short term variations in the thermohaline structure were related to the changes in the atmospheric forcing. Two distinct periods with statistically different mean temperature and salinity in the deep layer were detected among the analyzed 22 years. The overall vertical salinity (and density) gradient was much stronger and the halocline was sharper in the recent years than in the years 1987–1990. However, the summer mean vertical salinity and density gradients in the seasonal thermocline did not reveal large inter-annual variations. We suggest that a possible shift towards fresher waters in the Baltic Sea due to the climate change would result in the two-layer structure of water column in the deeper areas of the Gulf of Finland in summer. At the same time, a possible increase of sea surface temperature could lead to a strengthening of the vertical density stratification in the seasonal thermocline.
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Elken, J., Nõmm, M. & Lagemaa, P. 2011: Circulation patterns in the Gulf of Finland derived from the EOF analysis of model results. Boreal Env. Res. 16 (suppl. A): 84–102.

For the Gulf of Finland, we carried out the EOF (empirical orthogonal functions) analysis of hourly forecasts from the Baltic Sea operational HIROMB-SMHI model for the period 2006–2008. It is possible to distinguish two regions with a specific regime of circulation variability. The western region behaves like a wide channel. Dominant EOF modes at different sections have similar patterns and their time-dependent amplitudes are well correlated. A prevailing mode of currents (23%–42% of the variance) is barotropic (unidirectional over the whole section) and its oscillation (spectral peak at 24 h) is related to the water storage variation of the Gulf. A two-layer flow pattern (surface Ekman transport with deeper compensation flow, 19%–22%) reveals both inertial and lower frequencies. Highest outflow of surface waters occurs during north-easterly winds. The eastern wider region has more complex flow dynamics and only patterns that are nearly uniform over the whole Gulf were detected here. On the sea surface, quasi-uniform drift currents are deflected on the average by 40° to the right from the wind direction and they cover 60% of the circulation variance. Sea level variability is heavily (98%) dominated by nearly uniform changes which are caused by the water storage variations of the Gulf. Sea level gradients contain the main axis (23%) and transverse (17%) components, forced by winds of the same direction. The flows below the surface are decomposed also into the main axis (24%–40%) and transverse (13%–16%) components that are correlated with the sea level gradients according to the geostrophic relations.
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Lilover, M.-J. & Stips, A. K. 2011: An alternative parameterization of eddy diffusivity in the Gulf of Finland based on the kinetic energy of high frequency internal wave band. Boreal Env. Res. 16 (suppl. A): 103–116.

In July 1998, three time series of shear microstructure measurements (duration 13, 24 and 14 h, respectively) were performed in 3 different wind-forcing regimes as well as in 3 different background density stratification and current velocity shear situations at the entrance to the Gulf of Finland. We compared the "measured" eddy diffusivities with the diffusivities parameterized using the Richardson number, the Brunt-Väisälä frequency and with the diffusivities simulated using the two-equation k-ε turbulence closure. Summing up the discrepancy of all three time series, the methods applied resulted in a remarkable and consistent bias against the measured eddy diffusivity. Contrary to this result, the calculations with the new suggested parameterization scheme, which accounts for the internal wave kinetic energy of the super-inertial frequency band, fitted well for all three time series. Similarly, the modified k-ε simulations accounting for the super-inertial internal wave energy matched better the measured profiles.
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Ryabchuk, D., Kolesov, A., Chubarenko, B., Spiridonov, M., Kurennoy, D. & Soomere, T. 2011: Coastal erosion processes in the eastern Gulf of Finland and their links with geological and hydrometeorological factors. Boreal Env. Res. 16 (suppl. A): 117–137.

Potential reasons for the drastic intensification and step-like nature of coastal erosion in the Neva Bay area (to the east of the cape Peschany–Lebyazhye line), the easternmost part of the Gulf of Finland, are analysed based on field observations and hydrometeorogical data from adjacent areas. Beaches in this area consist of easily erodible Quaternary deposits that evolve under overall sediment deficit and are relatively vulnerable with respect to changes in the external forcing factors. It is demonstrated that the most extreme erosion events occur when high waves excited by long-lasting western or south-western storms attack the coast during very high storm surges in the absence of stable sea ice. Since 2004 the frequency of occurrence of such combinations has increased mostly owing to, late freezing of the bay and an increase in the number and severity of extreme erosion events in the future is likely. The coasts are also under gradually increasing anthropogenic pressure. Submarine mining operations in the nearshore and construction of large-scale coastal engineering structures such as the Flood Protection Facility may have considerable impact upon the coasts.
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Didenkulova, I. 2011: Shapes of freak waves in the coastal zone of the Baltic Sea (Tallinn Bay). Boreal Env. Res. 16 (suppl. A): 138–148.

The properties of extreme sea surface waves (freak waves) in shallow water and, particularly, their shape are analysed based on the high-resolution records of sea surface elevation in Tallinn Bay, the Baltic Sea, measured at the water depth 2.7 m from 21 June to 20 July 2008. The data set contains 97 freak waves, which occur in both calm and relatively rough weather conditions. It is shown that typical shapes of freak waves in the nearshore differ from those which are known for the deep sea. No groups of subsequent extreme waves, like the famous "three sisters" usually reported by eyewitnesses and measured instrumentally in the open sea, are found for the coastal zone. All freak waves in the records are single waves: 63% of them have positive, 19.5% sign-variable and 17.5% negative shape. It is shown that both the frequency of occurrence and the wave height of positive freak waves are correlated with the significant wave height. The height of sign-variable freak waves, which are observed only in relatively calm weather conditions, also changes in accordance with the significant wave height, while the height of negative freak waves shows no explicit dependence on the background wave height. It is found that 90% of all recorded freak waves have the height in the range from 2.0 to 2.3 times the significant wave height. About 10% of freak waves with the largest amplification (from 2.3 to 3.2 times the significant wave height) have a negative shape and their amplification factor decreases with an increase in the significant wave height.
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Erm, A., Alari, V., Lips, I. & Kask, J. 2011: Resuspension of sediment in a semi-sheltered bay due to wind waves and fast ferry wakes. Boreal Env. Res. 16 (suppl. A): 149–163.

Concurrently with the wind wave induced sediment recycling, large sections of the coast of Tallinn Bay are influenced by wakes generated by high speed vessels. Based on in situ measurements of surface waves, underwater irradiance and the fluxes of resuspended sediment, combined with counting of particles with FlowCAM and numerical modeling of wind waves, it is shown, that the anthropogenic resuspension plays a key role in the western part of Tallinn Bay during the relatively calm spring and summer seasons. The near bottom orbital velocities generated daily by fast ferries’ wakes are equivalent to those induced by wind waves excited by at least 18 m s–1 southwestern winds and 12 m s–1 northern winds. About 400 kg of sediment is resuspended and carried away from each meter of coastline annually.
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Lilover, M.-J., Pavelson, J. & Kõuts, T. 2011: Wind forced currents over the shallow Naissaar Bank in the Gulf of Finland. Boreal Env. Res. 16 (suppl. A): 164–174.

We performed current velocity observations on Naissaar Bank in northern Tallinn Bay, Gulf of Finland, for five weeks in late autumn 2008 using a bottom-mounted ADCP deployed at 8 m depth. Strong and variable, mainly southerly winds with speeds exceeding 10 m s–1 dominated in the area during 60% of the whole period. Bursts of seiche-driven currents with periods of 31, 24, 19.5, 16 and 11 h were observed after the passage of wind fronts. Inertial oscillations and diurnal tidal currents were relatively weak. The low-frequency current velocities gradually decreased toward the bottom at 3 cm s–1 over 4-m distance. The magnitude of the complex correlation coefficient between the current and wind for the whole series was 0.69, but it was much higher (up to 0.90) within the shorter steady wind periods. The current was rotated ~35° to the right from the wind. As an exception, during one period a counterclockwise surface-to-bottom veering of the current vector was observed. A topographically steered flow was seen either along isobaths of the bank during strong winds or along the ‘channel’ at the entrance to Tallinn Bay.
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Soomere, T., Zaitseva-Pärnaste, I. & Räämet, A. 2011: Variations in wave conditions in Estonian coastal waters from weekly to decadal scales. Boreal Env. Res. 16 (suppl. A): 175–190.

Historical visual observations and numerical hindcasts with the use of the WAM wave model and adjusted geostrophic winds are merged to reveal the basic features of the wave properties and to identify the variations in wave height in different scales in the coastal waters of Estonia. The visually observed wave properties from Vilsandi (1954–2008), Pakri (1954–1985) and Narva-Jõesuu (1954–2008) are compared against wave data hindcast for the entire Baltic Sea for 1970–2007. It is shown that the wave height follows the seasonal variation in wind speed with a maximum in October–January and with a substantial variability on weekly scales. The annual mean wave heights reveal nearly synchronous interannual variations along the entire coast of Estonia until the mid-1980s after which this coherence is lost. The length of the ice season is almost uncorrelated with the annual mean wave heights.
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Jaanus, A., Andersson, A., Olenina, I., Toming, K. & Kaljurand, K. 2011: Changes in phytoplankton communities along a north–south gradient in the Baltic Sea between 1990 and 2008. Boreal Env. Res. 16 (suppl. A): 191–208.

Evaluation of changes in Baltic Sea phytoplankton communities has been hampered by a lack of quantitative long-term data. We investigated changes in biomass of summer (June–September) phytoplankton over the last two decades (1990–2008) along a north–south gradient in the Baltic Sea. The areas were characterized by different temperature, salinity and nutrient conditions. Thirty taxonomic groups were selected for the statistical analysis. Increases in total phytoplankton, particularly cyanobacterial, biomass were observed in the Gulfs of Bothnia and Finland. In these two areas over the study period cyanobacteria also became abundant earlier in the season, and in the Curonian Lagoon Planktothrix agardhii replaced Aphanizomenon flos-aquae as the most abundant cyanobacterium. In general, water temperature was the most influential factor affecting the summer phytoplankton communities. Our data suggest that temperature increases resulting from climate change are likely to cause basin-specific changes in the phytoplankton communities, which in turn may affect overall ecosystem functioning in the Baltic Sea.
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Herkül, K., Kotta, J. & Pärnoja, M. 2011: Effect of physical disturbance on the soft sediment benthic macrophyte and invertebrate community in the northern Baltic Sea. Boreal Env. Res. 16 (suppl. A): 209–219.

Strong storms and ice scour are the most severe physical disturbances in the shallow water areas of the northern Baltic Sea. We studied experimentally the effects a physical disturbance — such as the removal of the surface sediment layer, vegetation, and benthic invertebrates and the timing of this disturbance (spring, summer) — had on the development of soft bottom macrophyte and invertebrate communities in a shallow bay. Disturbance had an immediate effect on the community in spring but not in summer. The lack of significant immediate effects in summer was attributed to a drifting algal mat that quickly introduced most of the local species to the newly established experimental plots. The springtime disturbance reduced the species richness and total biomass of phytobenthos in summer; the effect, however, was not detectable by autumn. Disturbance in spring decreased the total abundance and biomass of zoobenthos in autumn but not in summer. A summertime disturbance had no effect on the autumn benthic communities.
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Kelpšaitė, L., Dailidienė, I. & Soomere, T. 2011: Changes in wave dynamics at the south-eastern coast of the Baltic Proper during 1993–2008. Boreal Env. Res. 16 (suppl. A): 220–232.

Using data gathered by visual wave observations at three Lithuanian coastal observation sites during 1993–2008, we make an attempt to relate the recent changes in the intensity of coastal processes on the Lithuanian coast to changes in the local wave regime. There exist considerable interannual variations in the overall wave activity but no statistically significant trends in wave heights for the study period. The directional distribution of wave approach directions has become considerably narrower since about 2002. This feature is most prominent at Palanga where since 2002 almost all waves have approached from SW. This change apparently leads to a decrease in the sediment supply to the Curonian Spit and to a certain starvation of the Lithuanian coast.
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