Leaf dynamics and standing stocks of intertidal Zostera noltii Hornem. and Cymodocea nodosa (Ucria) Ascherson on the Banc d'Arguin (Mauritania)

Leaf dynamics and standing stocks of intertidal seagrasses were studied in the Baie d'Aouatif (Parc National du Banc d'Arguin, Mauritania) in April and September 1988. Standing stocks of Zostera noltii Hornem. suggest a unimodal seasonal curve similar to what is found for populations at higher latitudes. Also, leaf growth rates (0.03 cm² cm^–2 day^–1 on average) were similar to those found at higher latitudes in these months. Variation in leaf loss over tidal depth, time and different locations in the Baie d'Aouatif was larger and more often significant than variation in leaf growth. In general, Z. noltii beds in the Baie d'Aouatif had comparable leaf growth rates and standing stocks. In both months losses were almost always higher than or equal to growth.Variation in leaf loss over time was much higher in the plots that were situated high in the intertidal than in lower plots. This is explained by differences in susceptibility to sloughing, which is presumably higher in periods with low tide around noon for shallow depths.In an experiment using artificial shading nets, in situ leaf growth was affected negatively from 94% shading onwards. This shading was observed to reduce the light intensity reaching the seagrass bed to a level below the reported range of light compensation points for Z. noltii. Cymodocea nodosa (Ucria) Ascherson on average had higher leaf area and relative growth rates than Z. noltii and much lower loss rates, resulting in a positive net increase in September. Standing stocks were also higher than for Z. noltii. A mixed seagrass bed containing the above two species and Halodule wrightii Ascherson had the highest observed total biomass: 335 g m^–2 ash-free dry weight.     

Drivers of Wetland Conversion: a Global Meta-Analysis

Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability), mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors) are also identified as important causes of various types of land change (e.g., deforestation, desertification). Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have determined historic conversions.     

Linking clonal growth patterns and ecophysiology allows the prediction of meadow-scale dynamics of seagrass beds

Seagrasses are a group of 12 genera of monocotyledonous plants in four families that have successfully colonised shallow coastal seas, probably since the Cretaceous. Variations in light availability and water movement are prime environmental factors for the growth of these marine angiosperms. An overall similarity in growth form and modular clonal architecture allows the generalisation that small species have short-lived shoots with rapidly elongating rhizome axes, whilst the larger species have longer-lived shoots that do not expand rapidly with rhizomes. Annual rhizome elongation rates range between 2 cm and 4 m among species. This range in expansion capacity is correlated with rhizome diameter in an allometric fashion (y=191x^?1.5, r²=0.58, p<0.05). Rhizomes with a wider diameter also allow the storage of larger quantities of reserve carbohydrates to be mobilized during the adverse winter season at higher latitudes or for flowering. Repeated branching and the basal positioning of the meristems allow the formation and maintenance of seagrass meadows, and these are a prominent feature creating spatial heterogeneity on the sea floor down to a mean colonisation depth of 15.1±1.3 m (median 8 m, range 0.7–90 m, n=150). Spatial complexity is highest in multi-species seagrass beds, such as those of the Indo-Pacific region and Australia. Seagrass beds function as important coastal filters for nutrients and pollutants and display high carbon sequestration rates. Due to the recalcitrant nature of seagrass detritus, it forms a disproportionally high contribution (12%, but only 1% of productivity) to the carbon stored in ocean sediments. The services provided by these ecosystems to human society range from water quality improvement via nursery and feeding grounds for economically important fish to storm buffering and recreative amenity.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Ecosystem development in different types of littoral enclosures

Macrophyte growth was studied in two enclosure types (gauze and polythene) in a homogeneousPotamogeton pectinatus bed in Lake Veluwe (The Netherlands). The gauze was expected to allow for sufficient exchange with the lake to maintain similar seston densities, the polythene was expected to exclude fish activity and most water exchange. Polythene enclosures held higher totalP. pectinatus biomass (ash-free dry weight, AFDW) than the lake, gauze enclosures were intermediate. The enclosures had a higher abundance of other macrophyte species (Chara sp.,Potamogeton pusillus) than the lake. Seston ash content was not but seston AFDW, periphyton ash content and AFDW were lower in polythene than in gauze enclosures. The difference in plant biomass between gauze and polythene may be attributed to a difference in periphyton density and in seston AFDW due to zooplankton grazing (Rotatoria andDaphnia densities were higher in polythene enclosures). Since seston and periphyton AFDW and ash content were similar in lake and gauze enclosures, the intermediate macrophyte biomass in the gauze enclosures may be explained by reduced wave action and mechanical stress. Alternatively, phytoplankton inhibition by allelopathic excretions from the macrophytes may have caused the high macrophyte biomass in the polythene, and an absence of sediment-disturbing fish the intermediate biomass in the gauze enclosures. Creation of sheltered areas may favour macrophyte growth through both mechanisms and we conclude that this can be an important tool in littoral biomanipulation.     

Why do reed beds decline and fail to re‐establish? A case study of Dutch peat lakes

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Plant Species Composition Can Be Used as a Proxy to Predict Methane Emissions in Peatland Ecosystems After Land-Use Changes

Land-use change in peatlands affects important drivers of CH₄ emission such as groundwater level and nutrient availability. Due to the high spatial and temporal variability of such environmental drivers, it is hard to make good predictions of CH₄ emissions in the context of land-use changes. Here, we used plant species composition as a stable integrator of environmental drivers of CH₄ emissions. We used weighted averaging regression and calibration to make a direct link between plant species composition and CH₄ flux in an effort to predict values of CH₄ emission for a land-use gradient in two extensive peatland sites. Our predicted CH₄ emissions showed good fit with observed values. Additionally, we showed that a quick characterization of vegetation composition, by the dominant species only, provides equally good predictions of CH₄ emissions. The use of mean groundwater level alone for predicting emissions showed the same predictive power as our models. However, water level showed strong variability in time. Furthermore, the inverse relationship between water level and CH₄ emission can lead to higher errors in predictions at sites with higher CH₄ emission. The performance of our model was comparable with those of mechanistic models developed for natural wetland ecosystems. However, such mechanistic models require complex input parameters that are rarely available. We propose the use of plant species composition as a simple and effective alternative for deriving predictions of CH₄ emissions in peatlands in the context of land-use change.     

Periphyton density and shading in relation to tidal depth and fiddler crab activity in intertidal seagrass beds of the Banc d'Arguin (Mauritania)

Periphyton development was studied on microscopic glass slides and leaves of Zostera noltii Hornem. in an intertidal area in the Banc d'Arguin (Mauritania). The effects of shading, tidal depth and grazing activities by the fiddler crab Uca tangeri Eydoux were evaluated. For all experiments, periphyton ash content was high (52–93%) and ash-free dry weight ranged between 0.10–0.63 mg cm^–2. Slides accumulated more periphyton than leaves.Artificial shading (62–99%) for 13 days had no effect on periphyton densities on leaves. Increased tidal depth resulted in higher ash-free dry weight on slides, but in lower ash-free dry weight on leaves. Significant variation along the coastline also existed. The effect of fiddler crabs was studied using exclosures. Presence of fiddler crabs reduced periphyton density on slides, whereas light transmittance was increased. On leaves, no significant fiddler crab effect was found. This difference between leaves and slides was probably caused by a storm at the day before the end of the experiment, and by the higher periphyton density on slides as compared with leaves. As visual inspection during the experiment showed clear differences in appearance of leaves inside and outside the exclosures, the storm probably sloughed off mainly the older leaves, i.e. those on which the differences in periphyton cover were the highest.It is hypothesized that periphyton accumulation is higher with increased tidal depth, whereas fiddler crab grazing pressure also increases in this direction. The result is a decreased periphyton density with increased tidal depth.The presently found light extinction coefficients (mean 0.8 m^–1) and periphyton light attenuance (up to 25%) in Banc d'Arguin are not likely to affect seagrass leaf growth.     

Covariance in water- and nutrient budgets of Dutch peat polders: what governs nutrient retention?

Water and nutrient budgets were constructed for 13 low-lying peat polders in the Netherlands that varied in elevation relative to sea level (?0.2 to ?2.4 m below sea level), land use (7–70% of the total polder area covered by agriculture; largely dairy farming), and surface water prevalence (6–43%). Water balances were verified with chloride budgets and accepted when both met the criterion (total inflows ? total outflows)/(total inflows) <0.05. Apart from precipitation and evapotranspiration (overall means 913 vs. 600 mm), in- and outlet (171 vs. 420 mm) as well as in- and outward seepage (137 vs. 174 mm) were important items in the water budgets. Nutrient budgets, however, were dominated by terms related to agricultural land use (~60% of all inputs, 90% of N-removal and 80% of P removal) rather than water fluxes (8% and 5% of N and P inputs; 6 and 18% of outputs). After agriculture (200 kg N ha^?1 y^?1), mineralisation of the peat soil and atmospheric deposition appear to be important inputs (about 94 and 21 kg N ha^?1 y^?1). Major output terms were agricultural output (209 kg N ha^?1 y^?1) and denitrification (95 kg N ha^?1 y^?1). The average N budget was in balance (difference ~1 kg N ha^?1 y^?1), whereas P accumulated in most polders, particularly those under agriculture. The mean P surplus (15 kg P ha^?1 y^?1 in the 9 mainly agricultural polders) corresponds well with the accumulated difference observed elsewhere (700 kg P ha^?1 in the upper 50 cm in a nature reserve versus 1400 under agriculture) after over 50 years of dairy farming. Bulk retention of N and P in these polders is taking place in the peat soil, through temporary sorption to the matrix and N is lost through denitrification. In a principal components analysis combining land use, landscape pattern, water balance and nutrient budget terms, the three-first principal components explained 63% of the variability. The first component (PC) correlated strongly with the percentage of land under agriculture (r = 0.82) and negatively with the percentage covered by surface water (r = ?0.74). Most input and output terms of the nitrogen budget also correlated with this PC. The second PC covaried distinctly with the total area of a polder (r = ?0.79) and human population density at municipality level (r = 0.75). Phosphorus loads in inlet and outlet water correlated with this PC. This suggests that the variability in nutrient budgets among polders is largely governed by agricultural land use.