Meeting the challenge of scaling up processes in the plant–soil–microbe system

The scaling up of processes in the plant–soil–microbe system represents one of the greatest challenges facing environmental scientists and yet is essential for sustainable land management worldwide. The latter encompasses, for example, the mitigation of and adaptation to anthropogenic climate change, the bioremediation of industrially contaminated sites, catchment management of human pathogens such as Escherichia coli O157 and integrated crop management on the farm. Scaling up is also essential for the regional and global biogeochemical modelling that will inform policy-makers of the critical environmental factors driving climate change. Despite increasing understanding of the links between gene expression and process on a microscale, there is still much progress to be made when relating this to processes at the macroscale. In this paper, we explore the challenges this poses and examine key case studies of successful up-scaling.

The use of Kohonen neural networks for runoff–erosion modeling

Purpose

We investigated the application of Kohonen Neural Networks (KNNs) in order to estimate sediment yield based on runoff and climatological data in a semiarid region of Brazil. Accurate estimations of sediment yield are essential to improve the management of soil erosion in semiarid areas, where large quantities of sediments tend to be produced only periodically.

Materials and methods

The case study is an erosion plot within the São João do Cariri Experimental Basin, which is located in the semiarid portion of Paraíba State, Brazil. KNNs are unsupervised neural networks capable of reducing a multidimensional data set to a bidimensional matrix of features, which can be used for analysis and prediction purposes. A total of 60 rainfall events, which occurred between 1999 and 2002, were used to calibrate and test the model. The application of a multivariate linear regression (MLR) model was also carried out.

Results and discussion

Statistical indexes were used as criteria for evaluating the performance of the KNN and MLR models for the test data set. The correlation and relative bias of the KNN model estimations with those from observed data were 0.90 and ?4.39 %, respectively. A correlation of 0.70 and a relative bias of 15.63 % were found from the comparison of sediment yields obtained by the MLR model with those of the observed data. Analysis of the outcomes indicates that the KNN model, which is capable of detecting and extracting nonlinear trends, produced more reliable results than the regression model.

Conclusions

The KNN model results appear to be superior to those generated by the MLR model and suggest that the developed methodology may be applied to similar case studies.     

Environmental degradation in karst areas of Cambodia: A legacy of war?

Karst areas in Kampot Province, southwest Cambodia, have suffered relatively recent soil erosion and partial infilling of caves by the eroded sediment. This soil loss is most pronounced in localities that have been a focus of human activity, such as along pedestrian and vehicular access routes and in areas subject to vegetation clearing and agricultural activity, but it also occurs more widely across the hillslopes. In comparable karst environments elsewhere in Cambodia and neighbouring countries erosion is similarly evident in areas that have been subject to intensive human use, but in contrast to Kampot it is absent from the broader landscape. The soil degradation in the Kampot karst seems to require disturbance of the natural vegetation cover which stabilizes the soil cover in the other karsts, probably during the latter half of the 20th century. No major changes in deliberate land‐use at the study sites that might have triggered this erosion have been identified. However, this part of Cambodia was subject to heavy aerial bombardment between 1965 and 1973, and the karst hills and their caves were a particular focus of military activity. This bombing in turn facilitated ascent of the genocidal Khmer Rouge regime which drove virtually the entire population into a subsistence rural existence, and then further armed conflict prior to that regime's overthrow, both of which are likely to have generated additional environmental damage. Copyright © 2010 John Wiley & Sons, Ltd.     

Assessment of long-term barley–legume rotations in a typical Mediterranean agro-ecosystem: grain and straw yields

Traditional Mediterranean rainfed cereal/fallow systems are being replaced by cereal monoculture due to land-use pressure. Food or forage legumes in rotation with cereals are an alternative sustainable cropping system. Complex cropping systems can only be assessed by long-term trials. This 11-year rainfed barley-based rotation trial in northern Syria assessed rotation effects on yields of barley and legumes, with particular emphasis on the management of vetch. The mean order of barley grain yields from the rotations was: vetch for hay, vetch for grazing > fallow = medic = vetch for seed > lentil, and continuous barley. Straw yields followed a similar pattern. Nitrogen (60 kg ha^?1) increased grain (39%) and straw (65%) yields. The N fertilization of barley had no carryover effect on the alternative legume crops. Although there were no significant differences in seed or straw yield between lentil and vetch, seasonal rainfall influenced overall yields. Total biomass yields were in the order of vetch, medic and lentil. There is a compelling case for annual vetch paired with barley in rotations for the Mediterranean region. Thus, barley/vetch rotations can potentially enhance barley yields and improve soil quality, and provide valuable fodder for small ruminants as well in the region's agricultural systems.     

Influence of Salinity in the Bioavailability of Zn in Sediments of the Gulf of Cádiz (Spain)

This study assesses the effect of salinity in bioavailability and toxicity of Zn by means of laboratory bioassays by observing contamination in both sediment and water, accumulation of Zn in biological tissues, and histopathological damage in the gills and guts tissues of Ruditapes philippinarum clams, which were exposed to different types of sediments from the Gulf of Cádiz (SW Spain) as well as two dilutions of toxic mud coming from an accidental mining spill. With this objective, the coefficients of distribution (K _D) for Zn between overlying water and sediments were calculated, the histopathological frequencies in the tissues of the gills and guts of clams were determined, and the biota-sediment bioaccumulation factors as well as the bioaccumulation factors were quantified in the different stations. Results showed that the greatest histopathological damages appeared when the salinity values decreased. Statistical results showed that salinity was inversely correlated with histopathological damage (p?<?0.01) for the lesion index for gills. The most outstanding results were observed in the two dilutions of toxic mud (0.3% and 7.9%) at a salinity value of 10. Salinity was inversely correlated with the concentration of Zn in biological tissues (p?<?0.05) and inversely correlated with the concentration of Zn in water and sediment. Zn mobilization to the overlying water is produced when salinity values decrease.     

Lead, Zinc, Arsenic and Copper Pollution in the Alluvial Plain of a Mining Wadi: The Beal Case (Cartagena–La Union Mining District, SE Spain)

The distribution and mobility of heavy metals in the non-saturated zone of the alluvial plain of a wadi in the Cartagena–La Union mining district was investigated. The elemental chemistry of soils, in-depth sediments and different plant species (namely Hirsfeldia incana, Ditrichia viscosa and Piptatherum miliaceum) was carried out by using X-ray fluorescence and X-ray diffraction techniques. Potential mobility of metals was assessed by using lixiviation test runs (DIN 38414-S4). Concentrations detected in soils and sediments were higher than the acceptable limits reported in official regulations. Regarding metals mobility, values obtained for Pb, Zn and As exceed the limits established by European Union for DIN 38414-S4 leachates. Whilst the obtained leaching percentages for Pb, Cu and As were not especially high (<2%), Zn exhibit a very high leaching potential (up to 60% of the total metal content), involving potential risk of pollution events.     

The impact of vegetation and soil on runoff regulation in headwater streams on the east Qinghai–Tibet Plateau,China

Vegetation type is one of many factors that affect watershed hydrology and is an especially important influence on surface hydrological processes. Canopy and ground cover vegetation provide a natural cushion against the impact energy of rainfall in headwater portions of a stream basin, increasing water filtration into the soil and reducing surface runoff, but effects of different vegetation types are not fully understood. We sought to evaluate the capacity of different vegetation communities to regulate surface runoff in an alpine landscape. We collected water samples for stable hydrogen and oxygen isotopic analyses from precipitation, throughfall, soils, streams, and rivers and compared their isotopic signatures. Results indicated that different vegetation types had different capacities for water conservation. Forested vegetation types were best able to regulate surface runoff. Land use changes have dramatically affected water conservation in the study area in the past several decades; if forested land cover existed at the levels present in 1986 or 1974, the ability of the watershed to intercept surface runoff would increase by about 7% and 3%, respectively, over its capacity in 2000.     

Isoelectric focusing of β-glucosidase humic-bound activity in semi-arid Mediterranean soils under management practices

Changes in β-glucosidase enzyme–humic complexes and conventional parameters (pH, total organic C, total N, water-soluble C, and bulk density) were studied in an almond-cropped soil prone to erosion under a rehabilitation practice. The experimental plan included three soil slopes (0%, 2%, and 6%) and two type of fertilization (organic and mineral), with sampling of rhizosphere and inter-row soils. The enzyme humic complexes were extracted by pyrophosphate, purified by ultrafiltration of the organic extracts on molecular mass exclusion membranes (mol wt > 10⁴) and fractionated by isoelectric focusing technique (IEF). The IEF on polyacrylamide rod gels with a restricted pH gradient ranging between 6.0 and 4.0 gave five humic bands on the basis of the little differences of their electric charges (pI). Under both organic and mineral fertilization, β-glucosidase activity bound to the fractionated humic substances, especially in the pH range 4.5–4.2 of the rhizosphere soil, was higher than that of the inter-row soil. This also occurred in 6% slope where the enzyme activity was lower than in soil with lower slopes. The higher number of the β-glucosidase active humic bands in rhizosphere than inter-row soil, particularly for the 0% slope, may be due to the presence of humic molecules capable of preserving the enzyme molecules in the active form, other than to the higher microbial activity synthesizing and releasing the tested enzymes.     

Distribution of Metals in Vadose Zone of the Alluvial Plain in a Mining Creek Inferred from Geochemical, Mineralogical and Geophysical Studies: The Beal Wadi Case (Cartagena�CLa Union Mining District, SE Spain)

The assessment of metals dispersal in polluted mining areas is a very complex issue, usually needing data from several analytical techniques in a joint approach. The present work focuses on the impact of the mining activity on lowlands alluvial plain sediments from an ephemeral creek, their role as source or sink of pollution and the spatial distribution of metals within the zone. In-depth distribution of elements (As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, S, Ti and Zn) coming from mining activities was investigated by using X-ray fluorescence techniques and their mineralogical form using X-ray diffraction. A 2-D electrical resistance tomography field survey was carried out throughout at the creek bed to interpret the potential relationships between chemical, mineralogical and geophysical parameters. The application of leaching procedure (DIN 38414-S4 test) allows us to know the sediment??s heavy metals hazard and their potential mobility when changing redox conditions. From the results it was found that redox process of sulphur and the presence of carbonate influence the distribution of metals along the profile. In the present work, the precipitation of carbonates seems the most important process, especially for elements such as Zn and Mn. Secondary precipitation of sulphides enables the trapping of metals at sulphur-rich levels.     

Calibration of Hargreaves–Samani and Priestley–Taylor equations in estimating reference evapotranspiration in the Northwest of Iran

Accurate estimation of reference evapotranspiration (ET_o) is essential for water resources management and irrigation systems scheduling, especially in arid and semiarid regions such as Iran. In the present research, constant coefficients of Hargreaves–Samani (C_H–S) and Priestley–Taylor (C_P–T) equations were locally calibrated to estimate the ET_o based on the FAO–Penmen–Monteith (PM) method as standard method. For this purpose, meteorological data of eight synoptic stations located in the northwest of Iran were used during the period of 1997–2008. The outcomes showed that the values of C_H–S and C_P–T were 0.0026 (instead of 0.0023) and 1.68 (instead of 1.26), respectively. Also, at stations with high wind speed, the values of calibrated coefficients of C_H–S and C_P–T were maximum. Then, the estimated ET_o values using adjusted C_H–S and C_P–T coefficients were compared to the obtained actual ET_o values by PM method using root mean square error and mean bias error indices. The results indicated that the new calibrated H–S and P–T equations have good agreement with the PM method for estimation of the ET_o. Moreover, the equation of Ravazzani et al. was calibrated in the studied region. It was concluded that in general, the mentioned equation was shown better performance than original H–S equation.     

Do boundaries of soil animal and plant communities coincide? A case study of a Mediterranean forest in Russia

We studied the relationship between plant and soil animal communities by geostatistical analysis in a piedmont forest close to Novorossiysk (Southern Russia). Vegetation on the slope of a hill was an oak-ash-hornbeam forest, while the vegetation on the foot of the hill was a maple-ash-hornbeam forest. Two plots were studied each including both slope and foot habitats. On every plot samples collected formed a grid of 10 × 5 units with a 5 m distance between them. Soil macroinvertebrates were hand-sorted from the samples, and several soil parameters (soil, pebble, and litter mass, soil moisture) were measured.The analysis did not reveal coincidence between the boundaries of plant and soil animal communities on the bend of the hill. Soil animal communities of the plots were dominated by woodlice, diplopods, and insect larvae, reaching an abundance of 680–990 individuals m⁻² throughout the plots. Number of taxonomic groups per sample and overall animal abundance in the bend were the highest in both plots, whilst these parameters on the slope were the lowest. Variograms and maps of spatial distribution indicated that the boundary between soil animal communities was situated further up on the slope than the vegetation boundary. The size of the animal community was smaller than the size of plots sampled, what probably explained the lack of coincidence between the boundaries. There was a significant correlation between distribution of litter mass and parameters of soil animal communities, which was modulated by depth of soil layer and soil moisture. Soil parameters were more important for explaining boundaries between soil animal communities than plant communities in the forest considered.     

Effects of afforestation with four unmixed plant species on the soil–water interactions in a semiarid Mediterranean region (Sicily, Italy)

Purpose

An assessment of the effect of plant cover on the properties of four afforested soils in central Sicily was performed with the aim of discriminating among them after 60?years of afforestation.

Materials and methods

Chemical and biochemical soil analyses were coupled to fast field cycling (FFC) NMR relaxation investigations in order to monitor surface interactions of water in water-saturated soils.

Results and discussion

The traditional soil analyses revealed that the most stable soil properties such as soil texture and pH are not affected by 60?years of afforestation. Soils developed under eucalyptus trees showed larger amounts of hydrophilic organic matter as compared to the soils under pines and cypresses. FFC-NMR relaxometry data revealed that water, partitioned in clay-, loam-, and sand-type pores, showed longitudinal relaxation time values affected by the interactions with the soluble carbon content.

Conclusions

The results of the present study evidenced the potential of FFC-NMR relaxometry in differentiating the effect of diverse plant cover on chemical and hydrological properties of soils developed on the same parent material. In fact, in contrast with the traditional physicochemical and biochemical soil characterizations, which were unable to reveal differences among soils afforested with different plant species, FFC-NMR was capable of monitoring differences in water dynamics as affected by the presence of the most soluble soil organic material.     

Fractionation and Bioavailability of Arsenic in the Bed Sediments of the Anllóns River (NW Spain)

The arsenic bioavailability in the bed sediments from the Anllóns River (NW Spain) has been assessed by using several analytical approaches. A six-step sequential fractionation was compared to three general availability tests: the Toxicity Characteristic Leaching Procedure (TCLP) extraction, which estimates the leaching potential of As and its effect on the survival of microorganisms (Vibrio fischeri), an extraction with 1 M HCl extraction, which estimates the bioavailability to higher plants, and a physiologically based extraction test (PBET), which estimates the bioavailability to superior animals. Arsenic was found to be mainly associated to the least mobile fractions: bound to Fe-Al oxides and in the residual phase. Among the three single extractants considered, the PBET extracted the highest As concentrations (1–11% of the total As). The TCLP extracts showed toxicity to Vibrio fischeri whereas for the plants evaluated, aqueous extracts did not show adverse effects.     

Gradients of abundance and biomass across reserve boundaries in six Mediterranean marine protected areas: Evidence of fish spillover?

Marine protected areas (MPAs) are considered as an effective tool in marine coastal management, and considered able to enhance local fisheries through adult fish spillover. Indirect evidence of fish spillover could be obtained by horizontal gradients in fish abundance. To address this question, the existence of gradients of fish abundance and biomass across marine reserve boundaries was assessed in six Mediterranean MPAs using underwater visual censuses performed at various distances from the core of the MPA, in integral reserve (IR), to buffer zone (BZ) and fished areas. A reserve effect was evidenced with higher values of fish species richness (×1.1), abundance (×1.3), and biomass (×4.7) recorded inside MPAs compared to adjacent fished areas. Linear correlations revealed significant negative gradients in mean fish biomass in all the reserves studied after the effect of habitat had been removed, whereas negative gradients in abundance were less conspicuous. Generalized additive models suggested two main patterns of biomass gradients, with a sharp decrease at the IR-BZ boundary or at the BZ-fished area boundary. It was estimated that fish spillover beneficial to local fisheries occurred mostly at a small spatial scale (100s of metres). The existence of regular patterns of negative fish biomass gradients from within MPAs to fished areas was consistent with the hypothesis of adult fish biomass spillover processes from marine reserves and could be considered as a general pattern in this Mediterranean region.     

Analysis of runoff,sediment dynamics and sediment yield of subcatchments in the highly erodible Isábena catchment,Central Pyrenees

Purpose

The Isábena catchment (445 km²), Spain, features highly diverse spatial heterogeneity in land use, lithology and rainfall. Consequently, the relative contribution in terms of water and sediment yield varies immensely between its subcatchments, and also temporally. This study presents the synthesis of ~2.5 years of monitoring rainfall, discharge and suspended sediment concentration (SSC) in the five main subcatchments of the Isábena and its outlet.

Materials and methods

Continuous discharge at the subcatchment outlets, nine tipping bucket rainfall and automatic SSC samplers (complemented by manual samples), were collected from June 2011 until November 2013. The water stage records were converted to discharge using a rating curve derived with Bayesian regression. For reconstructing sediment yields, the data from the intermittent SSC sampling needed to be interpolated. We employed non-parametric multivariate regression (Quantile Regression Forests, QRF) using the discharge and rainfall data plus different aggregation levels of these as ancillary predictors. The subsequent Monte Carlo simulations allowed the determination of monthly sediment yields and their uncertainty.

Results and discussion

The stage–discharge rating curves showed wide credibility intervals for the higher stages, with great uncertainties associated with the discharge rates, especially during floods. The water yield of the subcatchments differed considerably. The entire catchment’s output was dominated by the northernmost subcatchment (~360 mm year^?1). The smaller, southern subcatchments featured much higher variability and lower runoff rates (55–250 mm year^?1). The SSCs exhibited a wide range and can exceed 100 g l^?1 for the central subcatchments, where most of the badlands are located. For the reconstruction of the sedigraphs, the QRF method proved suitable with Nash–Sutcliffe indices of 0.50 to 0.84. The specific sediment yield ranges from relatively low (32 t km^?2 year^?1) in the highly vegetated north to high values (3,651 t km^?2 year^?1) in areas with many badland formations.

Conclusions

The Isábena catchment shows high erosion dynamics with great variability in space and time, with stark contrasts even between adjacent subcatchments. The natural conditions make water and sediment monitoring and instrumentation very challenging; the measurement of discharge is particularly prone to considerable uncertainties. The QRF method employed for reconstructing sedigraphs and monthly yields proved well suited for the task.     

Assessment and prediction of changes in the reserves of organic carbon in abandoned soils of European Russia in 1990–2020

Experimental studies and the analysis of published data have shown that carbon reserves in soils generally increase upon soil exclusion from agricultural use. The rate of carbon accumulation in the abandoned soils depends on the soil type, the time elapsed since the soil abandoning (the restoration period), and the thickness of the layer for which the rate of carbon accumulation is determined. For the upper 20-cm-thick layer, it varies from 66 to 175 g C/m² per year in dependence on the type of soil and averages 111 g C/m² per year. The highest rate is typical of the first 10–15 years of soil restoration. According to our calculations, the carbon sequestration in the upper 20-cm-thick layer of Russian soils due to changes in land use was 184–673 Mt C in 1990–2005 and may reach 282–1030 Mt C by 2020.     

Optimizing Nitrogen Fertilizer–Use Recommendations for Winter Wheat in a Mediterranean‐Type Environment using Tissue Nitrate Testing

Abstract

Although nitrogen (N) fertilizer use is essential for economic yields of modern field crops, whether rainfed or irrigated, the underlying concern is to maximize nutrient‐use efficiency and avoid excessive N use that results in deterioration of water quality from the environmental standpoint as well in the interest as human and animal health. Soil testing for N forms and total plant N analysis can contribute to the efficient use of N, but both strategies have limitations. Accordingly, tissue testing of the growing crop has been promoted as an alternative approach. Although such tests have been widely used in the West to monitor the N status of crops, they are rarely used in developing countries. A 2‐year field trial examined the potential of tissue testing of rainfed wheat in a typical Mediterranean environment in the Cukurova region of southern Turkey, because observations from wells in the region had suggested increasing and excessive nitrate levels, most probably from fertilizer N use. The trial, in essence, compared different levels of N fertilizer application based on farmers' traditional application in addition to considering soil mineral N with tissue N based on a color index to refine N application recommendations. The measurements were taken in conjunction with observations on wheat yields. The study showed that using the combined approach of soil and tissue nitrate resulted in lowering the N fertilizer recommendations without any lowering of crop yields, clear evidence that farmers had been using excessive amounts of fertilizer N in the absence of limited or no official guidelines. Thus, such tests should be promoted to replace traditional fertilizer application practices as a simple and easily used tool to improve N‐use efficiency for the farmer, in addition to reducing negative environmental impacts of such use. The quick tests can help promote the awareness of the potential negative effects of overuse of N fertilizer.