Efimia M. Papatheodorou

Nematode community structure as indicator of soil functioning in European grassland soils

This investigation analyses whether soil nematode diversity is correlated with soil functional parameters to serve as bioindicator of soil functioning. The analysis focuses on the interrelations of nematofauna, microflora, and soil nitrogen pools. The sites studied represent six major European grassland types: Northern tundra, atlantic heath, wet grassland, seminatural temperate grassland, East European steppe, and mediterranean garigue. Continental and local climate gradients were combined to a wide and continuous range of microclimate conditions. Nematode richness, as indicated by the number of genera, was highest under temperate conditions and declined towards the climatic extremes. Differences in richness affected all nematode feeding types proportionally. Nematode richness was the only parameter among a range of 15 alternatives tested that exhibited consistent correlations with mass and activity parameters of both nematofauna and microflora in the mineral grassland soils (garigue, wet grassland, seminatural grassland, steppe). In the same soils, the nematode Maturity Index was the best indicator of nitrogen status. We conclude that a high nematode richness can generally be seen as a good indicator of an active nematofauna and microflora in mineral grassland soils, and hence as an indicator of the decomposition function. The prospects of exploiting nematode diversity as an indicator of soil functioning are critically discussed.

Design and evaluation of nematode 18S rDNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA

Abstract Consensus nematode 18S ribosomal DNA primers were designed by aligning available 18S sequences and identifying a variable region flanked by highly conserved regions. These primers were then used to amplify nematode 18S rDNA from whole soil community DNA extracted from a range of European grassland types. Cloning of the PCR amplicons (778 bp) followed by restriction digest analysis (RFLP) resulted in the recovery of 34 unique nematode sequences from the four grasslands studied. Comparison of these data with the limited number of 18S rDNA nematode sequences currently held in on-line databases revealed that all of the sequences could be assigned to known nematode taxa albeit tentatively in some cases. Two of the sequences recovered from the site in the Netherlands (wet, hay-grassland) were recovered in a clade that included a sequence of the genus Trichodorus whilst other sequences from this site showed similarity with 18S rDNA sequences of the genus Prismatolaimus (five sequences), Xiphinema (one sequence) and Enoplus (one sequence). Of the remaining sequences, two showed some affinity with Mylonchulus (UK, upland peat), four with Steinernema (UK) and one sequence with Mesorhabditis (Hungary, east European Steppe). Three sequences from the Netherlands and one from Hungary were recovered in a clade that included a sequence of the genus Pratylenchoides whilst three further sequences from the Netherlands and two from Hungary were recovered in a clade encompassing the genus Globodera. Of the remaining nine sequences, two (NL6, NL62) formed a distinct lineage within the Adenophorea with 90% bootstrap recovery in a paraphyletic clade that included sequences of Prismatolaimus and Trichodorus. Seven sequences (three from the Netherlands, three from the UK and one from Greece) were left unassigned though the tree topology suggested some relationship (58% bootstrap recovery) with the genus Cephalobus. To assess whether primers used to amplify 18S rDNA might be used to fingerprint genetic diversity in nematode communities in soil, the environmental sequence data were used to design a second set of primers carrying a GC-clamp. These primers amplified a 469 bp fragment internal to the region flanked by the primer set used to derive the nematode trees and were used to amplify 18S rDNA for subsequent analysis using denaturing gradient gel electrophoresis (DGGE). DGGE analysis of six major European grassland types revealed considerable genetic diversity between sites. However, the relationships seen with the DGGE data were inconsistent with previous studies where the same soils had been characterized with respect to functional and morphological diversity. To confirm that this second set of primers was amplifying nematode sequences, selected bands on the DGGE gels were extracted, PCR amplified and sequenced. The final alignment was 337 bases. These analyses revealed the presence of sequence signatures from the genera Paratrichodorus, Plectus, Steinernema, Globodera, Cephalobus and Pratylenchoides.

Abundance and diversity of the phyllosphere bacterial communities of Mediterranean perennial plants that differ in leaf chemistry

Summary.We studied the epiphytic bacterial communities of the summer leaves of eight perennial species naturally occurring in a Mediterranean ecosystem. The species differ in essential-oil content (from rich in essential oil to non-producers) and composition, and also in life form (from herbaceous species to tall shrubs). We compared the epiphytic bacterial communities on the basis of (i) their abundance, (ii) their metabolic profile (derived by use of the BIOLOG Ecoplate system) and (iii) richness and diversity of substrates that they use, as a measure of functional diversity. Among all species, the aromatic Melissa officinalis was the most abundantly colonized. The bacterial communities on the leaves of the aromatic Myrtus communis, Calamintha nepeta and Melissa officinalis, and also of Cistus incanus catabolized all 31 substrates offered; those on the evergreen-sclerophyllous species, Arbutus unedo and Quercus coccifera, catabolized only 14 and 17 substrates, respectively. Carbohydrates were consistently used abundantly by all communities, whereas carboxylic acids were most variably used. On average, the group of aromatic plants scored higher regarding bacterial abundance, and richness and diversity of substrates used by the bacterial communities on their leaves; the lowest values for both substrate-use indices were recorded in A. unedo. Bacterial abundance or richness or diversity of substrates used did not vary with leaf oil content. Abundance was positively correlated with both substrate-use indices. Results support claims that the antimicrobial effects of essential oils are not exerted so much under natural conditions as reports based on biassays with pathogens usually show. Although essential oils play a part in the microbial colonization of the phyllosphere, it is not likely that inhibition of phyllosphere bacteria is essential oils’ primary role, at least in the Mediterranean environment.

The effect of grazing on phenology and biomass allocation in Quercus coccifera (L.)

Abstract The spatial arrangement of above-ground tissues, the biomass allocation patterns, the root structure and the temporal variations in biomass were examined in grazed and ungrazed Quercus coccifera shrubs. Grazed shrubs exhibited lower values of individual leaf area and weight, and a higher number of leaves per shoot. This means that a grazed shrubs photosynthetic area is divided into more numerous, although smaller, units. In grazed shrubs, 60 % of the total biomass was invested in below-ground parts, while in ungrazed shrubs, the highest proportion of the biomass (50 %) was allocated to woody tissues. The root structure of Q. coccifera shrubs was characterized by high biomass allocation to coarse roots (65 %) and low allocation to fine ones (7 %). The allocation to coarse roots was significantly increased in grazed shrubs. The temporal variations in above- and below-ground biomass appeared to be grazing independent. Above- and below-ground plant biomass increase during the period from late spring to September, the most severe period for the Mediterranean ecosystem. The intrinsic features of Q. coccifera , coupled with features induced by grazing, probably favor its dominance in areas degraded by grazing.

Image analysis of soil micromorphology: feature extraction, segmentation, and quality inference

We present an automated system that we have developed for estimation of the bioecological quality of soils using various image analysis methodologies. Its goal is to analyze soilsection images, extract features related to their micromorphology, and relate the visual features to various degrees of soil fertility inferred from biochemical characteristics of the soil. The image methodologies used range from low-level image processing tasks, such as nonlinear enhancement, multiscale analysis, geometric feature detection, and size distributions, to object-oriented analysis, such as segmentation, region texture, and shape analysis.

Effects of the two carvone enantiomers on soil enzymes involved in the C, P, and N cycles

BackgroundEssential oils exert stimulatory or inhibitory effects on the size and activity of the soil microbial communities. Given that microbial biomass is the main source of soil enzymes, in this study, we examined how R-(-)- and S-(+)-carvone affect the activity of dehydrogenase, urease, and alkaline phospho-monoesterase, and the overall microbial activity, as expressed by soil respiration. Enzymatic and microbial activities were recorded every week, for a period of four weeks, during which the two carvone enantiomers were added twice, with a two-week interval, into soil samples. For all dependent variables, we analysed the deviations of the experimental from control values.ResultsTreatment per se had a significant effect only on urease. Its activity was inhibited in the S-carvone samples, while it was enhanced or inhibited, depending on the time of incubation, in the R-carvone ones. The activity of alkaline phospho-monoesterase was not affected by S-carvone, but it increased with R-carvone. Soil respiration markedly increased in presence of the two carvones with highest values being recorded in the R-carvone samples. None of the temporal patterns of the three enzymes’ activity followed the pattern of soil respiration.ConclusionsThe significant treatment by time interactions for the activities of all three enzymes indicates that responses are not consistent over time; this suggests differently functioning or structured microbial communities. Given their differing effects on soil enzymes, these compounds and the aromatic plants bearing them could find use in sustainable agriculture for the control of soil enzymes and, hence, the soil processes that they are associated with.

The effects of arbuscular mycorrhizal fungi and essential oil on soil microbial community and N-related enzymes during the fungal early colonization phase

The arbuscular mycorrhizal fungi (AMF) and the essential oils are both agents of sustainable agriculture, and their independent effects on the community of free-living soil microbes have been explored. In a tomato pot experiment, conducted in a sandy loam mixture, we examined the independent and joint effects of inoculation with the fungus Rhizophagous irregularis and the addition of Mentha spicata essential oil on the structure of the soil microbial community and the activity of soil enzymes involved in the N-cycle, during the pre-symbiosis phase. Plants were grown for 60 days and were inoculated with R. irregularis. Then pots were treated with essential oil (OIL) weekly for a period of a month. Two experimental series were run. The first targeted to examine the effect of inoculation on the microbial community structure by the phospholipid fatty acids analysis (PLFAs), and enzyme activity, and the second to examine the effects of inoculation and essential oil addition on the same variables, under the hypothesis that the joint effect of the two agents would be synergistic, resulting in higher microbial biomass compared to values recorded in singly treated pots. In the AMF pots, N-degrading enzyme activity was dominated by the activity of urease while in the non-inoculated ones by the activities of arylamidase and glutaminase. Higher microbial biomass was found in singly-treated pots (137 and 174% higher in AMF and OIL pots, respectively) compared with pots subjected to both treatments. In these latter pots, higher activity of asparaginase (202 and 162% higher compared to AMF and OIL pots, respectively) and glutaminase (288 and 233% higher compared to AMF and OIL pots, respectively) was found compared to singly-treated ones. Soil microbial biomasses and enzyme activity were negatively associated across all treatments. Moreover, different community composition was detected in pots only inoculated and pots treated only with oil. We concluded that the two treatments produced diverging than synergistic effects on the microbial community composition whereas their joint effect on the activity of asparaginase and glutaminase were synergistic.

Plant-induced differentiation of soil variables and nematode community structure in a Mediterranean serpentine ecosystem

Abiotic and biotic components of a serpentine Mediterranean soil were studied in terms of heavy metal and nutrient concentrations, microbial biomass, and structural and functional characteristics of the soil nematode community. We explored differentiations of the soil environment imposed by vegetation, sampling the bare soil and soil under Buxus sempervirens, Juniperus oxycedrus, Cistus creticus and Thymus sibthorpii. Organic matter, microbial biomass, nutrient availability and calcium/magnesium (Ca/Mg) ratio of the serpentine site were similar to those of degraded, non-serpentine Mediterranean ecosystems; the serpentine site showed potassium deficiency and high heavy metal load. Soil nematode abundance, especially of phytoparasites, was very low. Low enrichment and structure indices and high channel index values indicated a degraded, low-resource, stressful environment where fungal decomposition predominates. There was no differentiation of heavy metal concentrations among microsites. Bare soil exhibited high pH, low water content, low Ca/Mg (0.68), low nutrient concentrations, low abundance of most nematode groups, low values of maturity and plant parasitic indices, low nematode diversity and a distinct generic composition. Rhizosphere soil was differentiated according to the evergreen–sclerophyllous or seasonal–dimorphic habit of shrubs. This was reflected in soil nutrients and in all parameters of the soil nematode community.

The response of properties of soil cropped with shell beans and treated with disinfectant and fertiliser during the plant growing season

Disinfectants and fertilisers exert strong impact on soil processes by affecting the structure and the activity of the soil microbial community. Most relevant studies examined these impacts independently, under laboratory conditions and without crop cover. In this study, we have monitored the response of soil chemical, microbial, and biochemical properties to disinfectant and fertiliser treatments in field plots cultivated with beans. The measured properties comprised microbial C and N, asparaginase, gultaminase, urease, and acid phosphomonoesterase activities and contents of organic N, organic C, inorganic N, and inorganic P. We ran four different treatments using different combinations of chemical (metham sodium) and biological disinfectant (a mixture of neem cake and essential oils) and fertilisers (NPK 8-16-24 and cow manure) in plots cultivated with shell beans, while the control soil was neither treated nor cropped with beans. The data were expressed as percentage (%RC) in relation to the control values. The disinfectant and fertiliser treatments had less impact on soil properties compared to bean crop growth (except for microbial C and N, and content of organic C). In comparison to the control, higher activities of urease and asparaginase and content of inorganic N were recorded in bean cropped plots at the stage of seedlings (June), while higher activities of acid phosphomonoesterase and glutaminase and content of organic N were recorded at the stage of plant flowering (August). In October, the values of all properties were higher in the control plots compared to the treated plots. The joint effect of disinfectants x fertilisers affected the response of content of organic C and N and extractable P and glutaminase activity. The %RC of the properties exhibited more negative values in plots treated with chemical disinfectant and chemical fertiliser than in the other treatments. We suggested that the response of soil properties to disinfectants and fertilisers were influenced by the growth of P. vulgaris.

Spatial and temporal variations of soil function in a Mediterranean serpentine ecosystem

We investigated the variations in space and time of soil functionality in a Mediterranean serpentine soil for heavy metal and nutrient concentrations, microbial biomass and soil enzymatic activities (urease, dehydrogenase and alkaline phosphatase) in the rhizospheres of different plant species and in bare soil, during the humid and dry seasons of the year. Nutrients and heavy metals were also estimated in leaves of shrubs inhabiting the study area. Four species of serpentine-tolerant shrubs were present: the evergreen-sclerophyllous Juniperus oxycedrus and Buxus sempervirens and the phryganic Cistus creticus and Thymus sibthorpii. The most significant differentiation of the soil environment was between bare and rhizosphere soil, and was mainly driven by the availability of potassium. Spatial variations related to plant identity were clear but less important than temporal variations. There was no relationship between soil and foliar concentrations of nutrients and heavy metals. Higher foliar concentrations were recorded in the phryganic species. Finally, there was no enzyme inhibition due to the heavy metal load of the serpentine soil. Enzymatic activities were lower for bare soil samples, while their temporal variations probably followed the temporal variations of temperature and humidity imposed by the Mediterranean climate.