The network of interactions among soil quality variables and nematodes: short-term responses to disturbances induced by chemical and organic disinfection

Anthropogenic pressures that involve different kinds of inflows (chemical vs organic) to soils are likely to induce different responses of individual soil components as well as to affect the web of interactions between them. The aim of this paper was to explore whether chemical or organic disinfection constitute two different types of disturbance, regarding both their severity on individual soil components and the structural changes they induce on the network of interactions among soil biochemical variables and nematode functional guilds. Network analysis, a novel approach in the context of soil ecology, was used to explore these interactions.Different plots within a field cultivated conventionally with Phaseolus vulgaris for many years were disinfected either with metham sodium or with a mixture of plant-based alternatives (neem and essential oils). Control plots receiving no disinfectants were also included in our study. One month after the treatments were applied, we estimated microbial C and N, activities of asparaginase, glutaminase, urease and phosphatase, organic C and N, inorganic N and P as well as the functional diversity of nematodes.Chemical disinfection had a direct lethal effect on all nematodes, while the effect on the microbial community was less obvious, implying that at the time of sampling, microbial populations, especially bacterial ones had started to recover from disturbance. Urease and phosphatase activities were inhibited, which may partly be responsible for the reduced amounts of inorganic N and P. Organic disinfectants reduced microbial populations, mainly the fungal ones, but they did not inhibit enzyme activities. The availability of N and P increased and nematode abundance was not affected significantly.The results demonstrate the usefulness of network analysis in providing insight into the structure and robustness of the soil network and its response to disturbance. Despite the pronounced reduction in nematode numbers due to chemical disinfection, the importance of nematode guilds within the interaction network was amplified and a more compact network was formed. On the other hand, interactions within organic plots were found to be primarily dictated by soil biochemistry. Finally, the analysis showed that both types of disinfection increased the vulnerability of the interaction network and this was more pronounced in chemically treated plots.     

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

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.     

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.     

Response of soil chemical and biological variables to small and large scale changes in climatic factors

This paper studies the effect of large- and small-scale changes of soil temperature and humidity on soil microbial biomass C and N, ergosterol, carbon utilization potential, organic and inorganic N and rate of C and N mineralization at 25°C. Large-scale variations are identified with seasonal changes in temperature and humidity. To simulate small-scale changes, soil temperature and humidity were manipulated in the field. The treatment resulted in damping of temperature fluctuations and a decrease of soil humidity.The majority of the studied variables exhibit pronounced seasonality, showing a clear-cut distinction between summer (July–August) and winter (December). In summer, C mineralization rate and carbon utilization potential was high but microbial and fungal biomass (ergosterol) was low.C and N mineralization rate and microbial and fungal biomass were only affected by sampling date, demonstrating that gross parameters of biomass and activity of microorganisms are not affected by small-scale changes in temperature and humidity. In contrast, variables relating to N availability (organic N, NH₄⁺ and NO₃⁻, microbial biomass N) and carbon utilization potential of the microbial community were highly affected by small-scale changes in soil abiotic conditions. The results suggest that changes in N dynamics induced by small-scale changes of temperature and humidity are caused by shifts in the structure of the microbial community rather than by variations in microbial biomass.     

The study of secondary successional patterns in soil using network analysis: The case of conversion from conventional to organic farming

Soil disturbances that exert strong impacts on biota and their resources are also expected to induce changes in the web of interactions among soil variables. The objective of this paper was to explore the hypothesis that during the first years after the conversion from conventional to organic farming gradual changes occur in the correlations among the nematode, microbial and nutrient flow components, resulting in increased complexity of the soil system.To test this hypothesis, we used network analysis techniques to analyze data from conventional (Conv) and organic asparagus cultivations, as well as from the adjacent hedgerows (Hedg). Organic cultivations were managed organically for 2, 3 and 5 years (Org-2, Org-3, Org-5), representing thus steps along a gradient that corresponds to the duration of organic farming.The estimated network cohesion and centrality, as well as the key player metrics, showed that the correlation network of the newest organic systems, and mostly that of Org-3, was disorganized compared with that of Conv. This trend was reversed, and a complex and more cohesive network was formed in Org-5. In addition, by employing QAP techniques and Spearman rank correlation coefficients, inter-network correlations were estimated and similarities were found between the correlation network from Org-2 and that of Org-3. The structure of the latter was correlated with that from Org-5.Our results indicated that the conversion of a conventional system to organic induces a disturbance into the soil system routine, probably launching secondary successional changes in the interactions among soil components. These changes seem to involve the gradual destruction of existing interactions leading to the disorganization of the correlation network and the reconstruction of a more complicated one after 3-5 years.     

Predictability of soil succession patterns under different agricultural land use practices: Continual conventional cultivation versus transformation to organic cultivation or fallow periods

Changes in agricultural management practices create conditions that directly or indirectly promote the onset of secondary succession processes in the soil. Previous research has demonstrated that the succession of temperate forests follows the Markov principle, which states that the next state of a process depends only on the preceding state; hence, we set out to test this principle for soils subjected to different land uses over a 2 year period. Specifically, (1) continued conventional cultivation (i.e. the monoculture of shell beans, Phaseolus vulgaris L., with chemical fertilisers); (2) transformation of land-use from conventional cultivation to organic cultivation (shell beans fertilised with manure); and (3) transformation of land-use to a fallow state. The soil was sampled three times at specific shell bean growth stages (June, the seedling stage; August, mid-growth; October, one month after harvest) in both years, with various chemical and biochemical soil profiles being conducted (including carbon, nitrogen and phosphorus levels, and enzymatic activity). Correlations among successive soil chemical and biochemical profiles were stronger (two successive events: June and August, August and October) in the first year compared to the second year (one successive event: August and October) for the organic plots. For soils in which conventional land management was continued, significant correlation was only detected for one successive profile (August–October) in both years, whereas no significant correlation was obtained for any successive profiles in the fallow plots. Therefore, the Markov principle only holds for the entire cultivation period under certain conditions for bean crops; specifically, initial conventional cultivation followed by transformation to organic cultivation. In the case of continued conventional monoculture, the Markov principle is partially supported. In contrast, fallow plots did not follow any predictable pattern of changes in soil chemical and biochemical profiles. In conclusion, agricultural management causes soil succession processes to be predictable, due to the environmental homogeneity induced by manure and/or the limited plant effect, rather than natural processes.     

Spatial Variability of Soil Organic C,Inorganic N and Extractable P in a Mediterranean Grazed Area

In this paper, we studied the spatial variability of soil organic C (SOC), inorganic N (SIN) and extractable P (P_extr) in a grazed Mediterranean‐type vegetation formation. Sampling was conducted from a gently sloping area in northern Greece.. The grazing pressure was evenly distributed over the experimental area with the exception of an overgrazed passage zone 200–300 m from steeper foothills. Soil samples, from the upper 10 cm, were collected every 10 m along four replicate lines (400 m length with a distance of 10 m between lines). Sampling took place twice (October and February). Data were analysed by geostatistical tools, and spherical models were significantly fitted to the semivariograms. SOC in both samplings and SIN in the first one displayed moderate spatial dependence which indicates the non‐random distribution of their concentration. On the contrary, P_extr and SIN in winter exhibited weak spatial dependence, whereas P_extr in autumn showed spatial independence. For the parameters exhibiting spatial pattern, two scales of dependence were revealed: a fine scale within distances shorter than 10 m and a coarse scale varying between 80 and 130 m. The coarse distribution of SOC, SIN and P_extr invoked interplay among more predictable (composition of vegetation) and unpredictable (leaching, runoff) extrinsic factors, occurring at the landscape level. Specifically, SOC as a storage agent exhibited uniform spatial pattern in both samplings. By contrast, SIN by being susceptible to leaching exhibited time‐specific dependence, whereas P_extr which was affected by surface runoff displayed limited or even spatial independence. Copyright © 2012 John Wiley & Sons, Ltd.     

The response of soil biochemical variables to organic and conventional cultivation of Asparagus sp.

In this paper we aim to examine long-term effects caused by applying alternative management regimes to soil system, such as organic farming, and to compare them with short-term effects represented by seasonal agricultural steps such as fertilizing, harvesting, etc. To complete this task we focus on soil quality in organic and conventional fields. We compared soil biochemical variables among fields with different durations of organic cultivation (2, 3, 5 and 6 years) and one with conventional cultivation (CV). All fields were planted with a common perennial plant (Asparagus officinalis L.) and were subject to the same seasonal management cycle (fertilizing, crop harvest, incorporation of above-ground residues, etc.). Soil samples were collected four times throughout a year (March, May, September, December) corresponding to the main phases of the management cycle. The questions explored in this study were the following: (a) Do long-term changes due to the management regime (organic vs. conventional) have a greater effect upon soil variables than the seasonal (short-term) changes within the management cycle itself? (b) On the basis of soil biochemical status, can we distinguish between fields that have been under organic cultivation for different durations? (c) Do the importance of variables in fields’ distinction related to specific management phases?According to principal component analysis, we found that the soil biochemical status owed far more to the phase within the management cycle than to the management regime. Among sampling periods, December was characterized by greater heterogeneity of soil variables, which could be attributed to biomass laying on the soil surface which stimulated the microbial community with consequent changes in NH₄⁺, NO₃^?, N-mineralization and C-mineralization rate. The importance of soil variables in fields’ distinction was related to the specific management phase. The differences among fields, even in the cases of extractable P and organic N were not systematic. In addition, 10% of samples of the oldest organic field, shared common soil features with samples belonging to the newest organically cultivated field. This high intra-variability showed that none of the examined fields has developed systematically different soil characteristics. Therefore, our data show, at least for some crops, that indicators of soil quality (e.g. organic C and microbial biomass C) need not always improve with the duration of organic cultivation in a simple manner.