Functional and structural responses of bacterial and fungal communities from paddy fields following long-term rice cultivation

Purpose

Rice paddy soils undergo pedogenesis driven by periodic flooding and drainage cycles that lead to accumulation of organic matter and the stratification of nutrients and oxygen in the soil profile. Here, we examined the effects of continuous rice cultivation on microbial community structures, enzyme activities, and chemical properties for paddy soils along a chronosequence representing 0–700 years of rice cropping in China.

Materials and methods

Changes in the abundance and composition of bacterial and fungal communities were characterized at three depths (0–5, 5–10, and 10–20 cm) in relation to organic carbon, total nitrogen, dissolved organic carbon, microbial biomass carbon/nitrogen, and activities of acid phosphatase, invertase, and urease.

Results and discussion

Both soil organic carbon and total nitrogen increased over time at all three depths, while pH generally decreased. Microbial abundance (bacteria and fungi) and invertase and urease activity significantly increased with the duration of rice cultivation, especially in the surface layer. Fungal abundance and acid phosphatase activity declined with depth, whereas bacterial abundance was highest at the 5–10-cm soil depth. Profiles of the microbial community based on PCR-DGGE of 16S rRNA indicated that the composition of fungal communities was strongly influenced by soil depth, whereas soil bacterial community structures were similar throughout the profile.

Conclusions

Soil bioactivity (microbial abundance and soil enzymes) gradually increased with organic carbon and total nitrogen accumulation under prolonged rice cultivation. Microbial activity decreased with depth, and soil microbial communities were stratified with soil depth. The fungal community was more sensitive than the bacterial community to cultivation age and soil depth. However, the mechanism of fungal community succession with rice cultivation needs further research.

     

Assessment of changes in soil organic matter after invasion by exotic plant species

Invasive exotic plants can modify soil organic matter (SOM) dynamics and other soil properties. We evaluated changes in particulate organic matter (POM) and carbon (C) mineralisation in adjacent plots invaded by Solidago gigantea, Prunus serotina, Heracleum mantegazzianum and Fallopia japonica, and non-invaded control plots on different soils in Belgium. Litter decomposition of S. gigantea and P. serotina was compared to that of the native species Epilobium hirsutum, Betula pendula and Fagus sylvatica. Disregarding the differences in site characteristics (soil texture, parental material and plant species), we argued that the invasion by S. gigantea and P. serotina enhance SOM dynamics by increasing C mineralisation in 2 out of 3 sites invaded by S. gigantea and in 1 out of 3 sites invaded by P. serotina; C in coarse POM (cPOM, 4,000–250 μm) and fine POM (fPOM, 250–50 μm) in 1 site invaded by S. gigantea and C content in total POM (tPOM, 4,000–50 μm) and the organo-mineral fraction (OMF, 0–50 μm) in 1 site invaded by P. serotina. H. mantegazzianum and F. japonica slowed down SOM dynamics by reducing C mineralisation in three out of four sites; C and nitrogen (N) of fPOM in the invaded compared with the non-invaded plots at one site invaded by H. mantegazzianum. However, N content of cPOM (4,000–250 μm) was higher in the invaded sites by F. japonica compared with the non-invaded plots. Our results indicated that the effects of invasion by exotic plant species were not species-specific but site-specific.     

Using perlite as a substrate carrier for measuring microbial available phosphorus by respiration kinetics in soils

The release of CO₂ by soil microorganisms after the addition of nitrogen and glucose in excess and calibration additions of phosphorus has successfully been used to assess microbial available P, assuming the native soil P pool is then limiting respiration. However, in P-fixing soils and soils with high P content, carbon can be exhausted before the available soil P pool. It is not possible to simply increase the amount of glucose as then the glucose concentration would be lethal for microorganisms. A modified method was tested where soil is mixed with perlite. It was hypothesised that perlite, having a high water holding capacity, would dilute the concentration of glucose, while maintaining the bioavailability of added nutrients, thus avoiding carbon limitation. Factorial combinations of amount of soil and perlite (both adjusted to −25 kPa water potential) were tested to examine if perlite as such had any effect on the respiration. Five tropical soil samples with a sharp gradient in P availability and one N-limited compost material were used. The method successfully reduced the risk of carbon limitation. Microbial indices, such as basal respiration, substrate-induced respiration and maximum P-limited respiration, were directly proportional to the amount of soil in the experiments but unrelated to the amount of perlite, showing that perlite did not affect microbial measurements.     

Analysis of indigenous production methods and farm-based biodiversity of amochi (<Emphasis Type="Italic">Arisaema schimperianum</Emphasis> Schott) in two sub-zones of Southern Ethiopia

For the first time we report that diverse types of Arisaema schimperianum Schott locally called amochi, are grown and managed as an off-season food crop in Southern Ethiopia. Participatory Rural Appraisal (PRA) and formal survey studies on 204 households were conducted over two consecutive years (2003–2004) in Chencha and Dita sub zones of Southern Ethiopia, to identify indigenous production methods and farm based biodiversity of amochi. Amochi is propagated from seed tubers and tuber parts left in the soil from the preceding harvest and grow during the dry season, February to June. Average share of proportion in the annual household consumption from amochi tubers was 9% and 4% for Chencha and Dita respectively. Uncooked amochi is irritating in contact to skin and mouth. Fifteen amochi types were identified in Dita and 12 in Chencha. They differ in the level of irritation, maturity and yield. Rich farmers with large family size as a working force, large farm size to support larger number of livestock that is source of farmyard manure, have farms with larger diversity of amochi than their poor counterparts, suggesting that its diversity is influenced by house hold characteristics and favoured under relatively fertile soil conditions. In both sub zones women had better experience in identifying amochi types than men. Further study is needed to identify chemical contents; and genetic variation using morphologic and molecular traits, in order to develop a strategy to assess and utilise the existing genetic diversity.     

Powdery Mildew Resistance in a Collection of Chinese Barley Varieties

One hundred and forty-seven Chinese barley varieties maintained at the Gene Bank of the National Barley Improvement Centre, Zhejiang, and 84 progenies from these varieties were tested at the seedling stage for their reaction to 32 selected pathotypes of Blumeria graminis f. sp. hordei. Eighteen resistance spectra were identified comprising single or combined resistances from eight known (Ml(Bw), Ml(Ch), Mla7, Mla8, Mla9, Mla13, MlaRu4 and Mlg) and six unknown resistance genes. The most frequent gene was Ml(Bw), which was found in 69 varieties and previously detected in only a few European winter barley varieties. The genes Mla8 and Ml(Ch) were also often present, but other resistance genes were rare. After inoculation, considerably fewer pathogen colonies were observed in ‘Aiganqi’ and one line of ‘Tong5’. Twenty varieties were composed of lines with different resistance genes. China is likely to be a region of origin of the genes Ml(Bw), Mla7, as well as three unknown genes found in original landraces and perhaps another three unknown genes detected in cultivars bred in China. The resistances of varieties from the Zhejiang province and those originating from 11 other Chinese provinces were quite different. Unfortunately, none of the varieties are promising sources of resistance to powdery mildew and China does not seem to be a region suitable for identifying such sources.     

Comparison of genetic variation among accessions of <Emphasis Type="Italic">Aegilops tauschii</Emphasis> using AFLP and SSR markers

Genetic diversity of 54 accessions of Aegilops tauschii from five countries was assessed using sequence-tagged microsatellites (or simple sequence repeats, SSRs) and amplified fragment length polymorphisms (AFLPs). In the case of AFLP analysis, a total of 256 amplification products obtained, 234 of them were polymorphic across all the 54 accessions. A total of 224 fragments were obtained from the 24 SSR primers and 219 of fragments were polymorphic across all the genotypes screened. Based on both AFLP and SSR markers, the highest percentage of polymorphisms were obtained in Iranian and accessions of unknown origin. The highest polymorphic information content (PIC) value was observed for SSRs (0.82) while the highest marker index (MI) value was for AFLPs (8.5) reflecting the hyper-variability of the first and the distinctive nature of the second system. Principal co-ordinate analysis (PCO) revealed congruent patterns of genetic relationships for both data sets, but did not group accessions strictly according to their geographical origins. Poor correlation was found between AFLP and SSR marker loci. This low association may be due to low number of AFLP and SSR markers. These results show that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.     

Cation exchange capacity of density fractions from paired conifer/grassland soils

The cation exchange capacity (CEC) of a soil depends on the type and amount of both mineral and organic surfaces. Previous studies that have sought to determine the relative contribution of organic matter to total soil CEC have not addressed differences in soil organic matter (SOM) composition that could lead to differences in CEC. The objectives of this study were (1) to compare the CEC of two distinct SOM pools, the “light fraction (LF)” composed of particulate plant, animal, and microbial debris, and the “heavy fraction (HF)” composed of mineral-bound organic matter; and (2) to examine the effects of differences in aboveground vegetation on CEC. Soil samples were collected from four paired grassland/conifer sites within a single forested area and density fractionated. LF CEC was higher in conifer soils than in grassland soils, but there was no evidence of an effect of vegetation on CEC for the HF or bulk soil. LF CEC (but not HF CEC) correlated well with the C concentration in the fraction. The mean CEC of both fractions (per kg fraction) exceeded that of the bulk soil; thus, when the LF and HF CEC were combined mathematically by weighting values for each fraction in proportion to dry mass, the resulting value was nearly twice the measured CEC of bulk soil. On a whole soil basis, the HF contributed on average 97% of the CEC of the whole soil, although this conclusion must be tempered given the inflation of CEC values by the density fractionation procedure.     

Long-term effect of chemical fertilizer,straw, and manure on labile organic matter fractions in a paddy soil

To assess the effect of long-term fertilization on labile organic matter fractions, we analyzed the C and N mineralization and C and N content in soil, particulate organic matter (POM), light fraction organic matter (LFOM), and microbial biomass. Results showed that fertilizer N decreased or did not affect the C and N amounts in soil fractions, except N mineralization and soil total N. The C and N amounts in soil and its fractions increased with the application of fertilizer PK and rice straw. Generally, there was no significant difference between fertilizer PK and rice straw. Furthermore, application of manure was most effective in maintaining soil organic matter and labile organic matter fractions. Soils treated with manure alone had the highest microbial biomass C and C and N mineralization. A significant correlation was observed between the C content and N content in soil, POM, LFOM, microbial biomass, or the readily mineralized organic matter. The amounts of POM–N, LFOM–N, POM–C, and LFOM–C closely correlated with soil organic C or total N content. Microbial biomass N was closely related to the amounts of POM–N, LFOM–N, POM–C, and LFOM–C, while microbial biomass C was closely related to the amounts of POM–N, POM–C, and soil total N. These results suggested that microbial biomass C and N closely correlated with POM rather than SOM. Carbon mineralization was closely related to the amounts of POM–N, POM–C, microbial biomass C, and soil organic C, but no significant correlation was detected between N mineralization with C or N amounts in soil and its fractions.     

Genetic diversity of Syrian pistachio (<Emphasis Type="Italic">Pistacia vera</Emphasis> L.) varieties evaluated by AFLP markers

Pistachio (Pistacia vera L.) is a strategic nut tree species in the Middle East which holds comparative advantage over other fruit trees in view of its hardiness, income generation opportunities and benefits for the ecosystem. Yet pistachio cultivation depends on a very narrow genetic base, in spite of the existence of many varieties still marginally exploited. Syria is an important center of diversity for pistachio. A country wide ecogeographic survey in this country was carried out to determine the extent of pistachio genetic diversity and its use. As a whole, 114 accessions were collected from 37 farms to assess diversity at morphological and molecular level. Molecular evaluation was carried out using Amplified Fragment Length Polymorphism (AFLP) technique and performed using seven primer pair combinations. Results from the studies allowed the identification of 25 pistachio female varieties in Syria, some of which unique and described for the first time. Three groups of pistachio diversity were identified by cluster analysis which provides useful information about the distribution of genetic diversity in Syria for enhanced use and sustainable conservation.     

Response of denitrifying communities to successive soil freeze–thaw cycles

The effect of soil freeze–thaw cycles on the denitrification potential was examined based on the C₂H₂ inhibition method. The gross N₂O production curve of the soil sample (incubation with C₂H₂) showed minor changes between the freeze–thaw treatment and the unfrozen control. However, kinetics analysis revealed that the initial production rate, an indicator of the population density of denitrifying communities, decreased (P = 0.043) and the specific growth rate constant, an indicator of the activity of denitrifying communities, increased (P = 0.039) as a result of the freeze–thaw cycles in five of six soil samples examined. The increase in the specific growth rate constant suggested the stimulation of the activity of denitrifying communities that survived after the freeze–thaw cycles and may explain the minor suppression on the gross N₂O production in spite of decreasing the population density of denitrifying communities that was suggested by the initial production rate. The net N₂O production curve of the soil sample (incubation without C₂H₂) showed a remarkable change in one out of six soil samples, and in that one soil sample, N₂O release to the atmosphere was largely stimulated (7.6 times) by the freeze–thaw cycles. However, the stimulation of the N₂O release by the freeze–thaw cycles was even observed in two other selected soil samples (4.6 and 1.8 times), suggesting that an imbalance in the N₂O-producing and N₂O-reducing activities of denitrifying communities might complementally explain the N₂O release stimulated by the freeze–thaw cycles.