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.

     

Assessing the Impacts of Time-to-Detection Distribution Assumptions on Detection Probability Estimation

Abundance estimates from animal point-count surveys require accurate estimates of detection probabilities. The standard model for estimating detection from removal-sampled point-count surveys assumes that organisms at a survey site are detected at a constant rate; however, this assumption can often lead to biased estimates. We consider a class of N-mixture models that allows for detection heterogeneity over time through a flexibly defined time-to-detection distribution (TTDD) and allows for fixed and random effects for both abundance and detection. Our model is thus a combination of survival time-to-event analysis with unknown-N, unknown-p abundance estimation. We specifically explore two-parameter families of TTDDs, e.g., gamma, that can additionally include a mixture component to model increased probability of detection in the initial observation period. Based on simulation analyses, we find that modeling a TTDD by using a two-parameter family is necessary when data have a chance of arising from a distribution of this nature. In addition, models with a mixture component can outperform non-mixture models even when the truth is non-mixture. Finally, we analyze an Ovenbird data set from the Chippewa National Forest using mixed effect models for both abundance and detection. We demonstrate that the effects of explanatory variables on abundance and detection are consistent across mixture TTDDs but that flexible TTDDs result in lower estimated probabilities of detection and therefore higher estimates of abundance.Supplementary materials accompanying this paper appear on-line.     

Histopathology of infection and colonization of Quercus ilex fine roots by Phytophthora cinnamomi

Quercus ilex is one of the European forest species most susceptible to root rot caused by the oomycete Phytophthora cinnamomi. This disease contributes to holm oak decline, a particularly serious problem in the ‘dehesas’ ecosystem of the southwestern Iberian Peninsula. This work describes the host–pathogen interaction of Q. ilex and P. cinnamomi, using new infection indices at the tissue level. Fine roots of 6‐month‐old saplings inoculated with P. cinnamomi were examined by light microscopy and a random pool of images was analysed in order to calculate different indices based on the measured area of pathogen structures. In the early stages of invasion, P. cinnamomi colonizes the apoplast and penetrates cortical cells with somatic structures. On reaching the parenchymatous tissues of the central cylinder, the pathogen develops different reproductive and survival structures inside the cells and then expands through the vascular system of the root. Some host responses were identified, such as cell wall thickening, accumulation of phenolic compounds in the middle lamella of sclerenchyma tissues, and mucilage secretion blocking vascular cells. New insights into the behaviour of P. cinnamomi inside fine roots are described. Host responses fail due to rapid expansion of the pathogen and a change in its behaviour from biotrophic to necrotrophic.     

Characterization of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">melongenae</Emphasis> isolates from Turkey with ISSR markers and DNA sequence analyses

Fusarium oxysporum f. sp. melongenae (Fomg), causal agent of Fusarium wilt of eggplant, is a serious pathogen in open fields and greenhouses. Inter-simple sequence repeat (ISSR) banding profiles, sequence analyses of inter-transcribed-spacer (ITS), translation elongation factor 1-alpha (TEF-1α), and actin (actA) DNA regions were employed in this study to determine genetic diversity and population structure of Fomg isolates obtained from Turkey. For ISSR study, (ACTG)₅, (GACAC)₃, (GACA)₄, (GATA)₄, HVH(TG)₇ and (CA)₈RG primers were selected from a set of 16. Discriminative ability of the primers revealed with various indices including polymorphic information content (PIC), and mean PIC value was calculated as 0.26. The ISSR data revealed 31 loci belonging to 202 Fomg isolates and 14 of them were found to be polymorphic. The isolates on neighbor joining ISSR tree were grouped into two major clusters which separated Fomg and outgroup isolates. Population structure was investigated based on bayesian modeling and results indicated five subpopulations (K = 5, ?K = 205.42). Mean genetic and geographical distances among sampling locations revealed only a weak and insignificant correlation (r = 0.583, P = 0.06). Phylogenetic analyses were carried out with ITS, TEF-1α and actA DNA regions with a selected subset of 30 Fomg, along with one non-host and one outgroup isolates. Since ITS region were not able to provide a meaningful separation, TEF-1α and actA sequences of each organism were concatenated individually to build a dendrogram. The clustering tree successfully separated the Fomg, non-host and outgroup isolates in which all Fomg were located on the same branch, forming a monophyletic group in the dendrogram.     

Seasonal effect on infection and development of lesions caused by Cryphonectria parasitica in Castanea sativa

Seasonal variation in the development of chestnut blight, caused by Cryphonectria parasitica, was investigated by inoculating in situ chestnut trees and in vitro excised chestnut segments, at either monthly or 3‐monthly intervals throughout 30 months. Inoculations were made with conidia and mycelium of a virulent isolate and with mycelium of a hypovirulent isolate. Conidial inoculations of living sprouts or excised segments between May and July resulted in the greatest incidence of infection whereas inoculations in autumn and winter, in vitro as well as in situ, did not reveal any visible disease. However, from these symptomless inoculated stems, C. parasitica was isolated 3 months after inoculation. Inoculations with the mycelium of the virulent isolate always resulted in lesions, except in January 1999, and the greatest rate of lesion development occurred for inoculations made in the spring and summer. There was a significant seasonal effect on lesion development. Lesions caused by the hypovirulent isolate, smaller than those caused by the virulent isolate, followed a similar seasonal pattern. The same seasonal variations were observed for inoculations in vitro of excised segments. Relative water content (RWC) of chestnut bark significantly varied with bark sampling date. The rate of lesion development in sprouts significantly correlated with average minimum (ATn) and maximum (ATx) temperatures and the sum of rainfall during inoculation period, with the rate of lesion development measured in excised segments 10 days after inoculation (R10d) and with RWC measured on the day of inoculation. In multiple regression models, variables ATx and R10d best explained variation in lesion development.     

The efficiency of nitrogen in cattle manures when applied to a double‐annual forage cropping system

The use of cattle manure (CM) for fertilization presents challenges for optimizing nitrogen (N) use. Our work aimed to assess N efficiencies, in a 6‐year experiment with three biennial rotations of four crops: oat–sorghum (first year) and ryegrass–maize (second year) in a rainfed humid Mediterranean area of Spain. Fertilization treatments included the following: control (no N), 250 kg mineral N ha^?1 year^?1 (250MN), three CM rates (supplying 170, 250 and 500 kg N ha^?1 year^?1) and four treatments where the two lowest CM rates were complemented with either 80 or 160 kg mineral N ha^?1 year^?1. Treatments were distributed randomly in each of three blocks. Maximum dry‐matter yield (~44–49 t ha^?1 rotation^?1) was achieved in the third rotation, and only the control and the 170CM yielded significantly less. Within the limitations of the EU Nitrate Directive, the N steady state supply of 170CM always requires a complement of mineral N (80 kg N ha^?1) to maximize N agronomic efficiency. The maximum N‐fertilizer replacement value (250CM vs. 250MN) was 0·67, without significant differences between the two treatments in other N‐related efficiency indexes, which indicates that plants took advantage of residual‐N effects. Nitrogen losses by leaching in the 250CM treatment were around 5–7% of the N applied. This reinforces the sustainability of manure recycling in long cropping seasons.     

Genetic analysis and molecular mapping of quantitative trait loci in common bean against Pythium ultimum

Pythium ultimum is a soil pathogen that can cause seed decay and damage to roots in common bean. In this study, the response of a set of 40 common bean genotypes to P. ultimum and inheritance of the resistance in the 92 F? recombinant inbred lines (RIL) developed from a cross between Xana and Cornell 49242 was investigated by using emergence rate and seedling vigor. Emergence of the 40 genotypes showed a significant association between white seed coat and response to this pathogen. Among these, 11 common bean genotypes, all with colored seeds, exhibited a high percentage of emergence and seedling vigor not significantly different (P > 0.05) to noninoculated plants. Response of the RIL population revealed both qualitative and quantitative modes of inheritance. A major gene (Py-1) controlling the emergence rate was mapped in the region of the gene P, a basic color gene involved in control of seed coat color, located on LG 7. Using the RIL subpopulation with colored seeds, a significant quantitative trait loci (QTL) associated with the emergence rate (ER3(XC)) and another with seedling vigor (SV6(XC)) were identified on the LG 3 and 6, respectively. QTL SV6(XC) was mapped in the region of the gene V, another gene involved the genetic control of color. QTLs associated with seed traits were mapped in the same relative position as regions involved in responses to P. ultimum suggesting the possible implication of avoidance mechanisms in the response to this pathogen.     

Plant diversity of secondary forests in response to anthropogenic disturbance levels in montane regions of northeastern China

The effects of anthropogenic disturbances on forest structure and plant diversity of secondary forest ecosystems were evaluated based on the classification by site factors in the montane regions of northeastern China. Forty-five sample plots containing 720 sub-plots of overstory species (8 m × 8 m), 1,440 quadrats of understory species (2 m × 2 m), and 1,440 quadrats of herbaceous layer species (1 m × 1 m) were clustered into five groups (G1, G2, G3, G4 and G5) by site variables with Hierarchical Cluster Analysis. Meanwhile, the disturbance levels corresponding to the five groups were determined according to the factors influencing human disturbances (D0-G2, D1-G1, D2-G3, D3-G5, and D4-G4). Species diversities of overstory, understory, herbaceous layer and overall species were evaluated using species number, Margalef index, Pielou index, Shannon–Wiener index, and Simpson index; and β-diversities (Whittaker index, Cody index). Basal area of stands exhibited a decreasing trend along the disturbance level due to a gradual increase in the extraction of timber by the human disturbances. The indices of species diversity suggested that overstory and understory species were distributed evenly among the groups or disturbance levels. There were no absolutely dominant tree species in the secondary forest ecosystems. The differences in site factors and the current disturbance intensities were not intense enough to lead to loose changes in overstory and understory species. The species diversity indices exhibited the maximum values at D3 (G5) for herbaceous layer species; this may suggest that the current disturbance intensities were intense enough to lead the changes of herbaceous layer species. Three rare and endangered species (Juglans mandshurica, Fraxinus mandshurica and Acanthopanax senticosus) were found within the secondary forests. These rare and endangered species appeared in each clustered group or disturbance level, which suggested that the current disturbance intensity in the study area was not strong enough to influence the distribution of rare and endangered species. The current disturbances in the secondary forests may not lead to a decrease in stability and complexity of the overstory and understory species, but the higher disturbance level may be intense enough to change the habitat fitness for the herbaceous species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized authors.     

Lack of biocontrol capacity in a non-pathogenic mutant of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">melonis</Emphasis>

The aim of this study was to assess the biocontrol capacity of rev157, a non-pathogenic mutant of a pathogenic strain of Fusarium oxysporum f. sp. melonis (Fom24). Inoculated in association with the virulent parental strain, the mutant rev157 did not protect the host plant (muskmelon) against infection by Fom24. Applied on flax, a non-host plant, the mutant rev157 was not able to protect it against its specific pathogen F. oxysporum f. sp. lini. On the contrary the parental strain Fom24 did protect flax as well as a soil-borne biocontrol strain (Fo47). Since the mutant rev157 was affected neither in its growth in vitro nor in its capacity to penetrate into the roots, it can be speculated that the mutation has affected traits responsible for interactions within the plant. In F. oxysporum the pair of strains Fom24/rev157 is a good candidate to identify genes involved in the biocontrol capacity of F. oxysporum and to test the hypothesis of a link between capacity to induce the disease and capacity to induce resistance in the plant.     

Ecological impacts of small hydropower plants on headwater stream fish: from individual to community effects

Hydroelectricity is increasingly used worldwide as a source of renewable energy, and many mountain ranges have dozens or hundreds of hydropower plants, with many more being under construction or planned. Although the ecological impacts of large dams are relatively well known, the effects of small hydropower plants and their weirs have been much less investigated. We studied the effects of water diversion of small hydropower plants on fish assemblages in the upper Ter river basin (Catalonia, NE Spain), which has headwater reaches with good water quality and no large dams but many of such plants. We studied fish populations and habitat features on control and impacted reaches for water diversion of 16 hydropower plants. In the impacted reaches, there was a significantly lower presence of refuges for fish, poorer habitat quality, more pools and less riffles and macrophytes, and shallower water levels. We also observed higher fish abundance, larger mean fish size and better fish condition in the control than in impacted reaches, although the results were species‐specific. Accordingly, species composition was also affected, with lower relative abundance of brown trout (Salmo trutta) and Pyrenean minnow (Phoxinus bigerri) in the impacted reaches and higher presence of stone loach (Barbatula quignardi) and Mediterranean barbel (Barbus meridionalis). Our study highlights the effects of water diversion of small hydropower plants from the individual to the population and community levels but probably underestimates them, urging for further assessment and mitigation of these ecological impacts.