Soil fumigation and compost amendment alter soil microbial community composition but do not improve tree growth or yield in an apple replant site

Apple replant disease (ARD) is a disease complex that reduces survival, growth and yield of replanted trees, and is often encountered in establishing new orchards on old sites. Methyl bromide (MB) has been the fumigant used most widely to control ARD, but alternatives to MB and cultural methods of control are needed. In this experiment, we evaluated the response of soil microbial communities and tree growth and yield to three pre-plant soil treatments (compost amendment, soil treatment with a broad-spectrum fumigant, and untreated controls), and use of five clonal rootstock genotypes (M.7, M.26, CG.6210, G.30 and G.16), in an apple replant site in Ithaca, New York. Polymerase chain reaction (PCR)—denaturing gradient gel electrophoresis (DGGE) analysis was used to assess changes in the community composition of bacteria and fungi in the bulk soil 8, 10, 18 and 22 months after trees were replanted. PCR-DGGE was also used to compare the community composition of bacteria, fungi and pseudomonads in untreated rhizosphere soil of the five rootstock genotypes 31 months after planting. Tree caliper and extension growth were measured annually in November from 2002 to 2004. Apple yield data were recorded in 2004, the first fruiting year after planting. Trees on CG.6210 rootstocks had the most growth and highest yield, while trees on M.26 rootstocks had the least growth and lowest yield. Tree growth and yield were not affected by pre-plant soil treatment except for lateral extension growth, which was longer in trees growing in compost-treated soil in 2003 as compared to those in the fumigation treatment. Bulk soil bacterial PCR-DGGE fingerprints differed strongly among the different soil treatments 1 year after their application, with the fingerprints derived from each pre-plant soil treatment clustering separately in a hierarchical cluster analysis. However, the differences in bacterial communities between the soil treatments diminished during the second year after planting. Soil fungal communities converged more rapidly than bacterial communities, with no discernable pattern related to pre-plant soil treatments 10 months after replanting. Changes in bulk soil bacterial and fungal communities in response to soil treatments had no obvious correlation with tree performance. On the other hand, rootstock genotypes modified their rhizosphere environments which differed significantly in their bacterial, pseudomonad, fungal and oomycete communities. Cluster analysis of PCR-DGGE fingerprints of fungal and pseudomonad rhizosphere community DNA revealed two distinct clusters. For both analyses, soil sampled from the rhizosphere of the two higher yielding rootstock genotypes clustered together, while the lower yielding rootstock genotypes also clustered together. These results suggest that the fungal and pseudomonad communities that have developed in the rhizosphere of the different rootstock genotypes may be one factor influencing tree growth and yield at this apple replant site.     

Reciprocal transfer effects on denitrifying community composition and activity at forest and meadow sites in the Cascade Mountains of Oregon

In order to examine the effects of disturbance, vegetation type, and microclimate on denitrification and denitrifier community composition, experimental plots were established at the H. J. Andrews Experimental Forest in the Cascade Mountains of Oregon. Soil cores were reciprocally transplanted between meadow and forest and samples were collected after 1 and 2 years. Denitrifying enzyme activity (DEA) was measured using the acetylene block assay and terminal restriction length polymorphism profiles were generated with nosZ primers that target the gene coding for nitrous oxide reductase. Nitrate concentrations, C mineralization, and water content were measured to gain additional insights into soil properties controlling DEA. Meadow soils were significantly higher in DEA than forest soils, and the highest DEA levels were observed in cores transferred from the meadow into the forest. Nitrate concentrations were also different between forest and meadow soils, but did not correlate to DEA. DEA was higher in open versus closed cores, suggesting an association between denitrification and the rhizosphere. Denitrifier communities of undisturbed forest and meadow soils shifted through a 4-year period but remained distinct from each other. Similarly, denitrifier communities clustered by vegetation type of origin regardless of manipulation, suggesting that the overall denitrifier communities are well buffered against environmental changes.     

防病促生枯萎病拮抗菌“98-Ⅰ”对4种枯萎病防治效果研究

经 8年系统试验研究从 330个细菌菌株中筛选出 1株防病促生枯萎病拮抗菌“98 Ⅰ” ,经鉴定属蜡质芽孢杆菌。该菌对黄瓜枯萎病、西瓜枯萎病、青椒枯萎病和番茄枯萎病 4种土传病害均有显著防治效果 ,其平皿孢子萌发抑制率分别为 79 2 %、75 1%、72 3%和 95 7% ,且该菌对多种蔬菜有促生和促进种子发芽功效。     

Effects of three soil tillage systems on some biological activities in an Ultisol from southern Chile

Intensive tillage for annual crop production may be affecting soil health and quality. However, tillage intensity effects on biological activities of volcanic-derived soils have not been systematically investigated. We evaluated the effects of three different tillage practices on some biological activities of an Ultisol from southern Chile during the third year of a wheat–lupin–wheat crop sequence. Treatments were: no tillage with stubble burning (NTB), no tillage without stubble burning (NT) and conventional tillage with disk-harrowing and stubble burning (CT). Biological activities were evaluated in winter and summer at 0–200 mm and at three soil depths (0–50, 50–100 and 100–200 mm) in winter. Total organic C and N were significantly higher under no-tillage systems than CT. In general, NT increased C and N of microbial biomass in comparison with CT, especially in winter. Microbial biomass C was closely associated with microbial biomass N (r = 0.986, P < 0.05); acid phosphomonoesterase (r = 0.999, P < 0.05); β-glucosidase (r = 0.978, P < 0.05), and others. Changes in biological activities occurred mainly in the upper soil layer (0–50 mm depth) in spite of the short duration of the experiment. Biological activities could be used as practical biological indicators to apply the more appropriate management systems for increasing soil sustainability or productivity.     

长期施用化肥对红壤性水稻土中微生物生物量、活性及群落结构的影响

利用化肥长期定位试验,研究了施肥对土壤微生物生物量、活性及其群落结构的影响.结果表明:与不施肥相比,长期施用化肥不仅增加了土壤微生物生物量,而且导致了土壤微生物群落结构的分异.其中,有机无机配施处理和2倍NPK配施处理显著提高了土壤有机质含量、全N含量、土壤微生物生物量和土壤微生物活性.NPK均衡施肥处理对土壤有机质、土壤微生物生物量及其活性的影响小于非均衡施肥的处理(NP、NK、N、P、K),适当增施K肥有利于提高土壤微生物中真菌的比例.     

Short-term changes in nitrogen availability, gas fluxes (CO2, NO, N2O) and microbial biomass after tillage during pasture re-establishment in Rondônia, Brazil

Anthropogenic conversion of primary forest to pasture for cattle production is still frequent in the Amazon Basin. Practices adopted by ranchers to restore productivity to degraded pasture have the potential to alter soil N availability and N gas losses from soils. We examined short-term (35 days) effects of tillage prior to pasture re-establishment on soil N availability, CO₂, NO and N₂O fluxes and microbial biomass C and N under degraded pasture at Nova Vida ranch, Rondônia, Brazilian Amazon. We collected soil samples and measured gas fluxes in tilled and control (non tilled pasture) 12 times at equally spaced intervals during October 2001 to quantify the effect of tillage. Maximum soil NH₄⁺ and NO₃⁻ pools were 13.2 and 6.3 kg N ha⁻¹ respectively after tillage compared to 0.24 and 6.3 kg N ha⁻¹ in the control. Carbon dioxide flux ranged from 118 to 181 mg C–CO₂ m² h⁻¹ in the control (non-tilled) and from 110 to 235 mg C–CO₂ m² h⁻¹ when tilled. Microbial biomass C varied from 365 to 461 μg g⁻¹ in the control and from 248 to 535 μg g⁻¹ when tilled. The values for N₂O fluxes ranged from 1.22 to 96.9 μg N m⁻² h⁻¹ in the tilled plots with a maximum 3 days after the second tilling. Variability in NO flux in the control and when tilled was consistent with previous measures of NO emissions from pasture at Nova Vida. When tilled, the NO/N₂O ratio remained <1 after the first tilling suggesting that denitrification dominated N cycling. The effects of tilling on microbial parameters were less clear, except for a decrease in qCO₂ and an increase in microbial biomass C/N immediately after tilling. Our results suggest that restoration of degraded pastures with tillage will lead to less C matter, at least initially. Further long-term research is needed.     

Soil freeze-thaw cycle experiments: Trends, methodological weaknesses and suggested improvements

Although freeze-thaw cycles can alter soil physical properties and microbial activity, their overall impact on soil functioning remains unclear. This review addresses the effects of freeze-thaw cycles on soil physical properties, microorganisms, carbon and nutrient dynamics, trace gas losses and higher organisms associated with soil. I discuss how the controlled manipulation of freeze-thaw cycles has varied widely among studies and propose that, despite their value in demonstrating the mechanisms of freeze-thaw action in soils, many studies of soil freeze-thaw cycles have used cycle amplitudes, freezing rates and minimum temperatures that are not relevant to temperature changes across much of the soil profile in situ. The lack of coordination between the timing of soil collection and the season for which freeze-thaw cycles are being simulated is also discussed. Suggested improvements to future studies of soil freeze-thaw cycles include the maintenance of realistic temperature fluctuations across the soil profile, soil collection in the appropriate season and the inclusion of relevant surface factors such as plant litter in the fall or excess water in the spring. The implications of climate change for soil freeze-thaw cycles are addressed, along with the need to directly assess how changes in soil freeze-thaw cycle dynamics alter primary production.     

Fungal biomass in pastures increases with age and reduced N input

Previous studies have shown that soil fungal biomass increases towards more natural, mature systems. Shifts to a fungal-based soil food web have previously been observed with abandonment of agricultural fields and extensification of agriculture. In a previous field experiment we found increased fungal biomass with reduced N fertilisation. Here, we explore relationships between fungi, bacteria, N input and grassland age on real dairy farms in the Netherlands. We hypothesised that also in pastures that are still in production there is a negative relationship between fungal biomass and fertilisation, and that fungal biomass increases with grassland age in pastures that are still in production. We expected the fungal/bacterial biomass ratio to show the same responses, as this ratio has often been used as an indicator for management changes. We sampled 48 pastures from eight organic dairy farms. Sites differed in age and fertilisation rate. We determined fungal and bacterial biomass, as well as ergosterol (a fungal biomarker). Fungal and bacterial biomass and ergosterol, showed a negative relationship with N application rate, and correlated positively with organic matter percentage. In old pastures, fungal biomass and ergosterol were higher than in younger pastures. Because bacterial biomass responded in the same way as fungal biomass, the F/B ratio remained constant, and can therefore—in our data set—not be used as an indicator for changing management. We conclude that the changes in fungal and bacterial biomass were driven by changes in organic matter quality and quantity. The negative relationship we found between N application rate and fungal biomass adds to earlier work and confirms the presence of this relationship in pastures with relatively small differences in management intensities. Earlier studies on shifts in fungal biomass focused on ex-agricultural fields or restoration projects. Here we show that fungal biomass is also higher in older agricultural pastures.     

Respiration pattern and microbial use of field-grown transgenic Bt-maize residues

A 49-day incubation experiment was carried out with the addition of field-grown maize stem and leaf residues to soil at three different temperatures (5, 15, and 25 °C). The aim was to study the effects of two transgenic Bt-maize varieties in comparison to their two parental non-Bt varieties on the mineralization of the residues, on their incorporation into the microbial biomass and on changes in the microbial community structure. The stem and leaf residues of Novelis-Bt contained 3.9 μg g⁻¹ dry weight of the Bt toxin Cry1Ab and those of Valmont-Bt only 0.8 μg g⁻¹. The residues of the two parental non-Bt varieties Nobilis and Prelude contained higher concentrations of ergosterol (+220%) and glucosamine (+190%) and had a larger fungal C-to-bacterial C ratio (+240%) than the two Bt varieties. After adding the Bt residues, an initial peak in respiration of an extra 700 μg CO₂-C g⁻¹ soil or 4% of the added amount was observed in comparison to the two non-Bt varieties at all three temperatures. On average of the four varieties, 19-38% of the maize C added was mineralized during the 49-day incubation at the three different temperatures. The overall mean increase in total maize-derived CO₂ evolution corresponded to a Q₁₀ value of 1.4 for both temperature steps, i.e. from 5 to 15 °C and from 15 to 25 °C. The addition of maize residues led to a strong increase in all microbial properties analyzed. The highest contents were always measured at 5 °C and the lowest at 25 °C. The variety-specific contents of microbial biomass C, biomass N, ATP and adenylates increased in the order Novelis-Bt ? Prelude<Valmont-Bt ? Nobilis. The mineralization of Novelis-Bt residues with the highest Bt concentration and lowest N concentration and their incorporation into the microbial biomass was significantly reduced compared to the parental non-Bt variety Nobilis. These negative effects increased considerably from 5 to 25 °C. The transgenic Bt variety Valmont did not show further significant effects except for the initial peak in respiration at any temperature.     

DEHP对土壤脱氢酶活性及微生物功能多样性的影响

选用肥熟旱耕人为土(黄棕壤),设置了在土壤中施加100 mg kg-1 DEHP与不施加DEHP两个水平,盆栽试验研究了DEHP对土壤脱氢酶活性以及土壤微生物群落功能多样性的影响,以及植物在污染土壤中的修复作用。结果表明,施加DEHP显著抑制了土壤脱氢酶活性,30 d时与对照相比降低了约30%, 第60 d时尽管有缓慢的回升,但仍明显低于对照(p<0.05)。从BIOLOG反应的结果可以看出,DEHP也显著影响土壤微生物的功能多样性,土壤微生物群落的Shannon指数、Simpson指数、McIntosh指数和均度均显著低于无污染的对照,说明DEHP的污染导致了土壤微生物群落功能多样性的下降。种植植物对土壤脱氢酶和微生物活性有很明显的促进作用,并且在一定程度上缓解了DEHP的毒害作用,但并未消除DEHP对土壤微生物的影响。