Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA- and AOB-supported nitrification determined both in soil-water slurries and in unsaturated whole soil at field moisture. Soils were collected from stands of red alder (Alnus rubra Bong.) and Douglas-fir (Pseudotsuga menziesii Mirb. Franco) at three sites (Cascade Head, the H.J. Andrews, and McDonald Forest) on acidic soils (pH 3.9–5.7) in Oregon, USA. The abundances of AOA and AOB were measured using quantitative PCR by targeting the amoA gene, which encodes subunit A of ammonia monooxygenase. Total and AOA-specific (octyne-resistant) nitrification activities in soil slurries were significantly higher at Cascade Head (the most acidic soils, pH < 5) than at either the H.J. Andrews or McDonald Forest, and greater in red alder compared with Douglas-fir soils. The fraction of octyne-resistant nitrification varied among sites (21–74%) and was highest at Cascade Head than at the other two locations. Net nitrification rates of whole soil without NH₄⁺ amendment ranged from 0.4 to 3.3 mg N kg⁻¹ soil d⁻¹. Overall, net nitrification rates of whole soil were stimulated 2- to 8-fold by addition of 140 mg NH₄⁺-N kg⁻¹ soil; this was significant for red alder at Cascade Head and the H.J. Andrews. Red alder at Cascade Head was unique in that the majority of NH₄⁺-stimulated nitrifying activity was octyne-resistant (73%). At all other sites, NH₄⁺-stimulated nitrification was octyne-sensitive (68–90%). The octyne-sensitive activity—presumably AOB—was affected more by soil pH whereas the octyne-resistant (AOA) activity was more strongly related to N availability.     

Fungal and bacterial N2O production regulated by soil amendments of simple and complex substrates

Fungal N₂O production results from a respiratory denitrification that reduces NO₃⁻/NO₂⁻ in response to the oxidation of an electron donor, often organic C. Despite similar heterotrophic nature, fungal denitrifiers may differ from bacterial ones in exploiting diverse resources. We hypothesized that complex C compounds and substances could favor the growth of fungi over bacteria, and thereby leading to fungal dominance for soil N₂O emissions. Effects of substrate quality on fungal and bacterial N₂O production were, therefore, examined in a 44-d incubation after soils were amended with four different substrates, i.e., glucose, cellulose, winter pea, and switchgrass at 2 mg C g⁻¹ soil. During periodic measurements of soil N₂O fluxes at 80% soil water-filled pore space and with the supply of KNO₃, substrate treatments were further subjected to four antibiotic treatments, i.e., no antibiotics or soil addition of streptomycin, cycloheximide or both so that fungal and bacterial N₂O production could be separated. Up to d 8 when antibiotic inhibition on substrate-induced microbial activity and/or growth was still detectable, bacterial N₂O production was generally greater in glucose- than in cellulose-amended soils and also in winter pea- than in switchgrass-amended soils. In contrast, fungal N₂O production was more enhanced in soils amended with cellulose than with glucose. Therefore, fungal-to-bacterial contribution ratios were greater in complex than in simple C substrates. These ratios were positively correlated with fungal-to-bacterial activity ratios, i.e., CO₂ production ratios, suggesting that substrate-associated fungal or bacterial preferential activity and/or growth might be the cause. Considering substrate depletion over time and thereby becoming limited for microbial N₂O production, measurements of soil N₂O fluxes were also carried out with additional supply of glucose, irrespective of different substrate treatments. This measurement condition might lead to potentially high rates of fungal and bacterial N₂O production. As expected, bacterial N₂O production was greater with added glucose than with added cellulose on d 4 and d 8. However, this pattern was broken on d 28, with bacterial N₂O production lower with added glucose than with added cellulose. In contrast, plant residue impacts on soil N₂O fluxes were consistent over 44-d, with greater bacterial contribution, lower fungal contribution, and thus lower fungal-to-bacterial contribution ratios in winter pea- than in switchgrass-amended soils. Real-time PCR analysis also demonstrated that the ratios of 16S rDNA to ITS and the copy numbers of bacterial denitrifying genes were greater in winter pea- than in switchgrass-amended soils. Despite some inconsistency found on the impacts of cellulose versus glucose on fungal and bacterial leading roles for N₂O production, the results generally supported the working hypothesis that complex substrates promoted fungal dominance for soil N₂O emissions.     

Fractionation of the reference inoculum of epizootic rabbit enteropathy in discontinuous sucrose gradient identifies aetiological agents in high density fractions

Epizootic rabbit enteropathy (ERE) is a major cause of economic loss in intensive rabbit production. Since its first recognition in 1997, much work has been done to determine the pathogenic mechanisms of the disease and to identify the aetiological agent(s). Unfortunately, the quest for aetiology has only met with limited success despite the ability to reproduce the syndrome by inoculation of intestinal contents from field cases. These intestinal inocula contain a huge number of microorganisms which could all be involved in the aetiology of ERE. To decrease the number of putative agents, the French reference inoculum TEC3 was fractionated on a discontinuous sucrose gradient so that seven fractions (supernatant, 10%, 20%, 30%, 40%, 50% and pellet) were obtained. Specific-pathogen-free rabbits were inoculated with three out of these seven fractions (supernatant, 30%, and pellet). The objectives were: (1) to characterise the seven fractions by bacteriological examination; (2) to verify whether the aetiological agent was present in the fractions by inoculation of rabbits; (3) to assign the aetiological agent of ERE to a morphological group of pathogens; (4) to identify a fraction which could replace the reference inoculum TEC3 in applications such as cell cultures or egg inoculation. The results strongly suggest that ERE is a bacterial disease and does not have a viral or parasitic aetiology.     

冀北水稻田土壤细菌群落结构和多样性研究

为探讨冀北水稻田土壤细菌群落结构和多样性,以承德地区水稻主产区（河北隆化,河北滦平）稻田土壤为试验材料,采用高通量测序技术,对水稻大田土壤细菌群落结构和多样性进行研究。结果表明：不同地区水稻田土壤微生物多样性存在差异,其中样本ZYY.CKD9中微生物多样性最高且有益菌较多,主要有硫杆菌属（Thiobacillus）、拟衣藻属（Dechloromonas）和地杆菌属（Geobacter）;但也存在共有细菌菌群,如Kaistobacter、溶杆菌属（Lysobacter）、乳酸杆菌属（Lactobacillus）、Candidatus_Solibacter、硫杆菌属（Thiobacillus）、红长命菌属（Rubrivivax）、拟衣藻属（Dechloromonas）、Anaeromyxobacter、硝化螺旋菌属（Nitrospira）等;PCA分析结果显示,土壤细菌群落结构空间相关性不明显。这为冀北水稻田土壤修复、病害防治及功能菌肥开发,促进水稻高产栽培提供依据。     

沼泽红假单胞菌的抗氧化酶活性和对紫外线的吸收作用

对不同培养方式下沼泽红假单胞菌的5个菌株的菌体的抗氧化酶活性以及培养液的细胞和上清液对紫外线吸收作用进行了研究。结果表明,5个菌株的活细胞CAT活性普遍以好氧黑暗条件下的培养物高于微好氧光照条件下的,SOD活性则以微好氧光照条件下的培养物高于好氧黑暗条件的。5个菌株在好氧黑暗、微好氧光照培养条件下的细胞液和培养液的上清液在紫外线200～300nm波长范围有明显的吸收峰。     

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.     

2,4-二乙酰基藤黄酚产生菌在番茄根部的定殖及对番茄青枯病的防治

2,4-二乙酰基藤黄酚(2,4-DAPG)产生菌是荧光菌对土传病害进行生物防治的主要类群之一。室内筛选结果表明：供试的12个2,4-DAPG产生菌菌株对番茄青枯病菌均有不同程度的抑制作用,其中CPF、10抑菌效果最佳,抑菌带宽为3．5mm;而2P24、5J10次之,抑菌带宽为3．0mm。CPF10和2P24培养原液对番茄胚根的生长均有明显的抑制作用。CPF10和2P24根部定殖结果表明,两菌株均可在番茄幼苗根部大量定殖,根表细菌数量随着时间延长呈下降趋势但仍维持较高数量;而根内细菌数量有明显上升的趋势。CPF10和2P24对番茄青枯病均有一定的防治效果,其中2P24的防治效果最好。而CPF10在所有的处理中变异系数(CV)最小,防治效果最稳定。     

Effects of substrate sterilization,fungicide treatment,and mycorrhization helper bacteria on ectomycorrhizal formation of pedunculate oak (Quercus robur) inoculated with Laccaria laccata in two peat bare-root nurseries

Summary Pedunculate oak seedlings (Quercus robur) inoculated with the ectomycorrhizal fungus Laccaria lacata were grown for 1 year on fertilized sphagnum peat in two nurseries. Three factors affecting microbial populations in the substrate were studied, fungicide treatment of the seeds, peat disinfection before sowing (methyl bromide or steam pasteurization), and inoculation with mycorrhization helper bacteria. Treatment of acorns with Iprodione had no depressive effect on mycorrhiza formation. Both disinfection techniques were equivalent, stimulating or depressing mycorrhiza formation depending on the initial microflora in the peat. The introduction of two previously selected mycorrhization helper bacteria (one Pseudomonas fluorescens and one unidentified fluorescent pseudomonad), isolated from L. laccata sporocarps associated with Douglas fir—L. laccata ectomycorrhizas in other nurseries, significantly increased the mycorrhizal rate from 30 to 53% of the short roots. The implications of these results for the controlled mycorrhization of planting stocks and the specificity of mycorrhization helper bacteria are discussed.     

Microbial populations,enzyme activities and nitrogen-phosphorus-potassium enrichment in earthworm casts and in the surrounding soil of a pineapple plantation

Summary Total populations of bacteria and fungi, dehydrogenase activity (as a measure of total potential microbial activity), and urease and phosphatase activities were determined in earthworm casts and surrounding laterite soils planted to pineapple. The casts contained higher microbial populations and enzyme activities than the soil. Except for fungal populations, statistically significant (P = 0.05) increases were found in all other parameters. Microbial populations and enzyme activities showed similar temporal trends with higher values in spring and summer and lower values in winter. The earthworm casts contained higher amounts of N, P, K and organic C than the soil (P = 0.05). Selective feeding by earthworms on organically rich substrates, which break down during passage through the gut, is likely to be responsible for the higher microbial populations and greater enzyme activity in the casts.     

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.