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.     

Impact of inorganic nitrogen additions on microbes in biological soil crusts

Many studies have shown that changes in nitrogen (N) availability affect the diversity and composition of soil microbial community in a variety of terrestrial systems, but less is known about the responses of microbes specific to biological soil crusts (BSCs) to increasing N additions. After seven years of field experiment, the bacterial diversity in lichen-dominated crusts decreased linearly with increasing inorganic N additions (ambient N deposition; low N addition, 3.5 g N m⁻² y⁻¹; medium N addition, 7.0 g N m⁻² y⁻¹; high N addition, 14.0 g N m⁻² y⁻¹), whereas the fungal diversity exhibited a distinctive pattern, with the low N-added crust containing a higher diversity than the other crusts. Pyrosequencing data revealed that the bacterial community shifted to more Cyanobacteria with modest N additions (low N and medium N) and to more Actinobacteria and Proteobacteria and much less Cyanobacteria with excess N addition (high N). Our results suggest that soil pH, together with soil organic carbon (C), structures the bacterial communities with N additions. Among the fungal communities, the relative abundance of Ascomycota increased with modest N but decreased with excess N. However, increasing N additions favored Basidiomycota, which may be ascribed to increases in substrate availability with low lignin and high cellulose contents under elevated N conditions. Bacteria/fungi ratios were higher in the N-added samples than in the control, suggesting that the bacterial biomass tends to dominate over that of fungi in lichen-dominated crusts after N additions, which is especially evident in the excess N condition. Because bacteria and fungi are important components and important decomposers in BSCs, the alterations of the bacterial and fungal communities may have implications in the formation and persistence of BSCs and the cycling and storage of C in desert ecosystems.     

Interrelations of organism prevalence, specimen collection method, and host age, sex, and breed among 8,354 canine urinary tract infections (1969-1995)

Selected information was compiled from canine urinalyses and urine cultures conducted between January 1969 and December 1995. Eight thousand three hundred fifty-four microbial isolates (bacteria and fungi) included 4,873 isolates from females and 3,481 from males. Ten bacterial genera accounted for 96.3% of the urinary isolates, including Escherichia coli (44.1%), Staphylococcus spp. (11.6%), Proteus spp. (9.3%), Klebsiella spp. (9.1%), Enterococcus spp. (8.0%), and Streptococcus spp. (5.4%) as the 6 most common isolates in both genders of dogs. Among these 6 genera, female dogs were generally predisposed over males, although males had more urinary tract infections (UTIs) caused by Klebsiella spp. Distributions of ages at UTI diagnosis tended to be similar between genders. Infection with a single microbial species was responsible for >72% of UTIs in both genders. Among females, 40 breeds and a mixed-breed group represented 90.2% of all positive urine cultures, 88.4% of the individual dogs with UTIs. and 88.2% of the microbial isolations. Among males, these same 41 breed groups represented 87.9% of all positive urine cultures, 87.6% of the individual dogs, and 88.2% of the microbial isolations.     

不同温度对扬州盐水鹅品质的影响

[目的]为了保证扬州盐水鹅的卫生质量和品质。[方法]对扬州盐水鹅在不同保存温度下菌落总数、菌相和pH值的变化进行试验性观察。[结果]当菌落总数达到106 cfu/g、腿肌pH值为6.5以上时,均有异味产生;腐败过程中的优势菌种,37℃为肠球菌属和葡萄球菌属,20℃为变形杆菌属,4℃为假单胞菌属;对于当天制作并于中午出售的盐水鹅,其保存期限建议值为:37℃不超过7 h,20℃不超过24 h,4℃不超过6 d。[结论]该研究为建立健全可供盐水鹅新鲜度鉴定使用的卫生评价指标提供了依据。     

培养料不同pH对真姬菇生长的影响

探讨不同初始pH值对真姬菇菌丝生长及产量的影响,来确定栽培料最适的初始pH值.结果表明:栽培料以灭菌前初始pH值7.5～8.0,日长速最快,达到6.45～7.14 mm,其产量最高,达到246.5～248.6 g/袋.     

Dynamics of phosphatase activities in a cork oak litter (Quercus suber L.) following sewage sludge application

As part of a study of the processes involved in litter biodegradation following sewage sludge (SS) addition, the variations over 14 months of phosphatase activities in a cork oak litter (Quercus suber L.) were investigated. A field experimental design was carried out using the litter-bag method on both a fertilized plot receiving SS applications (twice ) and a control plot. Acid (APH) and alkaline (BPH) phosphatases were measured, along with several biotic and abiotic variables potentially involved in the regulation of these enzymes. These included moisture, temperature, pH, water-extractable inorganic P (P_W), culturable heterotrophic bacteria and fungi. Sludge addition had significant effects on all the variables measured. Indeed, sludge increased significantly BPH activities, available P_W, microbial densities (i.e. bacteria and fungi) and pH in the fertilized plot. In contrast, APH activities decreased significantly following sludge addition. As a consequence, the BPH/APH ratio increased markedly and immediately in the fertilized plot, but only after the 1st amendment. Following the 1st preconditioning SS amendment, the 2nd fertilization had fewer effects on biological variables, because of summer dryness. The different properties examined varied significantly with incubation time, and most were significantly related to the seasonal patterns of litter moisture in this Mediterranean forest ecosystem. Hence, sewage sludge application modified the intensity of microbial responses to environmental factors, but biological patterns regulating P turn-over were maintained.     

一株可降解苹果废弃枝条的生防细菌鉴定

筛选对废弃苹果枝条具有降解作用的细菌,为农业废弃物的资源化利用奠定基础。首先利用稀释涂布法从采集的带菌苹果枝段中分离,再通过羧甲基刚果红培养基和复筛培养基挑选出产纤维素酶的菌株,利用发酵培养基验证筛选菌株的纤维素降解能力,进行腐烂病（Valsa mali）的对峙试验并测定其生防潜力,最后通过菌落形态、显微观察和gyrA序列的16S rDNA分析对细菌进行鉴定。从采集的苹果枝条中共分离出3株细菌,其中X-2菌株对苹果枝条具有降解作用,其最适生长pH为8,最适生长温度为30 ℃左右。菌株分泌产生的滤纸酶（FPAase）、β-葡萄糖苷酶和羧甲基纤维素酶（CMCase）活力分别高达（12.78±0.03） U/mL、（8.63±0.64） U/mL和（8.36±0.02） U/mL,枝条纤维素降解率高达12.36%±0.44%,经过16S rDNA序列测定和Blast 同源序列检索,得出该生防菌株X-2为解淀粉芽孢杆菌 (Bacillus amyloliquefaciens)。菌株X-2可以满足废弃苹果枝条的降解需求,其在碱性条件下生长良好,有望应用于碱性地区废弃枝条纤维素的降解。