Short-term competition between crop plants and soil microbes for inorganic N fertilizer

Agricultural systems that receive high amounts of inorganic nitrogen (N) fertilizer in the form of either ammonium (NH₄⁺), nitrate (NO₃⁻) or a combination thereof are expected to differ in soil N transformation rates and fates of NH₄⁺ and NO₃⁻. Using ¹⁵N tracer techniques this study examines how crop plants and soil microbes vary in their ability to take up and compete for fertilizer N on a short time scale (hours to days). Single plants of barley (Hordeum vulgare L. cv. Morex) were grown on two agricultural soils in microcosms which received either NH₄⁺, NO₃⁻ or NH₄NO₃. Within each fertilizer treatment traces of ¹⁵NH₄⁺ and ¹⁵NO₃⁻ were added separately. During 8 days of fertilization the fate of fertilizer ¹⁵N into plants, microbial biomass and inorganic soil N pools as well as changes in gross N transformation rates were investigated. One week after fertilization 45-80% of initially applied ¹⁵N was recovered in crop plants compared to only 1-10% in soil microbes, proving that plants were the strongest competitors for fertilizer N. In terms of N uptake soil microbes out-competed plants only during the first 4 h of N application independent of soil and fertilizer N form. Within one day microbial N uptake declined substantially, probably due to carbon limitation. In both soils, plants and soil microbes took up more NO₃⁻ than NH₄⁺ independent of initially applied N form. Surprisingly, no inhibitory effect of NH₄⁺ on the uptake and assimilation of nitrate in both, plants and microbes, was observed, probably because fast nitrification rates led to a swift depletion of the ammonium pool. Compared to plant and microbial NH₄⁺ uptake rates, gross nitrification rates were 3-75-fold higher, indicating that nitrifiers were the strongest competitors for NH₄⁺ in both soils. The rapid conversion of NH₄⁺ to NO₃⁻ and preferential use of NO₃⁻ by soil microbes suggest that in agricultural systems with high inorganic N fertilizer inputs the soil microbial community could adapt to high concentrations of NO₃⁻ and shift towards enhanced reliance on NO₃⁻ for their N supply.     

Bacterial diversity in cucumber (Cucumis sativus) rhizosphere in response to salinity, soil pH, and boron

Soil salinity is a major factor relating microbial communities to environmental stress in the microbial selection process as stress can reduce bacterial diversity. In the San Joaquin Valley (SJV) of California, the problem of increasing salinity and consequently, decreasing crop productivity, due to reuse of saline drainage water are major concerns. An experiment was conducted in a closed, recirculating volumetric lysimeter system (VLS) consisting of 24 experimental plant growth units to determine the interactive effects of salinity, boron and pH on rhizosphere and non-rhizosphere microbial composition of cucumber (Cucumis sativus L. cv. Seminis Turbo hybrid). Plants in the VLS were irrigated from individual reservoirs containing a modified half-strength Hoagland's nutrient solution combined with salinity, boron (B), and pH treatments. The results indicated that salinity and pH were the most influential factors affecting the growth of plants and the effect of boron on the plant was more severe under slightly acidic conditions. Total bacterial DNA was extracted from rhizosphere and non-rhizosphere samples, and a 236-bp DNA fragment in the V3 region of the small subunit ribosomal RNA genes of eubacteria was amplified. The 16S rRNA and the products were subjected to denaturing gradient gel electrophoresis (DGGE) and sequencing. Analyses of bacterial diversity showed that the effects of salinity, boron, and pH were more severe on the rhizosphere bacterial population during the first week of growing cucumber, with decreasing impacts with plant growth. However, there was no salinity-B-pH interaction effects on plant biomass, but the effects were seen in the number of heterotrophic bacteria in the rhizosphere and on species richness and diversity during week seven of the study. These suggest that the effects of salinity-B-pH interactions may influence microorganisms first before plants and may pose long term effects on soil quality.     

Fate of prions in soil: Degradation of recombinant prion in aqueous extracts from soil and casts of two earthworm species

Prions represent the active agent in transmissible spongiform encephalopathy (TSE) diseases and can remain infective to mammals even after prolonged periods in soil. The influence of mesofauna on prion dispersal and degradation in soil, however, remains unknown. In this study the effect of earthworms on the retention/dissemination of TSEs in soil was evaluated using a model recombinant prion protein (recPrP) and aqueous extracts from soil and fresh casts of two earthworm species, Lumbricus terrestris and Aporrectodea caliginosa. Our results showed that earthworm gut-derived enzymes did not enhance the degradation of recPrP in comparison to soil, even though non-prion related proteolytic activity was higher in fresh worm excrements than in soil samples. Complete degradation of recPrP occurred in the aqueous extracts from all samples within up to 6 days at +15 °C. The proteolytic enzymes responsible for degrading recPrP were inhibited by aprotinin and leupeptin and studies in pure cultures suggested these were most probably of soil microbial origin.     

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.     

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.     

百草枯对土壤微生物影响的研究

研究了5种不同浓度百草枯对土壤微生物种群数量及土壤中细菌、放线菌和真菌生长速率的影响。结果表明,百草枯对土壤微生物的种群数量及土壤细菌、放线菌和真菌生长速率均具有一定的抑制作用,且随药剂浓度升高逐渐增强。加药后2～7d,对细菌种群抑制率为13.3%～100%,抑菌圈直径达0.07～0.93cm;对放线菌种群抑制率为8.6%～100%,抑菌圈直径达0～3.00cm;对真菌种群抑制率为7.6%～100%,生长速率的抑制率达1.4%～77.3%。抑制作用随加药时间延长又逐渐减弱。     

LiCl沉淀法提取富含荚膜的细菌基因组DNA

结合提取基因组DNA的CTAB法(hexadecyltrimethylammoniumbromide,十六烷基三甲基溴化铵)和用于提取海藻基因组DNA的LiCl法,设计了针对产生较多荚膜多糖细菌的DNA提取方法—LiCl沉淀法。通过电泳、分光光度计及16SrRNA基因扩增检测,证明LiCl沉淀法可以有效地提取产荚膜细菌基因组DNA,其片断大小约为23kb,不需进一步纯化即可用于后续分子生物学实验。     

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.     

The impact of protozoa on the availability of bacterial nitrogen to plants

Summary Microbial N from ¹⁵N-labelled bacterial biomass was investigated in a microcosm experiment, in order to determine its availability to wheat plants. Sterilized soil was inoculated with either bacteria (Pseudomonas aeruginosa alone or with a suspension of a natural bacterial population from the soil) or bacteria and protozoa to examine the impact of protozoa. Plant biomass, plant N, soil inorganic N and bacterial and protozoan numbers were determined after 14 and 35 days of incubation. The protozoa reduced bacterial numbers in soil by a factor of 8, and higher contents of soil inorganic N were found in their presence. Plant uptake of N increased by 20010 in the presence of protozoa. Even though the total plant biomass production was not affected, the shoot: root ratios increased in the presence of protozoa, which is considered to indicate an improved plant nutrient supply. The presence of protozoa resulted in a 65010 increase in mineralization and uptake of bacterial ¹⁵N by plants. This effect was more pronounced than the protozoan effect on N derived from soil organic matter. It is concluded that grazing by protozoa strongly stimulates the mineralization and turnover of bacterial N. The mineralization of soil organic N was also shown to be promoted by protozoa.Communication No. 9 of the Dutch Programme on Soil Ecology of Arable Farming Systems     

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.