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.     

汶川地震对岷江柏林土壤微生物群落及养分的影响

为了探索地震灾害对森林土壤肥力和微生物多样性的影响,以四川理县地震灾区不同受灾程度的岷江柏林土壤养分及细菌、古菌群落为调查对象,在受灾区选择2个典型土壤类型、7个人工岷江柏(Cupressus chenginana)林为调查对象,其中,在熊尔山调查点(山地褐土)选择1个受地震影响小的林分作为对照,3个受灾林分,在蒲溪沟调查点(山地棕壤)选择1个对照和2个受灾林分。结果表明:受地震影响,熊尔山和蒲溪沟两个研究区的p H平均值显著升高了11.5%。与对照相比,土壤有机质、全氮、碱解氮、速效磷、速效钾、有效铁、有效锰和有效铜的含量都出现显著下降(P0.05)。以干土计的细菌和古菌的基因拷贝数范围分别为2.42×10~7~5.81×10~7copies g~(-1)和1.77×10~6~5.66×10~6copies g~(-1),比对照降低了1~2个数量级。细菌数量高于古菌数量,而细菌和古菌均与土壤养分因子(土壤有机质,全氮,碱解氮,有效磷,速效钾,有效铁,有效锰)达到显著正相关水平,与土壤p H为极显著负相关,与有效铜含量没有显著相关关系。总之,地震破坏了土壤微生态环境,土壤细菌和古菌数量减少,土壤肥力降低,应进一步明确营养元素对土壤微生物影响的机理。     

Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest

Little is known about the organisms responsible for decomposition in terrestrial ecosystems, or how variations in their relative abundance may influence soil carbon (C) cycling. Here, we altered organic matter in situ by manipulating both litter and throughfall inputs to tropical rain forest soils, and then used qPCR and error-corrected bar-coded pyrosequencing to investigate how the resulting changes in soil chemical properties affected microbial community structure. The plot-scale manipulations drove significant changes in microbial community composition: Acidobacteria were present in greater relative abundance in litter removal plots than in double-litter plots, while Alphaproteobacteria were found in higher relative abundance in double-litter and throughfall reduction plots than in control or litter removal plots. In addition, the bacterial:archaeal ratio was higher in double-litter than no-litter plots. The relative abundances of Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were positively correlated with microbial biomass C and nitrogen (N), and soil N and C pools, while acidobacterial relative abundance was negatively correlated with these same factors. Bacterial:archaeal ratios were positively correlated with soil moisture, total soil C and N, extractable ammonium pools, and soil C:N ratios. Additionally, bacterial:archaeal ratios were positively related to the relative abundance of Actinobacteria, Gammaproteobacteria, and Actinobacteria, and negatively correlated to the relative abundance of Nitrospira and Acidobacteria. Together, our results support the copiotrophic/oligotrophic model of soil heterotrophic microbes suggested by Fierer et al. (2007).     

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.     

不同温度下尿素对水稻土甲烷产生及相关古菌群落的影响

水稻田是大气甲烷的重要排放源。尿素氮肥施用是提升水稻产量和品质的重要措施,但其对稻田土壤中产甲烷古菌的影响规律仍不清楚。通过模拟水稻生长季节可能的田间温度变化,本研究设置水稻土施加尿素(N,400 mg/kg干土)与未施加尿素两个处理,在15℃、25℃、37℃以及50℃下进行为期100天的厌氧培养,定期测定了培养过程中甲烷累积量以及土壤理化因子如p H、NH_4~+-N以及有机碳的变化,并运用基于16S r RNA基因的T-RFLP(末端限制性片段多态性分析)技术分析了产甲烷过程中古菌群落结构随时间的变化情况。结果表明:在中低温范围内(15~37℃),尿素对水稻土产甲烷有抑制作用,但在50℃高温下尿素对水稻土产甲烷量没有显著影响。尿素可能通过改变产甲烷古菌群落结构来影响甲烷的产生,在15~37℃范围内,尿素降低了水稻土产甲烷古菌群落的稳定性,增大了其在不同时间的差异性;而在50℃高温时,尿素对水稻土产甲烷古菌稳定性和差异性的影响不明显。不同温度下,尿素均降低了甲烷八叠球菌(Methanosarcinaceae)的丰度,且随着温度的变化,尿素对水稻土产甲烷机制的改变可能没有影响。     

三疣梭子蟹(Portunus trituberculatus)两种养殖塘水体古菌的季节变化

结合基于古菌16S rRNA 基因的末端限制性片段长度多态性(T-RFLP)技术与克隆测序技术对象山港三疣梭子蟹–脊尾白虾混养模式下改良塘 M1(塘底铺网、四周铺砂的养殖塘)以及传统塘M2(土塘)不同季节水体古菌群落结构和多样性进行分析。结果显示,M1、M2养殖塘水体古菌群落均由泉古菌门(Crenarchaeota)和广古菌门(Euryarchaeota)组成。M1、M2水体古菌群落组成在养殖初期较相似,但随着养殖时间的推移,古菌群落结构组成发生显著差异。M2养殖水体古菌群落结构随时间变化的差异性大于 M1,说明 M2养殖生态古菌群落稳定性低于 M1,底铺网、四周铺砂的改良措施可以减少古菌群落变化的幅度。相关性分析发现,多样性指数高时,古菌分布受环境的影响较小;2种养殖塘水体古菌分布受温度、溶解氧、总氮和总磷的影响较大。     

Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis

Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis （DGGE） with two primer pairs （344fGC/519r and 519f/915rGC） and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE proifles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no signiifcant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs;however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A （mcrA） gene fragments ampliifed with real-time PCR showed all samples possessed a single peak at 82＆#176;C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase （including diet factor） other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.     

Wildfire effects on the properties and microbial community structure of organic horizon soils in the New Jersey Pinelands

The frequency and intensity of wildfires are expected to increase in the coming years due to the changing climate, particularly in areas of high net primary production. Wildfires represent severe perturbations to terrestrial ecosystems and may have lasting effects. The objective of this study was to characterize the impacts of wildfire on an ecologically and economically important ecosystem by linking soil properties to shifts in microbial community structure in organic horizon soils. The study was conducted after a severe wildfire burned over 7000 ha of the New Jersey Pinelands, a low nutrient system with a historical incidence of fires. Soil properties in burned and non-burned soils were measured periodically up to two years after the fire occurred, in conjunction with molecular analysis of the soil bacterial, fungal and archaeal communities to determine the extent and duration of the ecosystem responses. The results of our study indicate that the wildfire resulted in significant changes in the soil physical and chemical characteristics in the organic horizon, including declines in soil organic matter, moisture content and total Kjeldahl nitrogen. These changes persisted for up to 25 months post-fire and were linked to shifts in the composition of soil bacterial, fungal and archaeal communities in the organic horizon. Of particular interest is the fact that the bacterial, fungal and archaeal communities in the severely burned soils all changed most dramatically during the first year after fire, changed more slowly during the second year after the fire, and were still distinct from communities in the non-burned soils 25 months post-fire. This slow recovery in soil physical, chemical and biological properties could have long term consequences for the soil ecosystem. These results highlight the importance of relating the response of the soil microbial communities to changing soil properties after a naturally occurring wildfire.     

Bacteria dominate ammonia oxidation in soils used for outdoor cattle overwintering

In areas used for cattle overwintering detrimental effects normally associated with grazing are intensified. Among the alterations observed, increases on the N availability and soil pH may highly influence structure of ammonia oxidizing microbes and thus influence nitrification pattern in soil. To evaluate this assumption, we assessed the abundance and diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in three sites with different degrees of animal impact (severe, moderate or no impact) of an overwintering pasture by means of qPCR and T-RFLP of amoA genes. In areas where no animal impact could be identified AOA was dominating over AOB. However, AOB abundance increased as the degree of animal impact enhances, becoming most dominant in the severely impacted site. Interestingly, the diversity of AOB was the highest in the severely impacted area, where AOA diversity was the lowest. Obviously the pressure imposed by altered environmental conditions created by cattle husbandry lead to the selection of AOB and AOA populations, adapted to alkaline pH and higher ammonia concentration.