Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils

Root-derived carbon (C) is considered as critical fuel supporting the interaction between plant and rhizosphere microbiome, but knowledge of how plant–microbe association responds to soil fertility changes in the agroecosystem is lacking. We report an integrative methodology in which stable isotope probing (SIP) and high-throughput pyrosequencing are combined to completely characterize the root-feeding bacterial communities in the rhizosphere of wheat grown in historical soils under three long-term (32-year) fertilization regimes. Wheat root-derived ¹³C was dominantly assimilated by Actinobacteria and Proteobacteria (notably Burkholderiales), accounting for nearly 70% of root-feeding microbiome. In contrast, rhizosphere bacteria utilizing original soil organic matter (SOM) possessed a higher diversity at phylum level. Some microbes (e.g. Bacteroidetes and Chloroflexi) enhancing in the rhizosphere were not actively recruited through selection by rhizodeposits, indicating a limited range of action of root exudates. Inorganic fertilization decreased the dependence of Actinobacteria on root-derived C, but significantly increased its proportion in SOM-feeding microbiome. Furthermore, significantly lower diversity of the root-feeding microbiome, but not the SOM-feeding microbiome, was observed under both organic and inorganic fertilizations. These results revealed that long-term fertilizations with increasing nutrients availability would decrease the preference of rhizosphere microbiome for root-derived substrates, leading to a simpler crop–microbe association.     

Diet and trophic niche of the endangered fish Garra ghorensis in three Jordanian populations

Garra ghorensis is a small riverine cyprinid fish endemic to the southern Dead Sea that is endangered through habitat loss and invasive species. Here, their diet and trophic niche were assessed in three Jordanian populations: an allopatric population, a population sympatric with native Capoeta damascina and a population sympatric with invasive Oreochromis aureus. Stomach content analyses of samples collected between February 2011 and January 2012 revealed that detritus and algae were prominent food items in their diets, with low dietary contributions of animal material. The most frequent and abundant macro‐invertebrates in intestines were Odonata nymphs and gastropod species. The calculation of trophic niche size from the stomach content data revealed that the niche of G. ghorensis (0.10) was generally smaller than sympatric C. damascina (0.24), with an overlap of 72%, whereas they had a larger trophic niche than sympatric O. aureus (0.20–0.13), with a niche overlap of 54%. These outputs were generally supported by stable isotope analyses of δ¹³C and δ¹⁵N completed on samples collected at the end of the 2011 growth season, although these indicated a greater contribution of animal material to assimilated diet. They also indicated that the trophic niche breadth [as standard ellipse area (SEA)] of C. damascina (4.18‰²) was higher than G. ghorensis (2.48‰²) and overlapped by 26%. For G. ghorensis, their SEA was slightly larger than O. aureus (4.33–4.00‰²), with an overlap of 27%. Although both methods indicated some sharing of food resources between sympatric fishes, there was no evidence suggesting detrimental outcomes for G. ghorensis and thus was not considered as a constraint on the status of their populations.     

Sheep excreta cause no positive priming of peat-derived CO2 and N2O emissions

Large areas of peatlands in Germany and the Netherlands are affected by drainage and high nitrogen deposition. Sheep grazing is a common extensive management activity on drained peatlands, in particular on nature protection areas. However, input of easily mineralisable material such as sheep excrements could enhance degradation of soil organic carbon (C_org), thereby increasing the effect of these ecosystems on national GHG budgets. Thus, a microcosm experiment on the influence of sheep excreta on GHG emissions from a histic Gleysol with strongly degraded peat was set up. The ¹⁵N and ¹³C stable isotope tracer technique was used to partition sources of CO₂ and N₂O. Labeled sheep faeces and urine were obtained by feeding enriched material. Undisturbed soil columns were treated with surface application of urine, faeces or mixtures of both in different label combinations to distinguish between direct effects and possible priming effects. Incubation was done under stable temperature and precipitation conditions. Fluxes as well as ¹⁵N and ¹³C enrichment of N₂O and CO₂, respectively, were measured for three weeks. Addition of sheep excreta increased emission of total CO₂ in proportion to the added carbon amounts. There was no CO₂ priming in the peat. No effect on CH₄ and N₂O was observed under the aerobic experimental conditions. The N₂O–N source shifted from peat to excreta, which indicates negative priming, but priming was not significant. The results indicate that sheep excreta do not significantly increase GHG emissions from degraded peat soils. Considering the degraded peatland preserving benefits, sheep grazing on peatlands affected by drainage and high nitrogen deposition should be further promoted.     

Integrated biomonitoring of airborne pollutants over space and time using tree rings,bark, leaves and epiphytic lichens

The integrated use of tree rings and outer tissues, and lichens, was tested for monitoring how pollutant concentrations vary in space and over time nearby an incinerator in industrial area in Central Italy. Trace elements in thalli of lichen Xanthoria parietina and in leaves, bark, wood of Quercus pubescens, as well as carbon, oxygen and nitrogen isotope ratios in tree rings were analyzed. Some trace elements in the leaves differed significantly between the plots, though this was not the case in lichens and bark. The values of δ¹³C and δ¹⁸O showed the same trend in all plots, while the values of δ¹⁵N were higher in the distal plot. The results indicated that trace elements were intercepted and collected by tree bark and leaves, as well as lichens, at low concentrations, and that they hardly entered into tree xylem tissues during the growing season to be stored into the woody tissues. Indeed, the study did not highlight marked changes over time and space, in accumulation of airborne pollutants in the selected biomonitors, most probably due to the low levels of industrial development. Nevertheless, the analysis of tree ring cores in combination with bark and leaves, and lichens might potentially contribute to depict historic impacts of airborne pollutants at pronounced concentrations.     

中亚哈萨克斯坦西部过去～30000年以来有机碳同位素变化及其意义

选取位于中亚干旱区哈萨克斯坦中西部的VA剖面作为研究对象,在AMS14C测年基础上,分析了该剖面记录的过去～30000年以来的有机碳同位素组成变化。结果表明:该剖面记录的过去～30000年以来有机质碳同位素值(δ13Corg)变化于-26.19‰--22.12‰之间,均值为-23.77‰,植被主要为C3植物,C4植物仅仅在末次冰盛期出现且其相对丰度极低。因此VA剖面土壤有机碳同位素组成变化主要反映的是C3植物对气候环境因子的响应,进一步对影响该地区植物碳同位素因素的分析发现,降水是控制该地区C3植物碳同位素变化的主要因素,即:降水增多导致C3植物碳同位素值偏负,可以用来指示研究区古降水变化趋势,CO2浓度以及温度仅仅在末次冰盛期对C3和C4植物相对丰度有一定的影响。     

稻田生物固氮研究进展及方向

稻田淹水产生的合适pH和氧化-还原条件为固氮微生物的固氮提供了适宜环境条件,使得稻田在多年不施氮肥条件下仍能维持一定产量,而旱地产量则逐年下降。随着化学氮肥用量的增加,导致了严重的环境污染,迫切需要增加生物固氮来保证粮食生产和减少环境污染。为发挥稻田生物固氮功能,我们对稻田生物固氮的研究方法、固氮量、固氮微生物、影响因素、调控及其研究方向进行综述,以期为稻田生物固氮研究提供参考。     

Microbial immobilization of ammonium and nitrate in relation to ammonification and nitrification rates in organic and conventional cropping systems

Agricultural systems that receive high or low organic matter (OM) inputs would be expected to differ in soil nitrogen (N) transformation rates and fates of ammonium (NH₄⁺) and nitrate (NO₃⁻). To compare NH₄⁺ availability, competition between nitrifiers and heterotrophic microorganisms for NH₄⁺, and microbial NO₃⁻ assimilation in an organic vs. a conventional irrigated cropping system in the California Central Valley, chemical and biological soil assays, ¹⁵N isotope pool dilution and ¹⁵N tracer techniques were used. Potentially mineralizable N (PMN) and hot minus cold KCl-extracted NH₄⁺ as indicators of soil N supplying capacity were measured five times during the tomato growing season. At mid-season, rates of gross ammonification and gross nitrification after rewetting dry soil were measured in microcosms. Microbial immobilization of NO₃⁻ and NH₄⁺ was estimated based on the uptake of ¹⁵N and gross consumption rates. Gross ammonification, PMN, and hot minus cold KCl-extracted NH₄⁺ were approximately twice as high in the organically than the conventionally managed soil. Net estimated microbial NO₃⁻ assimilation rates were between 32 and 35% of gross nitrification rates in the conventional and between 37 and 46% in the organic system. In both soils, microbes assimilated more NO₃⁻ than NH₄⁺. Heterotrophic microbes assimilated less NH₄⁺ than NO₃⁻ probably because NH₄⁺ concentrations were low and competition by nitrifiers was apparently strong. The high OM input organic system released NH₄⁺ in a gradual manner and, compared to the low OM input conventional system, supported a more active microbial biomass with greater N demand that was met mainly by NO₃⁻ immobilization.     

Purification and isotopic signatures (<Emphasis Type="Italic">δ</Emphasis><Superscript>13</Superscript>C, <Emphasis Type="Italic">δ</Emphasis><Superscript>15</Superscript>N, Δ<Superscript>14</Superscript>C) of soil extracellular DNA

The aim of this work was to obtain pure extracellular DNA molecules so as to estimate their longevity in soil by an isotope-based approach. Extracellular DNA molecules were extracted from all horizons of a forest soil and purified by the procedure of Davis (Purification and precipitation of genomic DNA with phenol–chloroform and ethanol. In: Davis LG, Dibner MD, Battey JF (eds) Basic methods in molecular biology. Appleton & Lange, Norwalk, 16–22, 1986) without (DNA1) or with (DNA2) a successive treatment with binding resins followed by elution. The two differently purified DNA samples were compared for their A₂₆₀/A₂₈₀ ratio, polymerase chain reaction (PCR) amplification and natural abundance of stable (¹³C and ¹⁵N) and radioactive (¹⁴C) isotopes. The purity index and the PCR amplification did not differentiate the efficiency of the two purification procedures. The isotopic signature of DNA was more sensitive and was strongly affected by the purification procedures. The isotopic measurements showed that the major contaminant of extracellular DNA1 was the soil organic matter (SOM), even if it is not possible to exclude that the similar δ ¹³C, δ ¹⁵N and Δ¹⁴C values of DNA and SOM could be due to the use of SOM-deriving C and N atoms for the microbial synthesis of DNA. For extracellular DNA2, extremely low values of Δ¹⁴C were obtained, and this was ascribed to the presence of fossil fuel-derived substances used during the purification, although in amounts not revealed by gas chromatography-mass spectrometry analysis. The fact that it is not possible to obtain contaminant-free DNA molecules and the potential use of soil native organic compounds during the microbial synthesis of DNA make it not achievable to estimate the age of soil extracellular DNA by radiocarbon dating.     

Compound specific plant amino acid δ15N values differ with functional plant strategies in temperate grassland

The distribution and natural abundance isotopic (δ¹⁵N) content of whole tissue and individual amino acids in plants in a temperate grassland were determined using ion chromatography (IC), continuous flow‐isotope ratio mass spectrometry (CF‐IRMS), and gas chromatography‐combustion‐isotope ratio mass spectrometry (GC‐C‐IRMS). The results showed that the selected plants (Lolium perenne, Juncus effusus, and Brachythecium rutabulum) differed in their amino acid content and distribution from the parent grassland soil. Bulk and individual amino acid δ¹⁵N isotope signatures were different between the plants, which concurred with their functional strategy in relation to the relative acquisition of available N sources. The individual amino acid δ¹⁵N values of histidine and phenylalanine could be used to differentiate between the three plant species.     

Alder-poplar associations: Determination of plant nitrogen sources by isotope techniques

Summary Three¹⁵N isotopic dilution methods (¹⁵N natural abundance, labelled mineral fertilizer, and organic matter) were used to determine the proportion of N derived from different available sources in seedlines ofAlnus glutinosa andPopulus nigra planted together or in monoculture under natural climatic conditions. The proportion of N derived from N₂ fixation in associated alders was appreciably higher than that determined in monoculture. The reduction of soil N uptake by associated alders contributed to an increase in total plant N and biomass production in associated poplars. When slightly N-labelled organic matter (alder leaf litter) was incorporated into the soil, 10–15% of its initial N content was recovered in poplar tissues, showing that this N source makes an important contribution to the N yield of associated non-fixing plants. There were no significant differences between the results obtained by¹⁵N natural abundance and those obtained by labelled fertilizer methods, suggesting that the ¹⁵N method could be used to evaluate annual N budgets in natural ecosystems.