The ratio of fungi and bacteria in the biomass of different types of soil determined by selective inhibition

Tundra, chernozem (virgin and arable), soddy-podzolic (coniferous forest, meadow, and arable), and grey forest (larch forest) soils were used to separate the contributions of fungi and bacteria to substrate-induced respiration (SIR) with the help of antibiotics. For soils with a high content of organic matter (tundra and chernozem: 12 and 8%, respectively), the procedure of selective inhibition of SIR has been optimized. This procedure consists in application of high concentrations of streptomycin (50–120 mg/g of soil) and cycloheximide (50–80 mg/g of soil) and decreasing the weight of the analyzed soil sample. Soils under study have shown the predominant contribution of fungi (63–82%) to the total SIR. The fungal-bacterial ratio in the soils of natural ecosystems (0–5 cm, without litter) was 4.3, 2.2, 1.5, and 1.5 for tundra soil, virgin chernozem, coniferous (soddy-podzolic soil), and larch (grey forest soil) forests, respectively. The lower layers of soddy-podzolic (5–10 cm) and grey forest (48–58 cm) soils showed a decrease in the fungal and increase in the bacterial component in the total SIR.     

中国农田土壤呼吸速率及驱动因子

土壤呼吸在全球碳收支中具有重要地位.研究中国典型农业区土壤呼吸的时空格局及影响因素,有助于构建区域尺度土壤呼吸定量评价模型,能够为评估中国乃至全球农业生态系统碳/源汇特征提供依据.本研究整合了2000~2012年中国农田生态系统土壤呼吸的主要研究成果,分析了华南、西南、华北、西北和东北5个典型农业区土壤呼吸的季节变化和区域差异,以及影响土壤呼吸的主要驱动因子.结果表明,5个典型农业区的土壤呼吸均存在明显的季节变化特征;中国农田生态系统年均土壤呼吸速率为(682.8±18.3)g C m?2.5个典型农业区年均土壤呼吸速率大小表现为华南区西南区华北区东北区西北区.全国农业土壤的年呼吸通量为(0.90±0.02)Pg C;水作和旱作两种土地利用类型间土壤呼吸速率差异显著(P0.05),旱作土壤呼吸速率约为水作的1.3倍;不同作物类型间土壤呼吸速率差异显著(P0.05),其排序为棉花玉米大豆水稻小麦;农田土壤呼吸与年均气温、土壤温度、土壤含水量和净初级生产力等影响因素呈显著正相关(P0.01),而与年均降水量的相关性不显著.     

Despite Long-Term Compost Amendment Seasonal Changes are Main Drivers of Soil Fungal and Bacterial Population Dynamics in a Tuscan Vineyard

The effect of long-term (8 years) compost treatments (compost or compost plus mineral fertilizer) on genetic structure of bacterial and fungal populations in both bulk soil and rhizosphere of grapevine (Vitis vinifera) was analyzed in respect to a control constituted by the soil treated with mineral fertilization. Soils were sampled in early summer (July), mid-summer (August), and before harvest (October). Bacterial and fungal populations were characterized by genetic fingerprints generated by the application of 16S rDNA and ITS rDNA Multiplex Terminal Fragment Length Polymorphism (M-TRFLP) technique. Compost induced no significant differences at any time on microbial communities from bulk soil samples, whereas seasonal variations significantly affected both bacterial and fungal populations as indicated by the Multi Dimensional Scaling (MDS) ordination method of the M-TRFLPs results. MDS analysis of grapevine rhizosphere M-TRFLPs showed that temporal separation was significant for the bacterial population only. Results suggested that soil microbial populations in vineyard productive ecosystems may be sensitive to environmental changes induced by seasonal variations and show a certain degree of resilience to different agricultural practices.     

Bacterial and Fungal Diversity of Quaternary Cave Sediment Deposits

The bacterial and fungal assemblages of clastic sediments collected from two caves located in north-western Romania were investigated by assessing ITS and 16S rRNA gene diversity. Bacterial members belonging to Chloroflexi, Nitrospirae, Proteobacteria, Firmicutes, Acidobacteria, Gemmatimonadetes, and fungal members of Ascomycota were identified. Except for Bacillus sp., all bacteria were related to uncultured or unknown species and the majority (86%) of the bacterial sequences from one of the caves had no close GenBank relatives. The bacterial sequences obtained clustered with species found in extreme environments. Half of the bacterial operational taxonomic units were clustered with clones isolated from deep subsurface sediments of a radioactively contaminated site in the USA. The present study represents the first attempt to identify microorganisms in Quaternary cave sediments.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Fungal and Bacterial Activity in Northern Peatlands

Selective inhibition of substrate-induced respiration with antibiotics cycloheximide and streptomycin sulphate provided insight into eukaryotic versus prokaryotic activities in surface peat soil of three Canadian peatlands. Prokaryotic and eukaryotic communities in peatlands are important in the net sequestration of atmospheric carbon dioxide and therefore play a unique role in global carbon cycling. Selective inhibition techniques were generally successful, with a maximum non-target inhibition of only 17%. Assuming that eukaryotic and prokaryotic activities were dominated by fungi and bacteria respectively, across 3 ecologically and hydrologically diverse and spatially dispersed peatlands, we demonstrated bacterial dominance in a bog and a poor fen both with acidic and primarily Sphagnum derived peat soil and in a near pH neutral wetter rich fen with sedge peat (fungal to bacterial activity ratio = 0.31 to 0.68). These results differ in that in other acidic environments, such as conifer forest soils, fungal to bacterial activity ratios are mostly greater than 1 indicative of fungal dominance.     

Fungal Taxa Target Different Carbon Sources in Forest Soil

Soil microbes are among the most abundant and diverse organisms on Earth. Although microbial decomposers, particularly fungi, are important mediators of global carbon and nutrient cycling, the functional roles of specific taxa within natural environments remain unclear. We used a nucleotide-analog technique in soils from the Harvard Forest to characterize the fungal taxa that responded to the addition of five different carbon substrates—glycine, sucrose, cellulose, lignin, and tannin-protein. We show that fungal community structure and richness shift in response to different carbon sources, and we demonstrate that particular fungal taxa target different organic compounds within soil microcosms. Specifically, we identified eleven taxa that exhibited changes in relative abundances across substrate treatments. These results imply that niche partitioning through specialized resource use may be an important mechanism by which soil microbial diversity is maintained in ecosystems. Consequently, high microbial diversity may be necessary to sustain ecosystem processes and stability under global change. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. K. K. T., M. A. B., and M. D. W. conceived the project. C. A. H. performed the molecular work and sequence alignments. M. A. B. performed the substrate-induced respiration experiment. S. D. A. and K. K. T. analyzed the data. C. A. H. wrote the article with input from the other authors.     

Soil Respiration in Different Agricultural and Natural Ecosystems in an Arid Region

The variation of different ecosystems on the terrestrial carbon balance is predicted to be large. We investigated a typical arid region with widespread saline/alkaline soils, and evaluated soil respiration of different agricultural and natural ecosystems. Soil respiration for five ecosystems together with soil temperature, soil moisture, soil pH, soil electric conductivity and soil organic carbon content were investigated in the field. Comparing with the natural ecosystems, the mean seasonal soil respiration rates of the agricultural ecosystems were 96%–386% higher and agricultural ecosystems exhibited lower CO₂ absorption by the saline/alkaline soil. Soil temperature and moisture together explained 48%, 86%, 84%, 54% and 54% of the seasonal variations of soil respiration in the five ecosystems, respectively. There was a significant negative relationship between soil respiration and soil electrical conductivity, but a weak correlation between soil respiration and soil pH or soil organic carbon content. Our results showed that soil CO₂ emissions were significantly different among different agricultural and natural ecosystems, although we caution that this was an observational, not manipulative, study. Temperature at the soil surface and electric conductivity were the main driving factors of soil respiration across the five ecosystems. Care should be taken when converting native vegetation into cropland from the point of view of greenhouse gas emissions.     

Deep Autotrophic Soil Respiration in Shrubland and Woodland Ecosystems in Central New Mexico

Quantifying the controls on soil respiration is important for understanding ecosystem physiology and for predicting the response of soil carbon reservoirs to climate change. The majority of soil respiration is typically considered to occur in the top 20–30 cm of soils. In desert soils, where organic matter concentrations tend to be low and plants are deeply rooted, deeper respiration might be expected. However, little is known about the depth distribution of respiration in dryland soils. Here we show that the average depth of soil respiration between pulse precipitation events is almost always greater than 20 cm and is frequently greater than 50 cm in two central New Mexico desert shrublands. The average depth of soil respiration in a pi?on-juniper woodland was shallower, between 5 and 40 cm. In the shrublands, 8‰ seasonal variations in the carbon isotope composition of soil-respired CO₂ (δ¹³C_r-soil) that correlate with vapor pressure deficit support root/rhizosphere respiration as the dominant source of soil CO₂. Such deep autotrophic respiration indicates that shrubs preferentially allocate photosynthate to deep roots when conditions near the surface are unfavorable. Therefore, respiration rates in these soils are not necessarily correlated with root biomass. The δ¹³C_r-soil values provide no evidence for CO₂ evolved from soil inorganic carbon. Our results also suggest that organic carbon cycling is rapid and efficient in these soils and that the δ¹³C value of CO₂ respired from soils in much of the southwestern US, and perhaps in other semiarid regions, varies seasonally by at least 4‰.     

Ecology of Soil Erosion in Ecosystems

Each year, about 75 billion tons of soil are eroded from the world's terrestrial ecosystems. Most agricultural land in the world is losing soil at rates ranging from 13 tons/ha/year to 40 tons/ha/year. Because soil is formed very slowly, this means that soil is being lost 13–40 times faster than the rate of renewal and sustainability. Rain and wind energy are the two prime causes of erosion from tilled or bare land. Erosion occurs when the soil lacks protective vegetative cover. Soil erosion reduces the productivity of the land by loss of water, soil organic matter, nutrients, biota, and depth of soil. The greatest threat to providing food for a rapidly growing human population is soil erosion. Abandoned, eroded agricultural land is replaced by clearing forested ecosystems. Received 17 February 1998; accepted 26 May 1998.     

Metal Toxicity Affects Fungal and Bacterial Activities in Soil Differently

Although the toxic effect of heavy metals on soil microorganism activity is well known, little is known about the effects on different organism groups. The influence of heavy metal addition on total, bacterial, and fungal activities was therefore studied for up to 60 days in a laboratory experiment using forest soil contaminated with different concentrations of Zn or Cu. The effects of the metals differed between the different activity measurements. During the first week after metal addition, the total activity (respiration rate) decreased by 30% at the highest level of contamination and then remained stable during the 60 days of incubation. The bacterial activity (thymidine incorporation rate) decreased during the first days with the level of metal contamination, resulting in a 90% decrease at the highest level of contamination. Bacterial activity then slowly recovered to values similar to those of the control soil. The recovery was faster when soil pH, which had decreased due to metal addition, was restored to control values by liming. Fungal activity (acetate-in-ergosterol incorporation rate) initially increased with the level of metal contamination, being up to 3 and 7 times higher than that in the control samples during the first week at the highest levels of Zn and Cu addition, respectively. The positive effect of metal addition on fungal activity then decreased, but fungal activity was still higher in contaminated than in control soil after 35 days. This is the first direct evidence that fungal and bacterial activities in soil are differently affected by heavy metals. The different responses of bacteria and fungi to heavy metals were reflected in an increase in the relative fungal/bacterial ratio (estimated using phospholipid fatty acid analysis) with increased metal load.     

Temperature Dependence of Soil Respiration Modulated by Thresholds in Soil Water Availability Across European Shrubland Ecosystems

Soil respiration (SR) is a major component of the global carbon cycle and plays a fundamental role in ecosystem feedback to climate change. Empirical modelling is an essential tool for predicting ecosystem responses to environmental change, and also provides important data for calibrating and corroborating process-based models. In this study, we evaluated the performance of three empirical temperature–SR response functions (exponential, Lloyd–Taylor and Gaussian) at seven shrublands located within three climatic regions (Atlantic, Mediterranean and Continental) across Europe. We investigated the performance of SR models by including the interaction between soil moisture and soil temperature. We found that the best fit for the temperature functions depended on the site-specific climatic conditions. Including soil moisture, we identified thresholds in the three different response functions that improved the model fit in all cases. The direct soil moisture effect on SR, however, was weak at the annual time scale. We conclude that the exponential soil temperature function may only be a good predictor for SR in a narrow temperature range, and that extrapolating predictions for future climate based on this function should be treated with caution as modelled outputs may underestimate SR. The addition of soil moisture thresholds improved the model fit at all sites, but had a far greater ecological significance in the wet Atlantic shrubland where a fundamental change in the soil CO₂ efflux would likely have an impact on the whole carbon budget.     

从药用植物根际土壤中分离出的2个中国新记录种(英文)

在进行黑龙江省药用植物根际土壤真菌多样性的研究中,分离获得了2个中国新记录种:蕨枝顶孢[Acremonium pteridii(J.C.Frankland)W.Gams]和穴形节皮菌的金孢属无性型[Chrysosporium anamorph ofArthro-derma cuniculi(Dawson)C.A.N.van Oorschot]。蕨枝顶孢的主要形态特征为分生孢子梗单生或二次及三次分支,具有1~3个隔膜,顶端着生单个分生孢子;分生孢子以假头状着生,卵形或者近圆形,内含1个油球。穴形节皮菌的金孢属无性型主要形态特征为短的侧分支与可育菌丝呈直角伸出,分生孢子具柄,生于短的突起上或者直立的侧分支上;分生孢子卵形或棍棒形,顶端钝圆,基部平截,大多数单胞,极少数为由2~3个细胞组成。文中对它们进行了详细的形态特征描述,标本保存于大连民族学院菌种保藏中心。     

草地群落的土壤呼吸

通过土壤呼吸作用向大气释放ＣＯ２是陆地生态系统碳循环的一个最主要的环节,也是人类活动影响下陆地生态系统对大气中ＣＯ２浓度产生影响,从而导致全球气候变化的关键生态学过程,因而成为全球碳循环研究中倍受关注的核心问题［３３,３７,３８］。１土壤呼吸的测定方...     

Long-Term Phosphorus Fertilization Impacts Soil Fungal and Bacterial Diversity but not AM Fungal Community in Alfalfa

Soil function may be affected by cropping practices impacting the soil microbial community. The effect of different phosphorus (P) fertilization rates (0, 20, or 40 kg P₂O₅ ha⁻¹) on soil microbial diversity was studied in 8-year-old alfalfa monocultures. The hypothesis that P fertilization modifies soil microbial community was tested using denaturing gradient gel electrophoresis and phospholipids fatty acid (PLFA) profiling to describe soil bacteria, fungi, and arbuscular mycorrhizal (AM) fungi diversity. Soil parameters related to fertility (soil phosphate flux, soluble P, moisture, phosphatase and dehydrogenase assays, and carbon and nitrogen content of the light fraction of soil organic matter) were also monitored and related to soil microbial ribotype profiles. Change in soil P fertility with the application of fertilizer had no effect on crop yield in 8 years, but on the year of this study was associated with shifts in the composition of fungal and bacterial communities without affecting their richness, as evidenced by the absence of effect on the average number of ribotypes detected. However, variation in soil P level created by a history of differential fertilization did not significantly influence AM fungi ribotype assemblages nor AM fungi biomass measured with the PLFA 16:1ω5. Fertilization increased P flux and soil soluble P level but reduced soil moisture and soil microbial activity, as revealed by dehydrogenase assay. Results suggest that soil P fertility management could influence soil processes involving soil microorganisms. Seasonal variations were also recorded in microbial activity, soil soluble P level as well as in the abundance of specific bacterial and fungal PLFA indicators of soil microbial biomass.     

Soil Drying As a Model for the Action of Stress Factors on Natural Bacterial Populations

The drying of soil samples reduced the abundance (especially of predominant species) and the diversity of bacteria isolated from these samples, making easier the isolation of rare bacterial species. Some bacterial species that were minor before soil drying became dominant in dried soil samples. In general, soil drying allowed the diversity of soil bacteria to be determined more adequately. The bacteria that were isolated from dried soil samples turned out to be resistant to gamma radiation (with LD₉₀ = 2.8–4.6 kGy) and desiccation. It is concluded that soil drying may serve as a model for the action of stress factors on natural bacterial populations. The hypothesis that periodic desiccation was the primary cause of formation of bacterial radioresistance in nature is discussed.     

Soil Carbon Dioxide Flux in Antarctic Dry Valley Ecosystems

The Antarctic dry valleys of southern Victoria Land are extreme desert environments where abiotic factors, such as temperature gradients, parent material, and soil water dynamics, may have a significant influence on soil carbon dioxide (CO₂) flux. Previous measurements of soil respiration have demonstrated very low rates of CO₂ efflux, barely above detection limits. We employed a modified infrared gas-analyzer system that enabled detection of smaller changes in CO₂ concentration in the field than previously possible. We measured diel CO₂ fluxes and monitored soil microclimate at three sites in Taylor Valley. Soil CO₂ flux ranged from –0.1 to 0.15 mol m^–2 s^–1. At two of the three sites, we detected a physically driven flux associated with diel variability in soil temperature. At these sites, CO₂ uptake (negative flux) was associated with dropping soil temperatures, whereas CO₂ evolution (positive flux) was associated with increases in soil temperature. These observations are corroborated by laboratory experiments that suggest that CO₂ flux is influenced by physically driven processes. We discuss four potential mechanisms that may contribute to physically driven gas exchange. Our results suggest there are strong interactions between biological and abiotic controls over soil CO₂ flux in terrestrial ecosystems of the Antarctic dry valleys, and that the magnitude of either may dominate depending on the soil environment and biological activity.     

Short-Term Response of Soil Enzyme Activity and Soil Respiration to Repeated Carbon Nanotubes Exposure

Nanomaterials such as single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) may repeatedly enter the soil environment with unknown adverse consequences. To provide the information on the effects of repeated exposure of CNTs, we determined the response of soil enzyme activity and soil basal respiration (SBR) through a two-week incubation of farmland soil repeatedly treated with different concentrations of CNTs (100, 200, 500 mg kg^?1 for SWCNTs and 100, 500, 1000 mg Kg^?1 for MWCNTs). The activities of catalase, alkaline phosphatase, and invertase and SBR were measured after one- and two-time treatments. The repeated contamination of SWCNTs and MWCNTs repressed the activity of alkaline phosphatase and invertase in the 14-day incubation. Alkaline phosphatase and invertase were more sensitive indicators of CNTs’ contamination than catalase and soil basal respiration. High concentration of the SWCNTs stimulated SBR while the lower concentration suppressed SBR. The recurred exposure of SWCNTs and MWCNTs repressed the activity of catalase and invertase. The obtained results indicated that the soil microorganisms were suppressed under repeated pollution, as suggested by the same suppressed response of SBR between SWCNTs and MWCNTs treatment, except for the concentration of 500 mg kg^?1.     

Effects of Fungal Bioaugmentation and Cyclodextrin Amendment on Fluorene Degradation in Soil Slurry

This study assesses the potential of fungal bioaugmentation and the effect of maltosyl-cyclodextrin amendment, as an approach to accelerate fluorene biodegradation in soil slurries. 47 fungal strains isolated from a contaminated site were tested in the biodegradation of fluorene. Results showed the greater efficiency of "adaptated" fungi isolated from contaminated soil vs. reference strains belonging to the collection of the laboratory. These assays allowed us to select the most efficient strain, Absidia cylindrospora, which was used in a bioaugmentation process. In the presence of Absidia cylindrospora, more than 90% of the fluorene was removed in 288 h while 576 h were necessary in the absence of fungal bioaugmentation. Maltosyl-cyclodextrin, a branched-cyclodextrin was chosen in order to optimize fluorene bioavailability and biodegradation in soil slurries. The results of this study indicate that Absidia cylindrospora and maltosyl-cyclodextrin could be used successfully in bioremediation systems.     

Mycorrhizal and Endophytic Fungal Colonization in Arrhenatherum elatius L. Roots According to the Soil Contamination in Heavy Metals

The aim of this work was to jointly study non-mycorrhizal (dark septate fungi) and mycorrhizal (arbuscular mycorrhizae) colonization along a large range of heavy metal pollution in soil in order to determine the effective contribution of each type of endophytes in relation to heavy metal uptake and tolerance. Hence, eight sites were chosen in the mining area of northern France with respect both to a large range of heavy metal contamination (Cd, Pb, Zn) and monospecific colonization by Arrhenatherum elatius. Root colonization with both arbuscular mycorrhizae (AM) and dark septate fungi (DSF) as well as spore density in rhizospheric soil were estimated in relation to soil characteristics. Mycorrhizal infestation (hyphae, arbuscules and vesicles) was adversely affected by soil pollution almost to exclusion. The intensity of colonization with DSF was very low in presence of AM in non-contaminated soils but higher in polluted soils. The effect of the fungal colonization on the heavy metal tolerance of Arrhenatherum elatius is discussed.     

毛竹林和阔叶林凋落物互置对土壤氮矿化的影响及微生物贡献

凋落物输入方式的改变导致凋落物数量和质量发生变化,进而对森林土壤氮矿化产生影响。选择未被入侵的次生阔叶林和毛竹入侵后形成的毛竹纯林为对象,对地表凋落物进行保留、去除与置换处理,采用室内培养法同时添加抗生素(链霉素和放线菌酮)分析真菌和细菌在土壤氮素矿化中的贡献。结果表明：(1)去除凋落物处理使阔叶林土壤净氨化速率增加27.0%,净硝化速率降低11.4%;毛竹林土壤净氨化速率增加23.4%。(2)置换凋落物处理使阔叶林土壤净氨化速率增加43.8%,净硝化速率降低33.5%;毛竹林土壤净硝化速率增加73.1%。(3)添加抗生素后,凋落物置换处理与对照相比,置换凋落物后阔叶林土壤真菌和细菌在净氨化中发挥主要作用;真菌在两种林分土壤净硝化中发挥主要作用,细菌在阔叶林土壤净硝化中发挥主要作用。(4)结合测定的凋落物化学性质可知,置换凋落物后引起真菌和细菌在土壤氮素矿化中贡献发生变化,是由于输入凋落物中木质素和纤维素含量的变化。综上,凋落物去除和置换改变了土壤氮素矿化速率,置换凋落物后改变了真菌和细菌对土壤氮素矿化的贡献。解析凋落物质量在土壤氮素矿化中的作用及微生物群落的相对贡献,有助于阐明毛竹入...