Arbuscular Mycorrhizas, Microbial Communities, Nutrient Availability, and Soil Aggregates in Organic Tomato Production

Effects of arbuscular mycorrhzal (AM) fungi on plant growth and nutrition are well-known, but their effects on the wider soil biota are less clear. This is in part due to difficulties with establishing appropriate non-mycorrhizal controls in the field. Here we present results of a field experiment using a new approach to overcome this problem. A previously well-characterized mycorrhizal defective tomato mutant (rmc) and its mycorrhizal wildtype progenitor (76R MYC+) were grown at an organic fresh market tomato farm (Yolo County, CA). At the time of planting, root in-growth cores amended with different levels of N and P, were installed between experimental plants to study localized effects of mycorrhizal and non-mycorrhizal tomato roots on soil ecology. Whilst fruit yield and vegetative production of the two genotypes were very similar at harvest, there were large positive effects of colonization of roots by AM fungi on plant nutrient contents, especially P and Zn. The presence of roots colonized by AM fungi also resulted in improved aggregate stability by increasing the fraction of small macroaggregates, but only when N was added. Effects on the wider soil community including nematodes, fungal biomass as indicated by ergosterol, microbial biomass C, and phospholipid fatty acid (PLFA) profiles were less pronounced. Taken together, these data show that AM fungi provide important ecosystem functions in terms of plant nutrition and aggregate stability, but that a change in this one functional group had only a small effect on the wider soil biota. This indicates a high degree of stability in soil communities of this organic farm.     

Species Diversity of Uncultured and Cultured Populations of Soil and Marine Ammonia Oxidizing Bacteria

Although molecular techniques are considered to provide a more comprehensive view of species diversity of natural microbial populations, few studies have compared diversity assessed by molecular and cultivation-based approaches using the same samples. To achieve this, the diversity of natural populations of ammonia oxidising bacteria in arable soil and marine sediments was determined by analysis of 16S rDNA sequences from enrichment cultures, prepared using standard methods for this group, and from 16S rDNA cloned from DNA extracted directly from the same environmental samples. Soil and marine samples yielded 31 and 18 enrichment cultures, respectively, which were compared with 50 and 40 environmental clones. There was no evidence for selection for particular ammonia oxidizer clusters by different procedures employed for enrichment from soil samples, although no culture was obtained in medium at acid pH. In soil enrichment cultures, Nitrosospira cluster 3 sequences were most abundant, whereas clones were distributed more evenly between Nitrosospira clusters 2, 3, and 4. In marine samples, the majority of enrichment cultures contained Nitrosomonas, whereas Nitrosospira sequences were most abundant among environmental clones. Soil enrichments contained a higher proportion of identical sequences than clones, suggesting laboratory selection for particular strains, but the converse was found in marine samples. In addition, 16% of soil enrichment culture sequences were identical to those in environmental clones, but only 1 of 40 marine enrichments was found among clones, indicating poorer culturability of marine strains represented in the clone library, under the conditions employed. The study demonstrates significant differences in species composition assessed by molecular and culture-based approaches but indicates also that, employing only a limited range of cultivation conditions, 7% of the observed sequence diversity in clones of ammonia oxidizers from these environments could be obtained in laboratory enrichment culture. Further studies and experimental approaches are required to determine which approach provides better representation of the natural community.     

柑橘丛枝菌根形态结构观察

以田间栽培的‘国庆1号’温州蜜柑(Citrus unshiu ‘Guoqing No.1’)/枳(Poncirus trifoliata)和‘国庆4号’温州蜜柑(C.unshiu ‘Guoqing No.4’)/枳为试材观察丛枝菌根的形态结构。结果表明,泡囊、丛枝、侵入点、根内菌丝、根外菌丝、根外厚垣孢子等结构出现在柑橘根系中,说明柑橘属于典型的丛枝菌根植物。丛枝菌根结构中泡囊出现概率较小,丛枝随处可见,侵入点多样化。丛枝菌根的结构主要存在柑橘根段的伸长区和成熟区,首次观察到根冠和分生区也有侵染。     

Higher Abundance of Ammonia Oxidizing Archaea than Ammonia Oxidizing Bacteria and Their Communities in Tibetan Alpine Meadow Soils under Long-term Nitrogen Fertilization

Increasing usage of nitrogen fertilizer for food production has resulted in severely environmental problems of nutrients enrichment. This study aimed to examine the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to a long-term nitrogen fertilization in Tibetan alpine meadow. The abundance and composition of both AOB and AOA were assessed using quantitative real-time PCR, cloning and sequencing techniques based on amoA gene under different fertilization gradient (0, 30, 60, 90, and 120 g m^?2 year^?1). Our results showed that, abundances of AOA amoA genes (ranging from 1.48 × 10⁹ to 2.00 × 10⁹ copies per gram of dry soil) were significantly higher than those of AOB amoA genes (1.25 × 10⁷ to 2.62 × 10⁸ copies per gram of dry soil) under fertilization scenario. The abundance of AOB amoA genes increased with increasing nitrogen fertilization, whereas fertilization had little effect on AOA abundance. Sequences of clone libraries of the different treatments revealed that AOB communities were dominated by representatives of Cluster 4, constituting 48.94–64.44% in each clone library. Sequences of Clusters 9, 1 and 2 were prevalent in soils under higher fertilization. All archaeal amoA sequences recovered were affiliated with the soil/sediment clade and marine sediment clade, and no significant difference was observed on the community structure among different fertilization treatments. Variations in the AOB community structure and abundance were linked to ammonium-N and soil pH induced by different fertilization treatments. These results showed that the abundance and structure of the AOB community respond to the fertilization gradient, not AOA.     

Evaluating Primers for Profiling Anaerobic Ammonia Oxidizing Bacteria within Freshwater Environments

Anaerobic ammonia oxidizing (anammox) bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE) fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r) for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r) was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library analysis, A438f/A684r was the most suitable primer set for multiple molecular assessments of anammox bacteria in freshwater environments.     

金沙江干热河谷(元谋段)的丛枝菌根

用碱解离、酸性品红染色法对金沙江干热河谷(元谋段)中生长的60种植物的丛枝菌根状况进行了调查。结果发现被调查植物中70％的植物形成丛枝菌根,干热河谷自然植物群落中的建群种大多具有丛枝菌根,一些莎草科、蓼科的植物也形成典型的丛枝菌根。丛枝菌根是干热河谷生态系统中的重要组成成分,在干热河谷的植被恢复中,必须同时考虑对地下植物共生真菌进行恢复。     

Detection of Methane Oxidizing Bacteria in Forest Soil by Monooxygenase PCR Amplification

Abstract Atmospheric methane oxidation by a spruce forest soil from Norway at 15°C was found to be maximal at a depth of ca 7 cm. Examination of the kinetics of this methane oxidation revealed an apparent Km of 403.1 nM and a Vmax of 2.2 nmol g^-1 dry weight soil h^-1. The low apparent Km suggested the presence of active methane oxidizing bacteria with a high affinity for methane. DNA was extracted from the 5–10 cm horizon, purified, and subjected to PCR amplification with primers directed toward the monooxygenase genes pmoA and amoA, which are essential for methane oxidation. Hybridization analysis of the clone library subsequently constructed revealed that 49% of the 76 cloned PCR fragments were putative methanotroph pmoA sequences and 16% were putative ammonium oxidizing nitrifier amoA sequences. Sequencing of 28 clones identified three major groups showing homology to pmoA from Methylococcus capsulatus, #-subdivision ammonia-oxidizers (amoA), and a new group of monooxygenase pmoA/amoA sequences.     

Arbuscular Mycorrhizas: Drivers or Passengers of Alien Plant Invasion

Observational and manipulative studies have revealed that alien plant invasions are an outcome of interplay between a myriad of biotic and abiotic factors operating at various spatio-temporal stages and scales. Despite the salient role of ubiquitous arbuscular mycorrhizal (AM) fungi in plant interactions, studies exploring the role of such symbionts in invasiveness of alien species and invasibility of communities are limited, in part because of difficult-culturablilty of AM fungi on artificial media and apparent complexities in manipulations of AM-plant interactions in field and laboratory experiments. Moreover, analysis of the AM-plant invasion studies conducted so far have yielded contradictory results with some indicating facilitation of invasion by AM fungi and others its inhibition. Other studies have indicated that arbuscular mycorrhizal symbiosis has no effect on invasiveness of alien plants. While arbuscular mycorrhizas may facilitate invasiveness of some alien plants, such plants may also potentially impact mycorrhizal community structure and functions in the invaded habitats in different ways. The present review addresses these paradoxically conflicting observations in the context of mutualism-commensalism-parasitism gradient that characterizes the relationship between AM fungi and their alien vs. native hosts and also discusses the influence of alien invasive plants on mycorrhizal community structure of invaded ecosystems. Through critical analysis of costs and benefits for invasive plants that associate with AM fungi in their introduced range, invasion-induced shifts in AM mutualism are evaluated in the context of their impact on native biodiversity. Underlining limitations of methodologies and experimental designs usually employed to understand AM-mediated plant invasiveness, we proposes herein some alternative frameworks and experimental approaches to overcome these limitations.     

一株氨氧化细菌的分离鉴定及其氨氧化特性

以城市污水处理工程的好氧活性污泥为菌源,通过富集、分离纯化,筛选出一株自养型氨氧化细菌CM-NRO14,进一步研究了该菌株的系统发育地位及氨氧化特性。根据菌株的形态学特征、生理生化特性及16S rDNA序列测定分析,确定该菌株属于亚硝酸单胞杆菌。CM-NRO14菌株的最大氨氧化速率24.54 mg/(L·d),利用氨的Km值45.66 mg/L,氨自身的抑制常数2401 mg/L,最大氨氧化速率的氨浓度331.2 mg/L。亚硝酸盐对氨氧化的抑制常数1524 mg/L。氨氧化的最适pH 7.79。氨氧化的最适温度34℃。菌株在初始氨氮浓度为180 mg/L,最佳氨氧化pH、温度条件下,4 d内氨氮降解率达到91.6%,菌株倍增时间2.94 d。     

Influence of Season and Plant Species on the Abundance and Diversity of Sulfate Reducing Bacteria and Ammonia Oxidizing Bacteria in Constructed Wetland Microcosms

Constructed wetlands offer an effective means for treatment of wastewater from a variety of sources. An understanding of the microbial ecology controlling nitrogen, carbon and sulfur cycles in constructed wetlands has been identified as the greatest gap for optimizing performance of these promising treatment systems. It is suspected that operational factors such as plant types and hydraulic operation influence the subsurface wetland environment, especially redox, and that the observed variation in effluent quality is due to shifts in the microbial populations and/or their activity. This study investigated the biofilm associated sulfate reducing bacteria and ammonia oxidizing bacteria (using the dsrB and amoA genes, respectively) by examining a variety of surfaces within a model wetland (gravel, thick roots, fine roots, effluent), and the changes in activity (gene abundance) of these functional groups as influenced by plant species and season. Molecular techniques were used including quantitative PCR and denaturing gradient gel electrophoresis (DGGE), both with and without propidium monoazide (PMA) treatment. PMA treatment is a method for excluding from further analysis those cells with compromised membranes. Rigorous statistical analysis showed an interaction between the abundance of these two functional groups with the type of plant and season (p?<?0.05). The richness of the sulfate reducing bacterial community, as indicated by DGGE profiles, increased in planted vs. unplanted microcosms. For ammonia oxidizing bacteria, season had the greatest impact on gene abundance and diversity (higher in summer than in winter). Overall, the primary influence of plant presence is believed to be related to root oxygen loss and its effect on rhizosphere redox.     

Influence of Land Use Intensity on the Diversity of Ammonia Oxidizing Bacteria and Archaea in Soils from Grassland Ecosystems

In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.     

Functional Ecology of Vesicular Arbuscular Mycorrhizas as Influenced by Phosphate Fertilization and Tillage in an Agricultural Ecosystem

Abstract

The importance of vesicular arbuscular mycorrhizas (VAM) in an agricultural crop production system depends largely on our ability, through soil management, to increase the effectiveness of the indigenous mycorrhizal fungal population. To do so requires a good understanding of the functional ecology of the symbiosis.

In this article, we discuss primarily our programs at Guelph, which have focused on two aspects of the symbiosis: the influence of phosphate (P) fertilization on colonization and the influence of soil disturbance by tillage on colonization and P absorption.

Although it is generally accepted that the level of colonization of roots by VAM fungi decreases with increased P availability, we have found that the decrease is not as marked as thought. A reasonable degree of colonization was observed at available P levels well above those required for maximum yield. We have also found that the reduction in colonization occurs to a greater extent in the roots growing in a fertilized zone than in those outside this zone. Thus, although a band application of fertilizer may markedly reduce colonization in the fertilized zone, the remainder of the root system would be well colonized, and have an increased ability to acquire phosphorus.

That soil disturbance by tillage reduces the effectiveness of the VAM symbiosis in maize was first observed in the early 1980s. Since then we have conducted numerous field and growth chamber experiments to determine the practical importance of this effect in crop production and to elucidate the mechanisms involved. Systems such as no-till and ridge-till have been shown to result in greater P absorption during early maize growth. They also result in earlier colonization in some, but not all, cases. We have not, as yet, observed a yield advantage as a result of the earlier P absorption. This may be because factors other than P nutrition are limiting yields with the reduced tillage systems. Our results do indicate quite clearly, however, that greater rates of P fertilizer are not required in reduced tillage systems, compared with systems that cause a greater degree of soil disturbance. We suggest that lesser rates of P fertilizer may be required, which would have both an economic and environmental impact.

Our studies to elucidate the mechanisms have led to the conclusion that the integrity of the extraradical mycelium from a previous crop is a critical factor in the greater early P absorption in undisturbed systems. It may also be important in rapid colonization of roots of newly developing seedlings. This latter effect, however, has been quite inconsistent in our studies. It is apparent that some unknown factor or factors, in addition to the integrity of the mycelium, is also critical.

The fact that a preexisting extraradical mycelium is important for early P nutrition under our field conditions led to the hypothesis that the mycelium from a previous crop retains its infectivity and is able to absorb and transport P to newly attached roots following an extensive period during which the soil is frozen. Experiments in which pouches containing soil with a root-free mycelium were exposed to freezing for differing lengths of time have provided evidence to support this hypothesis. Roots growing in undisturbed pouches removed from the field when the soil was frozen were rapidly colonized during a bioassay. Disturbance of the soil in these pouches invariably reduced P absorption by the bioassay plants and sometimes, but not always, reduced colonization.

A more thorough understanding of the mechanisms involved in the effect of disturbance on colonization would increase the potential for increasing the effectiveness of the VAM symbiosis in crop production through management practices.     

高效光合细菌菌剂对土壤微生物的影响

为了筛选在盆栽试验条件下适宜的高效光合细菌菌剂浓度以促进番茄生长,研究了高效光合细菌菌剂的3种浓度对番茄种植土壤中微生物特性的影响。试验结果表明：高效光合细菌菌剂的施用可以显著提高土壤中细菌和放线菌的数量,降低土壤中真菌数量;不同程度提高土壤脲酶、酸性磷酸酶和过氧化氢酶的活性。其中以稀释100倍的光合细菌菌剂+化肥处理效果最明显,稀释100倍的菌剂+化肥处理最有利于土壤中微生物的生长繁殖,对土壤环境的改善效果最显著。     

金沙江支流普渡河、小江干热河谷的丛枝菌根

调查具有不同植物群落的金沙江支流普渡河、小江干热河谷中91种常见植物的丛枝菌根真菌的侵染率及孢子密度。普渡河样地调查了56种植物,其中54种(96%)植物能形成典型的丛枝菌根,其平均孢子密度为1423±175/100g土;小江样地35种植物中有34种(97%)植物能形成典型的丛枝菌根,其平均孢子密度为601±103/100g土。单因素方差分析表明两个样地植物的AMF总感染率差异不显著,但其根际土壤中AMF孢子密度却存在显著差异,小江样地的AMF孢子密度明显低于普渡河样地。相关性分析表明,干热河谷植物的AMF感染率与其根际土壤中的AMF孢子密度之间不存在相关性。此外,调查还发现91种植物中,有61种植物(67%)在形成AM的同时,也被黑色有隔内生菌感染。     

丛枝菌根真菌对羊草生物量和氮磷吸收及土壤碳的影响

采用大田试验的方法在内蒙古锡林格勒草原进行牧草接种试验,通过灭菌和未灭菌两种土壤研究接种丛枝菌根真菌Glomus mosseae和Glomus claroidium对内蒙古典型草原优势种羊草生长的影响.结果显示,接种丛枝菌根真菌对羊草的地上部干重未产生显著影响,但向未灭菌土壤中接种能显著增加羊草根系量,同时接种G.mosseae显著增加了地上部的N、P含量及吸收量,有效地改善了植株N、P营养,提高了牧草品质;2种菌对根系的营养吸收影响不同,接种G.mosseae在灭菌土壤和未灭菌土壤中均能显著增加根系的N、P吸收量,而接种G.claroidium仅在土壤未灭菌状态下增加根系N、P吸收量;接种对土壤中的菌丝密度未产生显著影响,但接种后土壤中微生物量碳有增加的趋势,短期内难以观察到接种对土壤有机碳的影响.研究表明,丛枝菌根真菌能够提高牧草对N、P吸收,促进牧草的生长,改善牧草品质,增强牧草根际微生物量碳.     

电解海水的抑菌活性及对食品加工表面材料的消毒效果

为了考察直接电解海水消除细菌污染的可能性,本文将海水及海水稀释成不同浓度后通过氧化电解水装置进行电解不同时间后,所得酸性电解海水、碱性电解海水和中性电解海水对病原菌[埃希氏大肠杆菌(Escherichina coli)、沙门氏菌(Salmonella)、单核细胞增生李斯特菌(Listeria moncytogene)、摩化摩根(Morganella morganii)、副溶血性弧菌(Vibrio parahaemolyticus)]以及食品加工表面接触材料(地板砖、不锈钢板、瓷砖、手套、抹布)的消毒效果进行分析研究.结果表明,酸性电解海水具有良好的杀菌效果,能将107 CFU/mL的病原菌悬液在1 min内几乎全部杀死.碱性电解海水和中性水无明显的杀菌效果.通过模拟食品加工过程,对食品加工表面接触材料人为染菌,研究电解海水对表面材料的消毒效果,结果表明酸性电解海水仍能将表面材料含有的107CFU/cm2病原菌在5 min之内几乎全部杀灭.由此说明电解海水对食品加工表面接触材料具有明显的消毒效果,能取代以淡水为原料的电解水杀菌效果是高效廉价和不浪费淡水资源的一种理想消毒剂.     

Urban Tree Effects on Soil Organic Carbon

Urban trees sequester carbon into biomass and provide many ecosystem service benefits aboveground leading to worldwide tree planting schemes. Since soils hold ∼75% of ecosystem organic carbon, understanding the effect of urban trees on soil organic carbon (SOC) and soil properties that underpin belowground ecosystem services is vital. We use an observational study to investigate effects of three important tree genera and mixed-species woodlands on soil properties (to 1 m depth) compared to adjacent urban grasslands. Aboveground biomass and belowground ecosystem service provision by urban trees are found not to be directly coupled. Indeed, SOC enhancement relative to urban grasslands is genus-specific being highest under Fraxinus excelsior and Acer spp., but similar to grasslands under Quercus robur and mixed woodland. Tree cover type does not influence soil bulk density or C∶N ratio, properties which indicate the ability of soils to provide regulating ecosystem services such as nutrient cycling and flood mitigation. The trends observed in this study suggest that genus selection is important to maximise long-term SOC storage under urban trees, but emerging threats from genus-specific pathogens must also be considered.     

Organic Matter Stimulates Bacteria and Arbuscular Mycorrhizal Fungi in Bauhinia purpurea and Leucaena diversifolia Plantations on Eroded Slopes in Nepal

Erosion resulting from landslides is a serious problem in mountainous countries such as Nepal. To restore such sites it is essential to establish plant cover that protects the soil and reduces surface erosion. Mycorrhizal fungi growing in symbiosis with plants are essential in this respect because they improve both plant nutrient uptake and soil structure. We investigated the influence of organic matter and P amendment on recently produced biomass of bacteria and arbuscular mycorrhizal (AM) fungi in eroded slopes in Nepal. Eroded soil mixed with different types of organic matter or P was placed in mesh bags, which were buried around trees of Bauhinia purpurea and Leucaena diversifolia between June 2003 and December 2003 (the wet season) or between December 2003 and June 2004 (the dry season). Signature fatty acids were used to determine bacterial and AM fungal biomass after the 6‐month intervals. The amount and composition of AM fungal spores were analyzed in the mesh bags from the dry season. More microbial biomass was produced during the wet season than during the dry season. Furthermore, organic matter addition enhanced the production of AM fungal and bacterial biomass during both periods. The positive influence of organic matter addition on AM fungi could be an important contribution to plant survival in plantations on eroded slopes. Different AM spore communities and bacterial profiles were obtained with different organic amendments and this suggests a possible way of selecting for specific microbial communities in the management of eroded sites.     

Effects of Added Organic Matter and Water on Soil Carbon Sequestration in an Arid Region

It is generally predicted that global warming will stimulate primary production and lead to more carbon (C) inputs to soil. However, many studies have found that soil C does not necessarily increase with increased plant litter input. Precipitation has increased in arid central Asia, and is predicted to increase more, so we tested the effects of adding fresh organic matter (FOM) and water on soil C sequestration in an arid region in northwest China. The results suggested that added FOM quickly decomposed and had minor effects on the soil organic carbon (SOC) pool to a depth of 30 cm. Both FOM and water addition had significant effects on the soil microbial biomass. The soil microbial biomass increased with added FOM, reached a maximum, and then declined as the FOM decomposed. The FOM had a more significant stimulating effect on microbial biomass with water addition. Under the soil moisture ranges used in this experiment (21.0%–29.7%), FOM input was more important than water addition in the soil C mineralization process. We concluded that short-term FOM input into the belowground soil and water addition do not affect the SOC pool in shrubland in an arid region.