Seasonal population changes of myxomycetes and associated organisms in four woodland soils

Abstract The number of myxomycete plasmodium-forming units (PFUs) and associated microorganisms in soils from four woodland sites in the West of England were estimated at approximately monthly intervals over the course of a year, and other characteristics of the soils were determined. The numbers of PFUs were low except in an unusual high-phosphate woodland soil. This soil contained the fewest dictyostelid slime moulds. Conversely, the woodland soil with most dictyostelids contained the fewest PFUs. Naked soil amoebae were the most abundant phagotrophs. Myxomycetes were a comparatively small component of the phagotrophic community of the three typical woodland soils. Changes in the populations of naked amoebae, ciliates, myxomycetes and dictyostelids were sometimes synchronized with changes in the bacterial populations, which showed 9–35-fold seasonal variations in abundance at the four sites.     

The microbiology of soils under successive wheat crops in relation to take-all disease

Abstract Thirty-eight wheat fields in southern England were sampled in an attempt to correlate the amount of take-all disease with 35 microbiological and chemical measurements of soil. There was little correlation between field take-all and pot tests to determine soil infectivity. Myxogastrids were important components of the soil population, being up to half of the amoebal population, and most soils contained dictyostelids, reticulate amoebae and myxobacteria. Amoebae, ciliates, bacteria and saprophytic fungi were recorded for all soils. pH was a major determinant of soil populations, being clearly correlated with fungal abundance and with numbers of ciliates, dictyostelids and bacteria. Principal component analysis separated dictyostelids from the other soil amoebae and again showed the importance of pH in determining soil microbial populations. Take-all was negatively correlated with soil fertility and positively related to nematodes and myxobacteria, but this was probably an effect of take-all, and represented saprophytic growth on dead roots rather than being a cause. Reticulate amoebae and dictyostelids were both correlated with low levels of take-all. This study emphasises the large number of interrelated populations of soil microorganisms which could have an effect on the severity of take-all infections.     

Numerical abundance of myxomycetes (myxogastrids) in soils in the West of England

Abstract A most-probable-number technique was used to quantify the abundance of myxomycetes (myxogastrids) in soil samples taken from 23 'Sites of Special Scientific Interest' and one other site in the West of England. Associated organisms and soil conditions were also recorded. Sixteen of the 24 sites yielded myxomycete plasmodium-forming units (PFUs) in numbers averaging 230 cm⁻³ fresh soil. Where detectable in samples of grassland soil, the numbers ranged from 20–2750 cm⁻³, in woodland soil from 20–800 cm⁻³, and in sand dunes from 80–400 cm⁻³. Repeated sampling revealed changing numbers at single sites. The abundance of PFUs was correlated positively with numbers of soil amoebae, ciliates and nematodes, and with levels of magnesium and soil density, and negatively with organic matter content and levels of NH₄-nitrogen and phosphate. Each PFU probably corresponded to one or several uninucleate cells in the soil rather than to a plasmodium.     

Distribution and diversity of archaeal communities in selected Chinese soils

To understand the distribution and diversity of archaea in Chinese soils, the archaeal communities in a series of topsoils and soil profiles were investigated using quantitative PCR, T-RFLP combining sequencing methods. Archaeal 16S rRNA gene copy numbers, ranging from 4.96?×?10(6) to 1.30?×?10(8) copies?g(-1) dry soil, were positively correlated with soil pH, organic carbon and total nitrogen in the topsoils. In the soil profiles, archaeal abundance was positively correlated with soil pH but negatively with depth profile. The relative abundance of archaea in the prokaryotes (sum of bacteria and archaea) ranged from 0.20% to 9.26% and tended to increase along the depth profile. T-RFLP and phylogenetic analyses revealed that the structure of archaeal communities in cinnamon soils, brown soils, and fluvo-aquic soils was similar and dominated by Crenarchaeota group 1.1b and 1.1a. These were different from those in red soils, which were dominated by Crenarchaeota group 1.3 and 1.1c. Canonical correspondence analysis indicated that the archaeal community was primarily influenced by soil pH.     

Trophic interactions in soils as they affect energy and nutrient dynamics. III. Biotic interactions of bacteria,amoebae, and nematodes

Bacteria (Pseudomonas), amoebae (Acanthamoeba), and nematodes (Mesodiplogaster) were raised in soil microcosms with and without glucose additions. Nematode and amoebal grazing on bacteria significantly reduced bacterial populations by the end of a 24-day incubation period. Amoebal numbers decreased in the presence of nematodes with a corresponding increase in nematode numbers which reached a maximum of 230 nematodes/g of soil in the treatment with amoebae and glucose additions. After 24 days the nematode populations in the treatments without carbon additions were dominated by resistant dauer larvae indicating the unavailability of food. Although larval numbers were high in the treatments with glucose additions, the adult component of the population was still increasing at the end of the 24-day experiment. The effect of the presence of amoebae on nematode abundance was of the same magnitude as addition of 600g glucose-C.     

Community of dark-spored myxomycetes in ground litter and soil of taiga forest (Nizhne-Svirskiy Reserve,Russia) revealed by DNA metabarcoding

The diversity of dark-spored myxomycetes in forest ground litter and soil from four study plots across a fire chronosequence in Nizhne-Svirskiy Nature Reserve (northwest of Russia) was assessed by a DNA metabarcoding approach. The history of fire disturbances and the season of sampling influenced the composition of myxomycete assemblages. Several species showed substrate preferences different from what is known from fruiting body records. A high abundance of nivicolous species in the majority of the samples suggests that this ecological group constitutes a common element of soil microbial communities in lowland taiga forests. Four species are reported for the Leningrad region for the first time. Our results support the hypothesis that amoebae populations of myxomycetes may have much wider ecological niches than indicated by records of fructifications, and further environmental studies may provide valuable new insights on myxomycete ecology and distribution.     

土壤原生动物对川滇高山栎恢复时间的响应及生长季动态

青藏高原东缘生态环境脆弱, 森林频繁遭到砍伐, 生物多样性受到严重威胁, 森林砍伐后的生态恢复成为研究热点。原生动物在生态恢复中作为指示生物起着重要作用。本文就未砍伐、砍伐后不同恢复时期(20年、10年和1年)生的川滇高山栎(Quercus aquifolioides)林的土壤理化性质和原生动物在生长季的变化进行比较研究, 以探讨生长季不同月份、不同恢复期的原生动物数量变化规律, 分析土壤理化性质与其相关性。结果表明: (1)恢复10年和1年的林地的鞭毛虫数量(193个/g干土, 164个/g干土)显著高于原始林地(22个/g干土), 肉足虫在恢复1年的林地中数量最多(600个/g干土), 纤毛虫数量则随次生演替进程逐渐增多。(2)在生长季不同月份原生动物的数量呈先增加后减少的趋势。鞭毛虫和肉足虫的峰值分别出现在7月和8月, 而纤毛虫的数量在7、8、9月明显高于6月。(3)原生动物数量与土壤理化性质密切相关。鞭毛虫数量与pH值呈显著正相关(P = 0.019), 纤毛虫数量与铵态氮(P = 0.002)和碳氮比呈显著正相关(P = 0.022), 肉足虫数量与硝态氮(P = 0.008)和碳氮比(P = 0.016)呈显著负相关。结果显示, 三种原生动物数量在生长季不同月份表现出较大的波动性, 其数量变化受土壤理化性质等多种因素调控。纤毛虫数量对川滇高山栎林砍伐恢复有正响应, 而鞭毛虫、肉足虫数量有负响应。     

Variations in soil culturable bacteria communities and biochemical characteristics in the Dongkemadi glacier forefield along a chronosequence

The variations in the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tanggula Mountain were investigated. We examined low organic carbon (C) and nitrogen (N) contents and enzymatic activity, correlated with fewer bacterial groups and numbers in the glacier forefield soils. The soil pH values decreased, but the soil water content, organic C and total N significantly increased, along the chronosequence. The soil C/N ratio decreased in the early development soils and increased in the late development soils and it did not correlate with the soil age since deglaciation. The activities of soil urease, sucrase, protease, polyphenol oxidase, catalase, and dehydrogenase increased along the chronosequence. The numbers of culturable bacteria in the soils increased as cultured at 25°C while decreased at 4°C from younger soils to older soils. Total numbers of culturable bacteria in the soils cultured at 25°C were significantly positively correlated to the soil total N, organic C, and soil water content, as well as the activities of soil urease, sucrase, dehydrogenase, catalase, and polyphenol oxidase. We have obtained 224 isolates from the glacier forefield soils. The isolates were clustered into 28 groups by amplified ribosomal DNA restriction analysis (ARDRA). Among them, 27 groups and 25 groups were obtained from the soils at 25°C and at 4°C incubation temperatures, respectively. These groups are affiliated with 18 genera that belong to six taxa, viz, Actinobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, Alphaproteobacteria, and Betaproteobacteria. The dominant taxa were Actinobacteria, Gammaproteobacteria, and Bacteroidetes in all the samples. The abundance and the diversity of the genera isolated at 25°C incubation temperature were greater than that at 4°C.     

茶园及相邻林地土壤N2O排放的垂直分布特征

对茶园及相邻林地土壤N2O排放的垂直分布特征进行研究.结果表明: 在0～100 cm土层,茶园和林地土壤全氮（TN）、N₂O排放速率及积累量均随着土层增加而减少,且茶园均值大于林地.土壤pH、TN、水溶性有机氮(WSON)、微生物生物量氮(MBN)、NO₃^--N及NH₄⁺-N含量随着土层增加总体呈下降趋势,茶园各土层TN、WSON、MBN、NO₃^--N及NH₄⁺-N含量显著大于林地,而不同土层pH值均小于林地.茶园和林地土壤N₂O排放速率与TN、MBN及NH₄⁺-N含量呈显著正相关,而与pH相关性不显著.茶园土壤N₂O排放速率与NO₃^--N含量的相关性显著,与WSON的相关性不显著,而在林地土壤中呈相反趋势.0~100 cm土层内茶园 WSON/SON和N₂O N/MBN平均值大于林地,而MBN/SON平均值小于林地.这表明茶园土壤氮库有较高的代谢效率,N₂O排放速率较高,不利于土壤氮库的储量积累,也不利于维持土壤质量和持续利用的潜力.     

茶园及相邻林地土壤N2O排放的垂直分布特征

对茶园及相邻林地土壤N2O排放的垂直分布特征进行研究.结果表明: 在0～100 cm土层,茶园和林地土壤全氮（TN）、N₂O排放速率及积累量均随着土层增加而减少,且茶园均值大于林地.土壤pH、TN、水溶性有机氮(WSON)、微生物生物量氮(MBN)、NO₃^--N及NH₄⁺-N含量随着土层增加总体呈下降趋势,茶园各土层TN、WSON、MBN、NO₃^--N及NH₄⁺-N含量显著大于林地,而不同土层pH值均小于林地.茶园和林地土壤N₂O排放速率与TN、MBN及NH₄⁺-N含量呈显著正相关,而与pH相关性不显著.茶园土壤N₂O排放速率与NO₃^--N含量的相关性显著,与WSON的相关性不显著,而在林地土壤中呈相反趋势.0~100 cm土层内茶园 WSON/SON和N₂O N/MBN平均值大于林地,而MBN/SON平均值小于林地.这表明茶园土壤氮库有较高的代谢效率,N₂O排放速率较高,不利于土壤氮库的储量积累,也不利于维持土壤质量和持续利用的潜力.     

华西雨屏区不同退耕模式细根(包括草根)分解过程中土壤酶动态

采用原状土芯(intact core)法, 探讨了四川洪雅柳江退耕模式——光皮桦(Betula luminifera)与扁穗牛鞭草(Hemarthria compressa)复合模式(HN)、扁穗牛鞭草草地模式(NC)、柳杉(Cryptameria fortunei)人工林模式(LS)、光皮桦人工林模式(H)细根(包括草根)分解过程中土壤酶动态。结果表明: 1) HN下的土壤脲酶、蔗糖酶、酸性磷酸酶活性较大, LS下的土壤脲酶、酸性磷酸酶活性最小, 显著低于其他模式(p < 0.05)。2) HN、NC和LS下的土壤脲酶与细根(包括草根)分解速率显著相关, HN的蔗糖酶、NC的酸性磷酸酶、LS的多酚氧化酶活性与细根(包括草根)分解速率也呈显著正相关关系(p < 0.05)。3) 除H外, 土壤脲酶活性与细根C/N、纤维素绝对含量呈显著负相关关系(p < 0.05); 除NC外, 多酚氧化酶活性与细根纤维素绝对含量呈显著负相关关系。4)土壤脲酶活性与需氧固氮细菌或与真菌数量显著相关, HN下的土壤蔗糖酶活性与细菌和纤维素分解菌数量呈正相关关系, H与NC下的土壤酸性磷酸酶还分别与细菌和纤维素分解菌数量呈正相关关系(p < 0.05)。以上结果显示: 由光皮桦与扁穗牛鞭草不同生活型植物构成的复合模式有利于土壤酶活性的提高; 土壤脲酶活性高低能够反映这几种退耕模式细根(包括草根)分解速率的快慢, 细根(包括草根)的C/N是影响土壤脲酶活性的一个重要因素; 土壤酶活性与土壤真菌、需氧固氮细菌、纤维分解菌及细菌数量有关。     

In the shadow of Darwin: Anton de Bary’s origin of myxomycetology and a molecular phylogeny of the plasmodial slime molds

In his Origin of Species (John Murray, London, 1859), Charles Darwin described the theory of descent with modification by means of natural selection and postulated that all life may have evolved from one or a few simple kinds of organisms. However, Darwin’s concept of evolutionary change is entirely based on observations of populations of animals and plants. He briefly mentioned ‘lower algae’, but ignored amoebae, bacteria and other micro-organisms. In 1859, Anton de Bary, the founder of mycology and plant pathology, published a seminal paper on the biology and taxonomy of the plasmodial slime molds (myxomycetes). These heterotrophic protists are known primarily as a large composite mass, the plasmodium, in which single nuclei are suspended in a common ‘naked’ cytoplasm that is surrounded by a plasma membrane. Here we summarize the contents of de Bary’s 1859 publication and highlight the significance of this scientific classic with respect to the establishment of the kingdom Protoctista (protists such as amoebae), the development of the protoplasmic theory of the cell, the introduction of the concept of symbiosis and the rejection of the dogma of spontaneous generation. We describe the life cycle of the myxomycetes, present new observations on the myxamoebae and propose a higher-order phylogeny based on elongation factor-1 alpha gene sequences. Our results document the congruence between the morphology-based taxonomy of the myxomycetes and molecular data. In addition, we show that free-living amoebae, common protists in the soil, are among the closest living relatives of the myxomycetes and conclude that de Bary’s ‘Amoeba-hypothesis’ on the evolutionary origin of the plasmodial slime molds may have been correct.     

健康与凋萎病杨梅树体及根围菌群的差异

凋萎病是制约杨梅产业发展的严重病害。为了有效防控凋萎病,本研究分析了杨梅健康和感染凋萎病树体各部位及根表土和根围土中细菌和真菌群落的丰富度与多样性的差异。结果表明: 与健康树相比,病树根围土、根表土、根、枝干、枝皮和叶片的细菌和真菌丰富度均发生了显著变化,其中,根表土细菌和枝皮内真菌的丰富度和多样性均显著降低,而枝皮内细菌和根表土的真菌丰富度和多样性均显著升高。病树各部位及根表、根围土细菌和真菌的优势菌相对丰度在门、纲和属水平上发生了明显的变化,在病树枝干、根和根表土中的假单胞菌属及根表土、根围土中的镰刀菌属的相对丰度明显降低,病树根表土及根围土中青霉菌属的相对丰度明显增加。与凋萎病菌同属的拟盘多毛孢菌在病树根内显著减少,而在其他位置均大量增殖,其相对丰度与多数相对丰度较高的真菌呈正相关。本研究结果将为开发杨梅凋萎病的生态改良、培育健康树体和生物防治技术提供有效的理论依据。     

Bioremediation of experimental petroleum spills on mineral soils in the Vestfold Hills,Antarctica

The effect of nutrient and water enhancement on the biodegradation of petroleum was tested in Antarctic mineral soils. Nitrogen, phosphorus and potassium were applied in solution, with or without gum xanthan or plastic covers, to sites artificially contaminated with distillate. The effectiveness of these procedures was assessed by measuring changes in total petroleum hydrocarbons; heptadecane/pristane and octadecane/phytane ratios; in concentrations of major hydrocarbon components and in microbial numbers and activity.Significantly lower hydrocarbon concentrations were recorded after one year in soils treated with fertilizer solutions, but only in the surface 3 cm. These soils also showed lowered heptadecane/pristane and octadecane/ phytane ratios and had the highest levels of microbial activity relative to other plots. Soils treated with gum xanthan. or covered with plastic had the highest residual hydrocarbon levels. Both treatments inhibited evaporative loss of hydrocarbon, and there were indications that gum xanthan was utilized by the microbiota as an alternative carbon source to distillate. Higher temperatures were recordecd under the plastic but no stimulation of biodegradation was detected.Estimated numbers of metabolically active bacteria were in the range 10⁷ to 10⁸ g^–1 dry weight of soil, with an estimated biomass of 0.03 to 0.26 mg g^–1 soil. Estimated numbers of amoebae were in the range 10⁶ to 10⁷ g^–1 soil (biomass of 2 to 4 mgg^–1). The highest populations were recorded in fertilized, contaminated soils, the only soils where petroleum degradation was demonstrated.     

Interactions of Bacterial and Amoebal Populations in Soil Microcosms with Fluctuating Moisture Content

Sterilized soil samples (20 g of soil per 50-ml flask), amended with 600 μg of glucose-carbon and 60 μg of NH₄-N · g of dry soil⁻¹, were inoculated with bacteria (Pseudomonas paucimobilis) alone or with bacteria and amoebae (Acanthamoeba polyphaga). We used wet-dry treatments, which involved air drying the samples to a moisture content of approximately 2% and remoistening the samples three times during the 83-day experiment. Control treatments were kept moist. In the absence of amoebae, bacterial populations were reduced by the first drying to about 60% of the moist control populations, but the third drying had no such effect. With amoebae present, bacterial numbers were not significantly affected by the dryings. Amoebal grazing reduced bacterial populations to 20 to 25% of the ungrazed bacterial populations in both moisture treatments. Encystment was an efficient survival mechanism for amoebae subjected to wet-dry cycles. The amoebal population was entirely encysted in dry soil, but the total number of amoebae was not affected by the three dryings. Growth efficiencies for amoebae feeding on bacteria were 0.33 and 0.39 for wet-dry and constantly moist treatments, respectively, results that compared well with those previously reported for Acanthamoeba spp.     

The numbers of viable myxomycete cells in the alimentary tracts of earthworms and in earthworm casts

The numbers of 'plasmodium-forming units' (PFUs) of myxomycetes (mycetozoa or myxogastrids) in worm casts and soil were estimated by a most-probable-number method. Casts contained about five times more PFUs g dry wt˜' than did adjacent non-cast soil. Gut contents contained similar numbers to non-cast soil, but the proportion which was freezing resistant (and presumably in a resting stage) was greater. Numbers of PFUs in incubated worm casts increased rapidly, then fell. This transient increase probably accounts for the generally higher number observed in natural casts. Earthworms may serve as vectors of myxomycetes in soil.     

Density and diversity of protozoa in some arid Australian soils

This is the first extensive study of soil protozoa of arid lands. Twenty-six samples from litters, soils, termitaria, and a cyanobacterial crust, collected from central and south Australian arid lands, were analyzed for numbers and species of gymnamoebae, ciliates, and testacea. Amoebae ranged from 1,000-5,000/g of material, and were two orders of magnitude more abundant than ciliates. Both groups increased in abundance and species richness from bare soils through spinifex to mulga to chenopod vegetations. Testacea ranged 900-5,000/g with similar species richness throughout vegetations, but reached 11,900/g with a doubling of species in a refugium in Kings Canyon. The most prevalent species of amoebae, ciliates, and testacea were taxa associated with ephemeral and disturbed habitats (r-selection). The cyanobacterial crust might be considered a micro-refugium because it contained a number of non-encysting protozoa, including Thecamoeba sp. and Nassula picta, feeding on cyanobacterial filaments. The numbers and species richness of protozoa under shrubs were greater than in bare soils, supporting the resource island hypothesis that desert plants create soil heterogeneity by localizing soil fertility under their canopies.     

A method for the enumeration of myxomycetes in soils and its application to a wide range of soils

Abstract A standardised most-probable-number technique for estimating the number of myxomycete plasmodium-forming units (PFUs) in soils has been developed and tested experimentally. Application of the method to a local soil showed that the uppermost layers contained the most PFUs. Its application to 44 surface soils from various parts of the world detected myxomycetes in 36, of which 4 were desert soils. In general, highest numbers of PFUs (up to 9000·g⁻¹ soil) were recorded in grassland and agricultural soils. The nature of the PFUs has not been definitely resolved but they are probably myxamoebae, myxoflagellates and microcysts.     

Demographic and environmental causes of the decline of rural Song Thrushes Turdus philomelos in lowland Britain

We review current knowledge of demographic mechanisms and environmental factors implicated in the population decline of Song Thrushes Turdus philomelos in rural Britain since the mid-1970s, and present new analyses of regional variation in population changes. Increased mortality during the first year of life (from fledging to recruitment) is highlighted as a potential demographic mechanism having driven the population decline, while Song Thrushes in a rapidly declining farmland population were making too few nesting attempts to sustain local numbers. Breeding Song Thrushes are strongly associated with non-cropped habitats such as woodland edge, field boundaries, gardens and scrub; they make substantial use of grassland, but avoid cereals when foraging. Earthworms constitute a key component of Song Thrush diet and the availability of this prey is strongly influenced by moisture levels in surface soils. Several lines of evidence suggest that dry surface soils during summer are deleterious to the productivity and survival of Song Thrushes, and regional variation in the rates of population change in Britain during 1970–86 was negatively correlated with the extent of under-field drainage on farmland (the main function of which is to promote the drying of surface soils). Increasing dryness of agricultural soils and the loss of grassland from eastern arable counties have probably both contributed to the declines of rural Song Thrushes in Britain. Loss of hedgerows and scrub, and the degradation of woodland may also have contributed to population declines but the role of predators remains unclear. Recovery of rural Song Thrush populations requires challenging new policy initiatives that should aim to restore nesting cover (scrub and woodland understorey), grazed grassland in arable-dominated areas and damper soils in summer.     

不同土地利用方式下赤红壤生物学性状及其与土壤肥力的关系

以我国华南地区典型坡地的赤红壤为对象,研究了不同土地利用方式(新垦旱地、灌木林、桉树林及果园)下土壤微生物性状、酶活性及其与土壤肥力的关系.结果表明: 不同土地利用方式下土壤生物学性质差异极显著.其中,果园土壤的微生物数量和酶活性显著增加;新垦旱地土壤的呼吸速率显著增加,微生物数量、酶活性显著下降;灌木林和桉树林则介于果园和新垦旱地之间,且两者具有高度的相似性.不同土地利用方式下的土壤微生物数量和酶活性与土壤有机碳、大部分养分之间存在显著正相关;高有机质含量和高肥力水平的土壤有利于微生物的生长和酶活性的提高.