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.     

Seasonal population changes of myxomycetes and associated organisms in five non-woodland soils, and correlations between their numbers and soil characteristics

Abstract Microbial populations and other characteristics of five non-woodland soils from sites in the West of England were studied quantitatively over the course of a year, and special attention was paid to the changing abundance of myxomycetes. The latter, expressed as numbers of plasmodium-forming units (PFUs), were on average more abundant than in three representative woodland soils. During the year, instances were recorded in which rapidly increasing populations of bacteria were accompanied by increasing numbers of phagotrophic microorganisms, including myxomycetes, and others in which rapidly increasingly populations of phagotrophs were accompanied by falls in the numbers of bacteria. Oscillating predator-prey relationships were suggested. Myxomycetes were generally a significant component of the phagotrophic populations, even exceeding 50% of the total soil naked amoebae. Data on the biological and abiotic characteristics of woodland [3] and non-woodland soils were combined and statistically analysed for correlations. Myxomycete abundance was positively correlated with numbers of soil amoebae, ciliates, total bacteria, myxobacteria and nematodes, but inversely correlated with numbers of dictyostelid cellular slime moulds. It was positively correlated with soil pH and level of potassium, and negatively correlated with moisture content, organic matter content, and nitrogen/phosphorus ratio. Calculations suggest that the biomass of myxomycetes in temperate soils is commonly 6.4–64 mg dry weight · m⁻².     

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.     

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.     

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.     

What’s on your boots: an investigation into the role we play in protist dispersal

D. M. Wilkinson (2010, Journal of Biogeography, 37 , 393–397) suggested that anthropogenic dispersal is an understudied and potentially important factor in terrestrial protist biogeography. We investigated human footwear as a potential vector of dictyostelids, a diverse group of amoebae that includes both geographically restricted and cosmopolitan species. Eighteen pairs of boots were examined and dictyostelids were isolated from nearly all samples larger than 5.0 g. In total, six dictyostelid isolates were recovered, corresponding to four species –Dictyostelium minutum, D. sphaerocephalum, D. leptosomopsis and a new species, Polysphondylium sp. 1. Myxogastrid amoebae and acrasid‐like aggregations were also observed. Thus anthropogenic dispersal of naked amoebae appears to occur. The possible role of variations in dictyostelid fruiting body morphologies in dispersal potential is also discussed. These results support Wilkinson’s proposal and suggest that dictyostelids may be a useful group with which to study anthropogenic dispersal of terrestrial protists.     

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.     

Community Composition of Plant-parasitic Nematodes in Native and Cultivated Cerrados of Central Brazil

Communities of plant-parasitic nematodes collected from five different vegetation types (canopy woodland, savannah, gallery forest, cultivated perennial, and annual plants) and soils (yellowish red latosols, dark red latosols, arenosols, acrisols, and gleysols) were studied. Ninety percent of the soil samples collected from savannah contained at least four genera of plant-parasitic nematodes. The highest population densities were recovered from perennial plants and from acrisols. Nematodes from perennial and annual plants formed one cluster, which had a similar flexible-beta distance to that from the gallery forest. The distance in the native savannah and in canopy woodland was very different. Distance values for the soil aspect were similar for arenosols, yellowish, and dark red latosols. The value for acrisols was much larger than for the other soils.     

Novel soil lineages of Archaea are present in semi-arid soils of eastern Australia

The diversity of Archaea was studied in vertisolic and loam soils of a semi-arid region in Australia. Sampling was undertaken at an agricultural site, two grassland environments, and a brigalow (Acacia harpophylla) woodland. Archaeal community structure was profiled using amplified ribosomal DNA restriction analysis (ARDRA) combined with rDNA sequencing of an example of each restriction fragment length polymorphism type. Sequence comparison and phylogenetic analysis demonstrated that both crenarchaeotal and euryarchaeotal Archaea were present at oxic depths in the soil at all field sites. Along with previously described soil archaeal lineages, novel soil lineages and the deeply divergent Pendant-33 group of Euryarchaeota were also detected. A novel statistical method for comparing ARDRA derived data was demonstrated and implemented using the archaeal communities from the four field sites. Archaeal diversity, as measured by this method, was significantly higher in the agricultural site than at either of the grassland sites or the brigalow woodland.     

The nature of three ancient woodland soils in southern England

Abstract. Despite a wealth of published research on the nature of woodland soils, little is known about the nature of soils on sites that have supported woodland for many hundreds of years, namely ancient woodland. The properties and variability of soils in three ancient woods; one in the New Forest, Hampshire and two in Berkshire, were compared with those under recent woods. The acidity of ancient and recent woodland soils was high and remarkably similar. Only where cultivation of soils had preceded woodland establishment was soil acidity lower. The quantity of carbon in the soils studied was inversely related to soil acidity and the ancient woods had accumulated larger quantities of carbon than their recent counterparts. The quantities of Ca²⁺, Mg²⁺ and K⁺ were larger in the ancient woods except where prior cultivation had taken place. Total and organic phosphate contents of the ancient woodland soils were also consistently larger. The nature and pattern of soil variability in ancient woodland soils was quite distinct from that found in recent woods. Overall, the variability of soil acidity, carbon content and organic phosphate was larger in the ancient woodland soils but the pattern of variability differed between the soil properties. No clear association existed between the pattern of soil acidity and individual trees. At the surface of some of the woodland soils, however, carbon distribution appeared to be associated with individual trees. At depth in the ancient woodland soils, the association with the existing vegetation cover was not so clear. It is probable that the ancient woodland soils retained relict features of previous vegetation cover. Organic phosphate distribution was very strongly associated with the present vegetation cover. The pattern of distribution of organic phosphate appeared to be stronger than that of soil acidity and carbon content.     

Relationships between land snail assemblage patterns and soil properties in temperate-humid forest ecosystems

Aim The objectives were to (1) analyse the combined effects of soil pH, Ca content and soil moisture on total density and species richness of land snails in forest ecosystems, (2) explore relationships between the quantitative composition of snail assemblages and habitat characteristics, (3) investigate the relationships between soil pH and density of some of the most frequent species, and (4) compare the data with those from studies conducted in other temperate‐humid regions of Europe. Location Study sites were selected from 15 landscape types including different lithologies within the area of Baden‐Württemberg (35,000 km²), SW Germany. Methods Snails were recorded quantitatively from 83 study sites, with four plots representing a total of 0.25 m² per site. Topsoil samples from each site were analysed for pH, exchangeable Ca, and Ca content of carbonates. Three categories of soil moisture (dry, intermediate and wet) were established and defined according to the (climatic) water balance. Numbers of individuals and species were brought in relation to soil moisture and soil pH. Cluster analyses were conducted to identify groups of quantitatively similar snail species assemblages. Results Topsoil pH (2.7–7.5) and soil Ca contents were closely correlated. On dry soils, total snail density and species richness are generally low and do not change with pH, but clearly increase with increasing pH on intermediate moisture soils and on wet soils. On the latter, numbers of individuals and species are generally much higher compared with intermediate moisture sites at the same value of soil pH. Changes of density in relation to soil pH vary between species. Depending on the species, density increases only in the lower or only in the higher range of pH, is not related to pH, or decreases with increasing pH. Furthermore, these patterns vary within the same species depending on the region. This became evident from comparisons with other studies, particularly between sites in SW Germany and southern Scandinavia. From cluster analyses, subgroups of snail assemblages of high quantitative similarity were identified. Group formation is explained by soil pH to some extent, and one subgroup showed a connection with coniferous woodland sites on acidic soils. No further environmental factors available from our data could explain the clustering of snail assemblages more detailed. Main conclusions Soil moisture is the strongest determinant of snail density and species richness at undisturbed woodland sites, but effects of soil moisture and soil pH on these patterns are closely interrelated on intermediate moisture soils and wet soils. However, the quantitative species composition of the land snail assemblages is related to soil properties to a lower degree than snail density and species richness, and other habitat characteristics such as vegetation or litter quality, can be important for species dominance in addition.     

Dictyostelid cellular slime molds associated with grasslands of the central and western United States

Dictyostelid cellular slime molds (dictyostelids) associated with grassland ecosystems of the central and western United States were investigated at nine sites that included examples of the three major ecological types of grasslands (tall grass, mixed grass and short grass) generally recognized for the region. Samples of soil/humus collected from each site were examined with the Cavender method of isolating dictyostelids. For each of those six sites with well developed gallery forests present, an additional set of forest soil/humus samples was collected. A more intensive sampling effort was carried out at one site (Konza LTER) to assess the possible effects of burning and grazing on dictyostelid diversity and density. Twelve species of dictyostelids were recovered from grassland sites, whereas gallery forest sites yielded only nine species. Four cosmopolitan species (Dictyostelium giganteum, D. mucoroides, D. sphaerocephalum and Polysphondylium pallidum) were represented by the greatest densities of clones, with D. sphaerocephalum particularly common. The general pattern across all sites was that both species richness and density of dictyostelids decreased with decreasing precipitation. Samples collected from ungrazed grassland plots yielded higher numbers of both species and clones as compared to grazed plots, and the general pattern was for both values to increase as the interval between fires increased. For numbers of clones this correlation was statistically significant.     

Geophagy in chacma baboons: patterns of soil consumption by age class, sex, and reproductive state

Despite baboons' widespread distribution across Africa, geophagy among all subspecies has been poorly documented. We used video camera traps and soil analyses to investigate geophagy in chacma baboons (Papio cynocephalus ursinus) inhabiting the Western Cape of South Africa. During an 18‐month study, from August 2009 to January 2011, we continually monitored the largest and most frequently visited geophagy sites with camera traps for 545 days and captured soil consumption at one or more sites on 266 of those days (49%). In 3,500 baboon visits to geophagy sites, video camera traps captured 58.6 hr of geophagy. From these data, we evaluated site preference based on time spent consuming soil among these four geophagy sites. One hundred and seventy days of soil consumption data from the most frequently visited geophagy site allowed us to look for demographic trends in geophagy. Selected consumed soils from geophagy sites were analyzed for mineral, physical, and chemical properties. The baboons spent more time consuming white alkaline soils with high percentages of clay and fine silt, which contained higher concentrations of sodium than non‐white acidic soils that contained higher concentrations of iron. Our data indicate that pregnant chacma baboons spent more time consuming soil at monitored geophagy sites than baboons of any other age class, sex, or reproductive state. Based on analytical results, the soils consumed would be effective at alleviating gastrointestinal distress and possibly supplementing minerals for all age/sex classes, but potentially for different age/sex requirements. Am. J. Primatol. 74:48–57, 2012. © 2011 Wiley‐Liss, Inc.     

Distribution and ecology of dictyostelids in China

Dictyostelid cellular slime molds are a ubiquitous component of most soils, where they feed upon bacteria and other microbes and thus play an essential role in the soil ecosystem. Herein we review the available literature on dictyostelid cellular slime molds in China, especially their diversity and ecology. The patterns of distribution for these organisms in relation to the different habitats with which they are associated are analyzed and discussed. In addition, the assemblages of dictyostelids reported from China and the United States were compared. The CC value obtained (0.48) indicates that China and the United States are perhaps less similar than might be expected. Our data point out the need for further studies to characterize more completely the assemblages of dictyostelids associated with particular vegetation types or particular regions throughout the world.     

Vertical distribution of the free-living amoeba population in soil under desert shrubs in the Negev desert, Israel

A field study was designed to examine the effect of desert shrubs on the dynamics of free-living amoebae in arid soil. Soil samples from 0- to 50-cm depths were collected at 10-cm intervals in each of the four seasons. The vertical distributions of the four main morphological types of amoebae, grouped according to their mobility, and of small flagellate populations were measured under the canopies of Hammada scoparia and Atriplex halimus, shrubs belonging to the chloride-absorbing xerohalophytes. The result obtained from the field study demonstrated that the total number of protozoa was significantly higher during the wet seasons (winter and spring) than during the dry seasons. The protozoan population was more diverse under the canopy of H. scoparia during the wet seasons, reaching 8,000 individuals per 1 g of dry soil, whereas during the dry seasons, the populations were higher under the canopy of A. halimus, with a mean of 250 individuals. The protozoan population in the deeper layers (40 to 50 cm) was found to be as active as that in the upper layers, demonstrating that, in the desert, soil columns below 20 cm are fertile and worth studying. The type 1 amoebae (e.g., Acanthamoeba and Filamoeba spp.) were the most abundant throughout the study period, and their numbers were significantly higher than those of the other amoeba types.     

Local Adaptation of Metallicolous and Non‐Metallicolous Anthyllis vulneraria Populations: Their Utilization in Soil Restoration

Restoration of metalliferous mine soils requires using plant species tolerant to high metal concentrations and adapted to nutrient‐poor soil. Legumes can increase plant productivity through N₂‐fixation, but they are often scarce in metalliferous sites. We examined survival, growth, and tolerance of four populations of a legume, Anthyllis vulneraria, from two metalliferous (MET) Zn‐Pb mine sites, Avinières (AV) ([Zn‐EDTA] = 26,000 mg/kg) and Eylie (EY) ([Zn‐EDTA] = 4,632 mg/kg), and two non‐metalliferous (NMET) sites located in the south of France with the aim to select the most appropriate populations for restoration of mined soils. In a common garden experiment, plants from each population were reciprocally grown in soil from the provenance of each population. The two NMET populations exhibited high mortality and low growth rates in soil from the mined sites. The AV MET exhibited a high growth rate in metalliferous soils, but showed high mortality in non‐metalliferous soils. The growth of the EY MET was very low in the AV‐contaminated soil, but was the highest of all populations in moderately and non‐metalliferous soils. Plants from the AV MET population showed a high growth and survival in metalliferous soil and would be appropriate in the restoration of metal‐contaminated sites (>30,000 mg Zn kg^?1). The EY MET population would be adapted to the restoration of moderate metal‐contaminated soils (<30,000 mg Zn kg^?1). Taking into account the broad distribution of A. vulneraria, these two populations could be suitable for the restoration of derelict mine sites in mediterranean and temperate regions of Europe and North America.     

Eumycetozoa?=?Amoebozoa?: SSUrDNA Phylogeny of Protosteloid Slime Molds and Its Significance for the Amoebozoan Supergroup

Amoebae that make fruiting bodies consisting of a stalk and spores and classified as closely related to the myxogastrids have classically been placed in the taxon Eumycetozoa. Traditionally, there are three groups comprising Eumycetozoa: myxogastrids, dictyostelids, and the so-called protostelids. Dictyostelids and myxogastrids both make multicellular fruiting bodies that may contain hundreds of spores. Protostelids are those amoebae that make simple fruiting bodies consisting of a stalk and one or a few spores. Protostelid-like organisms have been suggested as the progenitors of the myxogastrids and dictyostelids, and they have been used to formulate hypotheses on the evolution of fruiting within the group. Molecular phylogenies have been published for both myxogastrids and dictyostelids, but little molecular phylogenetic work has been done on the protostelids. Here we provide phylogenetic trees based on the small subunit ribosomal RNA gene (SSU) that include 21 protostelids along with publicly available sequences from a wide variety of amoebae and other eukaryotes. SSU trees recover seven well supported clades that contain protostelids but do not appear to be specifically related to one another and are often interspersed among established groups of amoebae that have never been reported to fruit. In fact, we show that at least two taxa unambiguously belong to amoebozoan lineages where fruiting has never been reported. These analyses indicate that we can reject a monophyletic Eumycetozoa, s.l. For this reason, we will hereafter refer to those slime molds with simple fruiting as protosteloid amoebae and/or protosteloid slime molds, not as protostelids. These results add to our understanding of amoebozoan biodiversity, and demonstrate that the paradigms for understanding both nonfruiting and sporulating amoebae must be integrated. Finally, we suggest strategies for future research on protosteloid amoebae and nonfruiting amoebae, and discuss the impact of this work for taxonomists and phylogenomicists.     

On the abundance of marine naked amoebae on the surface of five species of macroalgae

Abstract Naked amoebae constituted a numerically significant component of the surface microbial community of five species of seaweeds. They were most abundant in the summer months on the brown macrophytes, Fucus and Laminaria , where numbers up to 23 cells cm⁻² of algal surface were recorded. This implies that littoral algal stands can support populations of up to 3.2 × 10⁶ amoebae m⁻². A total of 27 different species were recognized and, of these, six species were less than 10 μm in length, a size class overlooked in previous studies. Damaged tissue contained higher numbers of amoebae, up to 43 cells cm⁻², presumably due to higher bacterial densities and increased shelter at these sites. Some amoebae may have been utilizing algal carbon exudates directly, especially isolates of Trichosphaerium , which showed evidence of algal digestion. The numbers of amoebae found in this study suggest that these protozoa may play a significant, and previously overlooked, role in the cycling of estuarine carbon.     

Ecological distribution of Spirillum lipoferum Beijerinck.

A survey in various countries revealed that the N2-fixing Spirillum lipoferum Beijerinck is a very common root and soil inhabitant in the tropics. More than half of the grass root and soil samples collected in tropical countries (four African countries and Brazil) contained abundant S. lipoferum populations, while less than 10% of the samples collected in temperate South Brazil, Kenya, and the U.S.A. contained the organism. There is a pronounced vegetation effect. Panicum maximum seems the most favorable among the forage grasses, while few positive samples were found under virgin tropical forest. Legume roots contained less S. lipoferum than adjacent soils. More than 80% of the samples from cereal roots (maize, sorghum, wheat, and rye) grown in fields fertilized with PK and Mo, in Rio de Janeiro State, were positive. Maize and sorghum grown under similar conditions in Wisconsin contained less than 10% of positive samples, but when maize fields were inoculated 90% of the root samples contained S. lipoferum. Alluvial soils were more favorable than eroded hill soils. Occurrence in soil was strongly pH-dependent with a pH around 7, being optimal (correlation coefficient r = 0.90). Sporadic occurrence was observed even in soils with pH 4.8. Surface-sterilized P. maximum roots collected from soils with pH ranging from 4.8 to 7.2 contained high S. lipoferum numbers which did not correlate with soil pH (r = 0.41). Amendment with malate of acid soils was not very effective in increasing nitrogenase (N2-ase) activity, but in two soils with pH above 6.4, high N2-ase activity was obtained after 16 to 48 h of incubation. In two soils from a temperate climate region, inoculation with S. lipoferum increased N2-ase activity produced through malate amendment.