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.     

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.     

Distribution and diversity of soil protozoa in the McMurdo Dry Valleys of Antarctica

The polar desert soils of the McMurdo Dry Valley region support a limited water film community dominated by flagellates, amoebae, and nematodes. This study describes the protozoa and compares their distribution to nematodes. In 50 samples collected from 12 locations, rotifers and tardigrades were infrequent, and ciliates and testacea were rare. Soil protozoa occurred at all sites but the dominant nematode, Scottnema lindsayae (Timm 1971), did not, indicating soil habitat factors limiting nematode distribution are not limiting to protozoa. In contrast to the nematode species, which are all endemic to Antarctica, there were no endemic protozoan morphospecies found in our samples. The protozoan abundance was several orders of magnitude greater than that of the nematodes, and the species diversity was much greater. Most of the protozoa grew better at lower incubation temperatures. The ubiquitous distribution of protozoa suggests their importance in soil food webs and nutrient cycling in the dry valleys.     

Distribution and activity of microorganisms in subsurface sediments of a pristine study site in Oklahoma

Distribution and activity of microorganisms in surface soil and subsurface sediments were studied in depth profiles of six different microbial biomass and activity indicators (total direct counts, number of cells capable of electron transport system activity, viable cell plate counts, most Probable numbers of protozoa, and 4-hydroxybenzoate-degrading microorganisms, and ATP content). The profiles showed the same general trends on two different dates (January and June 1985). Seasonal variations were noted, but they were not extreme. Biomass and activity values declined sharply with depth in the unsaturated zone, reaching minima in a clay confining layer in the interface zone between 3 and 4 m. Contiguous 10-cm samples from the interface zone showed significant textural and microbiological variability. Higher and more stable biomass and activity values were detected in the saturated zone, the highest being a very permeable gravelly loamy sand layer at approximately 7.5 m. In this layer, viable counts were nearly equal to total counts and they approached the viable counts in surface soil. Surface-type protozoa and cyanobacteria also were detected in this layer, suggesting that it was connected hydrologically to a nearby river. Lowest values were detected in an underlying bedrock clay layer at 8 m, which, despite its impermeability and low viable counts, did contain measurable total counts, 4-hydroxybenzoate-degrading microorganisms, and ATP. Correlations were noted between sediment texture and microbial activity (i.e., sandy texture=high activity, clayey texture=low activity), but other hydrogeological and geochemical factors probably also influenced microbial distribution and activity in the profile.     

Heterotrophic flagellates, centrohelid heliozoa and filose amoebae from marine and freshwater sites in the Antarctic

Heterotrophic flagellates, centrohelid heliozoa and filose amoebae were recorded from cultures derived from water collected at marine and freshwater sites in the Antarctic. Marine samples were collected in the vicinity of Prydz Bay, southeast Antarctica and freshwater samples from Sombre Lake on Signy Island and Crooked and Druzhby Lakes in the Vestfold Hills. Thirty-five species were identified. One new species, Kiitoksia kaloista (Protista incertae sedis), is described. The other species have been previously reported from other geographic locations, providing no evidence for endemism in protozoan species found in Antarctica. Received: 23 September 1996 / Accepted: 28 December 1996     

The SSU rDNA coding region of a filose amoeba contains a group I intron lacking the universally conserved G at the 3'-terminus

We sequenced small subunit ribosomal DNA (rDNA) PCR-fragments of sizes 2.3 kb and 2.9 kb isolated from a culture of the red alga, Porphyra spiralis var. spiralis. Phylogenetic analysis of the 2.3-kb fragment showed that it encoded the sequence of a contaminant filose amoeba. The Nuclearia-like amoeba (named strain N-Por) was identified with scanning electron microscopy. Its rDNA sequence was positioned with strong bootstrap support within a diverse protist assemblage that includes filose amoebae, chlorarachniophytes, cercomonads, and Plasmodiophora brassicae. The rDNA of N-Por contained a group I intron at the conserved 943 position that remarkably, had a U at the 3'-terminus rather than the universally conserved G.     

Estimating the growth potential of the soil protozoan community

We have developed a method for determining the potential abundance of free-living protozoa in soil. The method permits enumeration of four major functional groups (flagellates, naked amoebae, testate amoebae, and ciliates) and it overcomes some limitations and problems of the usual 'direct' and 'most probable number' methods. Potential abundance is determined using light microscopy, at specific time intervals, after quantitative re-wetting of air-dried soil with rain water. No exogenous carbon substrates or mineral nutrients are employed, so the protozoan community that develops is a function of the resources and inhibitors present in the original field sample. The method was applied to 100 soil samples (25 plots x 4 seasons) from an upland grassland (Sourhope, Southern Scotland) in the UK. Median abundances for all four functional groups lie close to those derived from the literature on protozoa living in diverse soil types. Flagellates are the most abundant group in soil, followed by the naked amoebae, then the testate amoebae and ciliates. This order is inversely related to typical organism size in each group. Moreover, preliminary evidence indicates that each functional group contains roughly the same number of species. All of these observations would be consistent with soil having fractal structure across the size-scale perceived by protozoa. The method described will be useful for comparing the effects on the soil protozoan community of different soil treatments (e.g. liming and biocides).     

Novel cultured protists identify deep-branching environmental DNA clades of cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia

We describe three new orders of filosan Cercozoa, five new deep-branching genera, eight new species of Thaumatomonas, Reckertia, Spongomonas, Rhogostoma, Agitata, Neoheteromita and Paracercomonas, sequence their 18S rDNA, and construct 18S rDNA trees for 148 Cercozoa. Our phylogeny indicates that Filosa were ancestrally gliding flagellates; non-flagellate filose amoebae evolved from them five times independently. The new genera are more closely related to environmental DNA sequences than cultured organisms. Tremula longifila, a zooflagellate glider on both flagella (unlike other Cercozoa), is the most divergent filosan (Tremulida ord. n.). Micrometopion nutans is a eukaryote-eating gliding zooflagellate like Metopion and Metromonas. Minimassisteria diva is a widespread trimorphic marine amoeboflagellate granofilosan. Peregrinia clavideferens, a non-testate, scale-bearing, filose amoeba, branches deeply in Thaumatomonadida, which are probably sisters to Spongomonadida. Nudifila producta is a filose amoeboflagellate related to Clautriavia and Marimonadida (ord. n., e.g. Pseudopirsonia, Auranticordis). We substantially revise Imbricatea, now including Spongomonadida, and Thecofilosea to include Phaeodaria. Thecofilosea and Imbricatea and Thecofilosea are sisters, both arguably ancestrally rigid gliding flagellates with ventral pseudopod-emitting grooves. Scale-free Ovulinata parva is sister to Paulinella, so imbricate silica scales can be lost. Internal hollow silica skeletons evolved twice in Thecofilosea (Ebriida, Phaeodaria) or were multiply lost. Protaspa replaces preoccupied 'Protaspis'.     

Soil fauna communities and microbial respiration in high Arctic tundra soils at Zackenberg, Northeast Greenland

The soil fauna communities were described for three dominant vegetation types in a high arctic site at Zackenberg, Northeast Greenland. Soil samples were extracted to quantify the densities of mites, collembolans, enchytraeids, diptera larvae, nematodes and protozoa. Rates of microbial respiration were also assessed. Collembolans were found in highest densities in dry heath soil, about 130,000 individuals m⁻², more than twice as high as in mesic heath soils. Enchytraeids, diptera larvae and nematodes were also more abundant in the dry heath soil than in mesic heath soils, whereas protozoan densities (naked amoeba and heterotrophic flagellates) were equal. Respiration rate of unamended soil was similar in soil from the three plots. However, a higher respiration rate increase in carbon + nutrient amended soil and the higher densities of soil fauna (with the exception of mites and protozoa) in dry heath compared to the mesic heath soils indicated a higher decomposition rate here.     

Abundance and productivity of protozoa in chalk streams

The distribution and abundance of protozoa in two chalk streams were studied. Particular attention was given to the ciliates and amoebae associated with the dominant submerged macrophyte, Ranunculus penicillatus . Highest numbers of protozoa occurred in habitats in the stream where the current velocity was reduced. Mean standing crops of ciliates, flagellates and amoebae were 32.5, 2.9 and 2.0 mg dry wt m⁻² of stream bed respectively. Estimates of production and respiration rates by field populations of ciliates and amoebae were made for one type of habitat within the streams. The results are compared with published data on the productivity of protozoa in other habitats and of other invertebrates within the chalk stream ecosystem. The limitations of such productivity estimates are discussed.     

Role of Microniches in Protecting Introduced Rhizobium leguminosarum biovar trifolii against Competition and Predation in Soil

The importance of microniches for the survival of introduced Rhizobium leguminosarum biovar trifolii cells was studied in sterilized and recolonized sterilized loamy sand and silt loam. The recolonized soils contained several species of soil microorganisms but were free of protozoa. Part of these soil samples was inoculated with the flagellate Bodo saltans, precultured on rhizobial cells. The introduced organisms were enumerated in different soil fractions by washing the soil, using a standardized washing procedure. With this method, free organisms and organisms associated with soil particles or aggregates >50 μm were separated. The total number of rhizobia was influenced slightly (silt loam) or not at all (loamy sand) by the recolonization with microorganisms or by the addition of flagellates alone. However, when both flagellates and microorganisms were present, numbers of rhizobia decreased drastically. This decrease was more than the sum of both effects separately. Nevertheless, populations of rhizobia were still higher than in natural soil. In the presence of flagellates, higher percentages of rhizobia and other microorganisms were associated with soil particles or aggregates >50 μm than in the absence of flagellates. In recolonized soils, however, the percentages of particle-associated rhizobia were lower than in soils not recolonized previous to inoculation. Thus, the presence of other microorganisms hindered rhizobial colonization of sites where they are normally associated with soil particles or aggregates.     

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。     

Persistence of free-living protozoan communities across rearing cycles in commercial poultry houses

The introduction and survival of zoonotic bacterial pathogens in poultry farming have been linked to bacterial association with free-living protozoa. To date, however, no information is available on the persistence of protozoan communities in these environments across consecutive rearing cycles and how it is affected by farm- and habitat-specific characteristics and management strategies. We therefore investigated the spatial and temporal dynamics of free-living protozoa in three habitats (pipeline, water, and miscellaneous samples) in three commercial poultry houses across three rearing cycles by using the molecular fingerprinting technique denaturing gradient gel electrophoresis (DGGE). Our study provides strong evidence for the long-term (ca. 6-month) persistence of protozoa in broiler houses across consecutive rearing cycles. Various free-living protozoa (flagellates, ciliates, and amoebae), including known vectors of bacterial pathogens, were observed during the down periods in between rearing cycles. In addition, multivariate analysis and variation partitioning showed that the protozoan community structure in the broiler houses showed almost no change across rearing cycles and remained highly habitat and farm specific. Unlike in natural environments, protozoan communities inside broiler houses are therefore not seasonal. Our results imply that currently used biosecurity measures (cleaning and disinfection) applied during the down periods are not effective against many protozoans and therefore cannot prevent potential cross-contamination of bacterial pathogens via free-living protozoa between rearing cycles.     

Selective grazing of methanotrophs by protozoa in a rice field soil

Biological methane oxidation is a key process in the methane cycle of wetland ecosystems. The methanotrophic biomass may be grazed by protozoa, thus linking the methane cycle to the soil microbial food web. In the present study, the edibility of different methanotrophs for soil protozoa was compared. The number of methanotroph-feeding protozoa in a rice field soil was estimated by determining the most-probable number (MPN) using methanotrophs as food bacteria; naked amoebae and flagellates were the dominant protozoa. Among ten methanotrophic strains examined as a food source, seven yielded a number of protozoa comparable with the yield with Escherichia coli [10⁴ MPN (g soil dry weight)⁻¹], and three out of four Methylocystis spp. yielded significantly fewer numbers [10²–10³ MPN (g soil dry weight)⁻¹]. The lower edibility of the Methylocystis spp. was not explained either by their growth phase or by harmful effects on protozoa. Incubation of the soil under methane resulted in a higher number of protozoa actively grazing on methanotrophs, especially on the less-edible group. Protozoa isolated from the soil demonstrated a grazing preference on the different methanotrophs consistent with the results of MPN counts. The results indicate that selective grazing by protozoa may be a biological factor affecting the methanotrophic community in a wetland soil.     

Phylogeny and classification of phylum Cercozoa (Protozoa)

The protozoan phylum Cercozoa embraces numerous ancestrally biciliate zooflagellates, euglyphid and other filose testate amoebae, chlorarachnean algae, phytomyxean plant parasites (e.g. Plasmodiophora, Phagomyxa), the animal-parasitic Ascetosporea, and Gromia. We report 18S rRNA sequences of 27 culturable zooflagellates, many previously of unknown taxonomic position. Phylogenetic analysis shows that all belong to Cercozoa. We revise cercozoan classification in the light of our analysis and ultrastructure, adopting two subphyla: Filosa subphyl. nov. a clade comprising Monadofilosa and Reticulofilosa, ranked as superclasses, ancestrally having the same very rare base-pair substitution as all opisthokonts; and subphylum Endomyxa emend. comprising classes Phytomyxea (Plasmodiophorida, Phagomyxida), Ascetosporea (Haplosporidia, Paramyxida, Claustrosporida ord. nov.) and Gromiidea cl. nov., which did not. Monadofilosa comprise Sarcomonadea, zooflagellates with a propensity to glide on their posterior cilium and/or generate filopodia (e.g. Metopion;Cercomonas; Heteromitidae – Heteromita, Bodomorpha, Proleptomonas and Allantion) and two new classes: Imbricatea (with silica scales: Euglyphida; Thaumatomonadida, including Allas, Thaumatomastix) and Thecofilosea (Cryomonadida; Tectofilosida ord. nov. – non-scaly filose amoebae, e.g. Pseudodifflugia). Reticulofilosa comprise classes Chlorarachnea, Spongomonadea and Proteomyxidea (e.g. Massisteria, Gymnophrys, a Dimorpha-like protozoan). Cercozoa, now with nine classes and 17 orders (four new), will probably include many, possibly most, other filose and reticulose amoebae and zooflagellates not yet assigned to phyla.     

Coprozoic Protozoa from Wyoming Mammals

SYNOPSIS. Coprozoic protozoa from elk, bison, bear, moose, coyote, marmot, cattle, horse, sheep and man were kept in feces at 4° C. for 2–6 months. During that time in most of the samples there developed the flagellates Cercomonas sp., Copromonas ruminantium and Monas communis; the amoebae Vahlkampfia sp. and Sappinia diploidea , and ciliates of the Nyctotherus type, and an unidentified smaller species. There was a correlation between numbers of protozoa and bacteria. The same species of protozoa in soil or in soil mixed with boiled feces failed to live. Coprozoic protozoa may require certain essential metabolites from bacteria as do true parasites. The wide variation in appearance of cysts made it practically impossible to identify the protozoa with certainty in that stage. Reliance had to be on motile forms which readily developed in the cold cultures.     

Structure of filose amoeba <Emphasis Type="Italic">Rhogostoma minus</Emphasis> Belar 1921 (Cryomonadida,Cercozoa) cell

The structure of the unicellular cell of filose amoeba, Rhogostoma minus Belar, 1921, is studied. Zoospores, cysts, and multinuclear plasmodia have not been found. The cell is covered by a thin shell made out of organic matter. Narrow and branched pseudopodia arise from the pseudostome. The vesicle-shaped nucleus, endoplasmic reticulum, microbodies, and Golgi apparatus are of a usual structure. The oval-shaped mitochondria carry tubular cristae. No flagellar apparatus, fibrillar structures, or extrusive organelles have been found. The amoeba feeds on bacteria. The phylogeny of R. minus in regard to other filose amoebas and flagellates is discussed.     

Biomass control in waste air biotrickling filters by protozoan predation

Two protozoan species as well as an uncharacterized protozoan consortium were added to a toluene-degrading biotrickling filter to investigate protozoan predation as a means of biomass control. Wet biomass formation in 23.6-L reactors over a 77-day period was reduced from 13.875 kg in a control biotrickling filter to 11.795 kg in a biotrickling filter enriched with protozoa. The average toluene vapor elimination capacity at 1 g/m3 toluene and 64 m3/(m3. h) was 31.1 g/(m3. h) in the control and 32.2 g/(m3. h) in the biotrickling filter enriched with protozoa. At higher toluene inlet concentrations, toluene degradation rates increased and were slightly higher in the biotrickling filter enriched with protozoa. The lower rate of biomass accumulation after the addition of protozoa was due to an increase of carbon mineralization (68% as compared to 61% in the control). Apparent biomass yield coefficients in the control and enriched trickling filter were 0.72 and 0.59 g dry biomass/g toluene, respectively. The results show that protozoan predation may be a useful tool to control biomass in biotrickling filters, however, further stimulation of predation of the biomass immobilized in the reactor is required to ensure long-term stability of biotrickling filters.     

Distribution of aerobic bacteria,protozoa, algae,and fungi in deep subsurface sediments

The distribution of microorganisms in deep subsurface profiles was determined at three sites at the Savannah River Plant, Aiken, South Carolina. Acridine orange direct counts (AODC) of bacteria were highest in surface soil samples and declined to the 10⁶ to 10⁷ per gram range in the subsurface, but then did not decline further with depth. In the subsurface, AODC values varied from layer to layer, the highest being found in samples from sandy aquifer formations and the lowest in clayey interbed layers. Sandy aquifer sediments also contained the highest numbers of viable bacteria as determined by aerobic spread plate counts (CFU) on a dilute heterotrophic medium. In some of these samples bacterial CFU values approached 100% of the AODC values. Viable protozoa (amoebae and flagellates, but no ciliates) were found in samples with high bacterial CFU values. A variety of green algae, phytoflagellates, diatoms, and a few cyanobacteria were found at low population densities in samples from two of the three boreholes. Low numbers of fungi were evenly distributed throughout the profiles at all three sites. Microbial population density estimates correlated positively with sand content and pore‐water pH, and negatively with clay content and pore‐water metal concentration. A large diversity of prokaryotic and eukaryotic microorganisms was found in samples with high population densities. A survey of bacterial strains isolated from subsurface samples revealed associations of gram‐positive bacteria with high clay sediments and gram‐negative bacteria with sandy sediments. The ability to deposit lipophilic storage material (presumably poly‐ß‐hydroxybutyrate) was found in a high proportion of isolates from sandy sediments, but only rarely in isolates from high clay sediments.     

凡口铅锌矿湿地处理系统的土壤原生动物

20 0 1年 12月 ,在广东省韶关市凡口铅锌矿湿地处理系统中采集土壤样品 ,采用Singh和Stout的培养法对土样中的原生动物进行定性、定量研究。共发现原生动物 4 2种 ,对照区和湿地每克风干土壤中原生动物的平均丰度分别为 2 377和 113,三大类土壤原生动物丰度中鞭毛虫占优势 ,多于纤毛虫和肉足虫。通过原生动物种类、丰度与土壤理化参数的统计分析说明铅锌尾矿对土壤原生动物群落的危害极大。通过土壤原生动物丰度和物种相似性聚类分析结果反映出正在使用的湿地 3土壤受污染严重 ,已停止使用的湿地 1和湿地 2中的胁迫效应已有所减轻 ,湿地 4中也存在胁迫效应。在整个湿地系统中根系土壤原生动物丰度差异说明 ,4种类型植物对土壤中重金属毒性效应的去除能力大小顺序为类芦>香蒲 >油草 >芒。最后 ,还探讨了造成土壤中鞭毛虫占优势原因 ,主要由土壤特殊的孔隙结构和土壤原生动物的食源决定