Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment.
(73/2707)
Soil structure depends on the association between mineral soil particles (sand, silt, and clay) and organic matter, in which aggregates of different size and stability are formed. Although the chemistry of organic materials, total microbial biomass, and different enzyme activities in different soil particle size fractions have been well studied, little information is available on the structure of microbial populations in microhabitats. In this study, topsoil samples of different fertilizer treatments of a long-term field experiment were analyzed. Size fractions of 200 to 63 microm (fine sand fraction), 63 to 2 microm (silt fraction), and 2 to 0.1 microm (clay fraction) were obtained by a combination of low-energy sonication, wet sieving, and repeated centrifugation. Terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes were used to compare bacterial community structures in different particle size fractions. The microbial community structure was significantly affected by particle size, yielding higher diversity of microbes in small size fractions than in coarse size fractions. The higher biomass previously found in silt and clay fractions could be attributed to higher diversity rather than to better colonization of particular species. Low nutrient availability, protozoan grazing, and competition with fungal organisms may have been responsible for reduced diversities in larger size fractions. Furthermore, larger particle sizes were dominated by alpha-Proteobacteria, whereas high abundance and diversity of bacteria belonging to the Holophaga/Acidobacterium division were found in smaller size fractions. Although very contrasting organic amendments (green manure, animal manure, sewage sludge, and peat) were examined, our results demonstrated that the bacterial community structure was affected to a greater extent by the particle size fraction than by the kind of fertilizer applied. Therefore, our results demonstrate specific microbe-particle associations that are affected to only a small extent by external factors. (+info)
Toxocara spp. eggs in public squares of Sorocaba, Sao Paulo State, Brazil.
(74/2707)
The visceral larva migrans (VLM) is a syndrome observed in human infection with helminth larval eggs such as the Toxocara spp. that usually infects dogs and cats. Among the risk factors involved in the occurrence of VLM, particularly important is the size of these animal populations. Sorocaba is a city with a dog population twice as large as that recommended by the World Health Organization. This fact has led to a survey of the presence of Toxocara spp. eggs in public square soils of this city. Thirty squares were selected, fifteen located in the outskirts of the city and fifteen downtown. Soil samples were collected from five distinct sites in the same area. The material was homogenized and drained and 100 g was mixed with a saturated solution of magnesium sulfate and 5% potassium iodine. The floating material was analyzed under the light microscope. Toxocara spp. eggs were found in 16 squares, nine of which were located in the outskirts of the city and seven downtown. It was concluded that Sorocaba squares present a high rate of contamination with Toxocara spp. eggs. The squares in the outskirts of the city presented a higher occurrence of these eggs in comparison with those downtown, although the difference was not statistically significant (p > 0.05). (+info)
The long-distance abscisic acid signal in the droughted plant: the fate of the hormone on its way from root to shoot.
(75/2707)
Abscisic acid (ABA) is a potent molecule that certainly modifies stomatal behaviour and plant water loss and probably acts to modify the growth of leaves. The hormone is synthesized both in the leaves and the roots of the plant and in the soil and may move freely from plant to soil and soil to plant. It can also move rapidly through the plant in both the xylem and the phloem and will partition between different compartments in different tissues largely as a function of pH. It is described here how perturbations in soil conditions around the roots and the water status of the air can modify the fluxes of ABA around the plant and its accumulation in different compartments and different tissues. These fluxes can be interpreted as signals of different stresses imposed on the plant and consideration is given to how different perturbations can exert subtle changes which are manifest as modified shoot growth rates and functioning. Most emphasis in the discussion is placed upon the plant's responses to the imposition of soil and atmospheric drought. (+info)
Simultaneous recovery of RNA and DNA from soils and sediments.
(76/2707)
Recovery of mRNA from environmental samples for measurement of in situ metabolic activities is a significant challenge. A robust, simple, rapid, and effective method was developed for simultaneous recovery of both RNA and DNA from soils of diverse composition by adapting our previous grinding-based cell lysis method (Zhou et al., Appl. Environ. Microbiol. 62:316-322, 1996) for DNA extraction. One of the key differences is that the samples are ground in a denaturing solution at a temperature below 0 degrees C to inactivate nuclease activity. Two different methods were evaluated for separating RNA from DNA. Among the methods examined for RNA purification, anion exchange resin gave the best results in terms of RNA integrity, yield, and purity. With the optimized protocol, intact RNA and high-molecular-weight DNA were simultaneously recovered from 19 soil and stream sediment samples of diverse composition. The RNA yield from these samples ranged from 1.4 to 56 microg g of soil(-1) dry weight), whereas the DNA yield ranged from 23 to 435 microg g(-1). In addition, studies with the same soil sample showed that the DNA yield was, on average, 40% higher than that in our previous procedure and 68% higher than that in a commercial bead milling method. For the majority of the samples, the DNA and RNA recovered were of sufficient purity for nuclease digestion, microarray hybridization, and PCR or reverse transcription-PCR amplification. (+info)
Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays.
(77/2707)
We report on the development and validation of a simple microarray method for the direct detection of intact 16S rRNA from unpurified soil extracts. Total RNAs from Geobacter chapellei and Desulfovibrio desulfuricans were hybridized to an oligonucleotide array consisting of universal and species-specific 16S rRNA probes. PCR-amplified products from Geobacter and Desulfovibrio were easily and specifically detected under a range of hybridization times, temperatures, and buffers. However, reproducible, specific hybridization and detection of intact rRNA could be accomplished only by using a chaperone-detector probe strategy. With this knowledge, assay conditions were developed for rRNA detection using a 2-h hybridization time at room temperature. Hybridization specificity and signal intensity were enhanced using fragmented RNA. Formamide was required in the hybridization buffer in order to achieve species-specific detection of intact rRNA. With the chaperone detection strategy, we were able to specifically hybridize and detect G. chapellei 16S rRNA directly from a total-RNA soil extract, without further purification or removal of soluble soil constituents. The detection sensitivity for G. chapellei 16S rRNA in soil extracts was at least 0.5 microg of total RNA, representing approximately 7.5 x 10(6) Geobacter cell equivalents of RNA. These results suggest that it is now possible to apply microarray technology to the direct detection of microorganisms in environmental samples, without using PCR. (+info)
Axial differences in community structure of Crenarchaeota and Euryarchaeota in the highly compartmentalized gut of the soil-feeding termite Cubitermes orthognathus.
(78/2707)
Methanogenesis represents an important electron sink reaction in the hindgut of soil-feeding termites. This is the first comprehensive analysis of the archaeal community structure within the highly compartmentalized intestinal tract of a humivorous insect, combining clonal analysis and terminal restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the archaeal communities in the different gut compartments of Cubitermes orthognathus. We found that the morphological and physicochemical heterogeneity of the gut is reflected in a large phylogenetic diversity and pronounced axial differences in the composition of the archaeal gut microbiota, notably among those clones or ribotypes that could be assigned to methanogenic taxa. Comparative analysis of the relative frequencies of different archaeal lineages among the small-subunit rRNA gene (SSU rDNA) clones and their corresponding T-RF indicated that the archaeal community in the anterior, extremely alkaline hindgut compartment (P1) consists mainly of members of the Methanosarcinaceae, whereas Methanobacteriaceae and Methanomicrobiales predominate in the subsequent, more posterior compartments (P3/4a and P4b). The relative abundance of Thermoplasmales increased towards the rectum (P5). SSU rDNA sequences representing Crenarchaeota, which have not yet been reported to occur in the intestinal tracts of arthropods, were detected in all gut sections. We discuss how the spatial distribution of methanogenic populations may be linked to axial heterogeneity in the physicochemical gut conditions and to functional adaptations to their respective ecological niches. (+info)
The position of localized soil compaction determines root and subsequent shoot growth responses.
(79/2707)
Plants growing in soils typically experience a mixture of loose and compact soil. The hypothesis that the proportion of a root system exposed to compact soil and/or the timing at which this exposure occurs determines shoot growth responses was tested. Broccoli (Brassica oleracea var. italica cv. Greenbelt) seedlings were grown in pot experiments with compact, loose and localized soil compaction created by either horizontal (compact subsoils 75 or 150 mm below loose topsoil) or vertical (adjacent compact and loose columns of soil) configurations of loose (1.2 Mg m(-3)) and compact (1.8 Mg m(-3)) soil. Entirely compact soil reduced leaf area by up to 54%, relative to loose soil. When compaction was localized, only the vertical columns of compact and loose soil reduced leaf area (by 30%). Neither the proportion of roots in compact soil nor the timing of exposure could explain the differing shoot growth responses to localized soil compaction. Instead, the strong relationship between total root length and leaf area (r(2)=0.92) indicated that localized soil compaction reduced shoot growth only when it suppressed total root length. This occurred when isolated root axes of the same plant were exposed to vertical columns of compact and loose soil. When a single root axis grew through loose soil into either a shallow or deep compact subsoil, compensatory root growth in the loose soil maintained total root length and thus shoot growth was unaffected. These contrasting root systems responses to localized soil compaction may explain the variable shoot growth responses observed under heterogeneous conditions. (+info)
Seed reserve-dependent growth responses to temperature and water potential in carrot (Daucus carota L.).
(80/2707)
Both temperature and soil moisture vary greatly in the surface layers of the soil through which seedlings grow following germination. The work presented studied the impact of these environmental variables on post-germination carrot growth to nominal seedling emergence. The rapid pre-crook downward growth of both the hypocotyl and root was consistent with their requirement for establishment in soil drying from the surface. At all temperatures, both hypocotyl and root growth rates decreased as water stress increased and there was a very distinct temperature optimum that tended to occur at lower temperatures as water stress increased. A model based on the thermodynamics of reversible protein denaturation was adapted to include the effects of water potential in order to describe these growth rate responses. In general, the percentage of seedlings that reached the crook stage (start of upward hypocotyl growth) decreased at the extremes of the temperature range used and was progressively reduced by increasing water stress. A model was developed to describe this response based on the idea that each seedling within a population has lower and upper temperature thresholds and a water potential threshold which define the conditions within which it is able to grow. This threshold modelling approach which applies growth rates within a distribution of temperature and water potential thresholds could be used to simulate seedling growth by dividing time into suitable units. (+info)