Distribution of Heterotrophic Bacteria in Lake Shira

A study of the horizontal and vertical distribution of heterotrophic bacteria in brackish Lake Shira in summer periods showed that mesophilic bacteria dominated in all areas of the lake, whereas psychrotolerant bacteria dominated in the metalimnion and hypolimnion of its central part. Nonhalophilic bacteria were mostly mesophilic and dominated in coastal waters. Most psychrotolerant bacteria were able to grow in the presence of 5–10% NaCl. Heterotrophic bacteria isolated in different regions of the lake were identified to a generic level. The isolates were classified into autochthonous and allochthonous microorganisms on the bases of their distribution pattern in the lake water, halotolerance, and ability to grow at low temperatures.     

The Effect of Resource Islands on Abundance and Diversity of Bacteria in Arid Soils

Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample’s origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are more abundant under the shrub canopy, while barren soils are characterized by a higher abundance of Actinobacteria. The bacterial communities in the Mediterranean soils were similar in both patch types. These results correspond to the hypothesis of “resource islands”, suggesting that shrub canopies provide a resource haven in low-resource landscapes. Yet, a survey of the physicochemical parameters of inter- and under-shrub soils could not attribute the changes in bacterial diversity to soil moisture, organic matter, or essential macronutrients. We suggest that in the nutrient-poor soils of the arid and semi-arid sites, bacteria occupying the soil under the shrub canopy may have longer growth periods under favorable conditions, resulting in their increased biomass and altered community composition.     

Patchiness in the Distribution of Planktonic Heterotrophic Bacteria in Lakes

By using conventional dilution plating procedures, the heterotrophic planktonic bacteria in Lake Washington were found to be distributed in small-scale (<1.0 ml) and large-scale (>1 m in horizontal distance) patches. Recommendations are made on sampling and enumeration procedures to minimize the effect of patchiness on obtaining an accurate estimate of bacterial numbers.     

Two new Umbelliferae of the Chihuahuan Desert

Two apparently calcicolous species of apioid Umbelliferae,Aletes calcicola andDonnellsmithia coahuilensis, are described from the Chihuahuan Desert of Coahuila, Mexico.     

Oak Bark Allometry and Fire Survival Strategies in the Chihuahuan Desert Sky Islands,Texas, USA

Trees may survive fire through persistence of above or below ground structures. Investment in bark aids in above-ground survival while investment in carbohydrate storage aids in recovery through resprouting and is especially important following above-ground tissue loss. We investigated bark allocation and carbohydrate investment in eight common oak (Quercus) species of Sky Island mountain ranges in west Texas. We hypothesized that relative investment in bark and carbohydrates changes with tree age and with fire regime: We predicted delayed investment in bark (positive allometry) and early investment in carbohydrates (negative allometry) under lower frequency, high severity fire regimes found in wetter microclimates. Common oaks of the Texas Trans-Pecos region (Quercus emoryi, Q. gambelii, Q. gravesii, Q. grisea, Q. hypoleucoides, Q. muehlenbergii, and Q. pungens) were sampled in three mountain ranges with historically mixed fire regimes: the Chisos Mountains, the Davis Mountains and the Guadalupe Mountains. Bark thickness was measured on individuals representing the full span of sizes found. Carbohydrate concentration in taproots was measured after initial leaf flush. Bark thickness was compared to bole diameter and allometries were analyzed using major axis regression on log-transformed measurements. We found that bark allocation strategies varied among species that can co-occur but have different habitat preferences. Investment patterns in bark were related to soil moisture preference and drought tolerance and, by proxy, to expected fire regime. Dry site species had shallower allometries with allometric coefficients ranging from less than one (negative allometry) to near one (isometric investment). Wet site species, on the other hand, had larger allometric coefficients, indicating delayed investment to defense. Contrary to our expectation, root carbohydrate concentrations were similar across all species and sizes, suggesting that any differences in below ground storage are likely to be in total volume of storage tissue rather than in carbohydrate concentration.     

Decomposition of roots in a Chihuahuan Desert ecosystem

Summary Mass losses of tethered buried roots of two woody shrubs and two herbaceous annuals buried in plots irrigated at 25 mm·month^-1, 6 mm·week^-1 and no irrigation were measured. At the end of 1 year, 10–15% of the mass of the herbaceous annual roots remained and 60% of the mass of woody shrub roots remained. There were no differences in mass loss attributable to added water. Rates of mass losses of roots in the Chihuahuan Desert were equal to or higher than those reported from mesic ecosystems. Roots of woody shrubs had relatively constant C:N ratios through the experiment. There was significant N immobilization in Baileya multiradiata roots. Percent mass loss of grass roots, Erioneuron pulchellum, and herbaceous annual roots, B. multiradiata, in plots with termites was 62% and in plots without termites was 15%. These data suggest that subterranean termites are responsible for most of the mass loss and mineralization of carbon and nitrogen in dead grass and herbaceous roots in the northern Chihuahuan Desert.     

Distribution,Diversity, and Activities of Sulfur Dioxygenases in Heterotrophic Bacteria

Sulfur oxidation by chemolithotrophic bacteria is well known; however, sulfur oxidation by heterotrophic bacteria is often ignored. Sulfur dioxygenases (SDOs) (EC 1.13.11.18) were originally found in the cell extracts of some chemolithotrophic bacteria as glutathione (GSH)-dependent sulfur dioxygenases. GSH spontaneously reacts with elemental sulfur to generate glutathione persulfide (GSSH), and SDOs oxidize GSSH to sulfite and GSH. However, SDOs have not been characterized for bacteria, including chemolithotrophs. The gene coding for human SDO (human ETHE1 [hETHE1]) in mitochondria was discovered because its mutations lead to a hereditary human disease, ethylmalonic encephalopathy. Using sequence analysis and activity assays, we discovered three subgroups of bacterial SDOs in the proteobacteria and cyanobacteria. Ten selected SDO genes were cloned and expressed in Escherichia coli, and the recombinant proteins were purified. The SDOs used Fe²⁺ for catalysis and displayed considerable variations in specific activities. The wide distribution of SDO genes reveals the likely source of the hETHE1 gene and highlights the potential of sulfur oxidation by heterotrophic bacteria.     

PCR-DGGE Comparison of Bacterial Community Structure in Fresh and Archived Soils Sampled along a Chihuahuan Desert Elevational Gradient

The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation of long-term patterns in bacterial species richness and community structure that was not available with previous technology. However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing microbial community dynamics for particular ecosystems or landscapes.     

Soil microarthropods from the Chihuahuan Desert of New Mexico

An account is given of the soil- and litter-dwelling microarthropods collected under three species of desert shrub in southern New Mexico. Particular attention is paid to the acarine component which represents 80% of the microarthropod fauna. Comparisons made with samples collected one hour after wetting show that only the Collembola respond rapidly to changes in the moisture content of the soil. The results of the study suggest that the depth and stability of the surface litter determine the degree to which microarthropod activity is affected by the application of water.     

Plant regulation of soil nutrient distribution in the northern Chihuahuan Desert

Vegetation throughout the southwestern United States has changed from perennial grassland to woody shrubland over the past century. Previous studies on the development of islands of fertility focused primarily on only the most limiting, plant-essential element, soil nitrogen (N). The research presented here addressed the question of whether other plant-essential elements, namely phosphorus (P) and potassium (K), showed similar concentration gradients under the desert shrub Larrea tridentata, creosotebush. It also examined whether the spatial distribution of N, P, and K differed from that of essential, but non-limiting nutrients, namely calcium (Ca), magnesium (Mg), and sulfur (S), and non-essential elements, namely sodium (Na), chloride (Cl), and fluoride (F). Within adjacent grassland and shrubland plots, surface soils were collected under and between vegetation and analyzed for a suite of soil nutrients. Soil nutrient distribution followed a uniform pattern that mirrored the spatial homogeneity of bunchgrasses in the grassland, but followed a patchy distribution that mirrored the spatial heterogeneity of individual shrubs in the shrubland. The main differences were that in the grassland, all elements were uniformly distributed, but in the shrubland the plant-essential elements, nitrogen, phosphorus, and potassium, were concentrated under the shrub canopy, and the non-limiting and non-essential elements were either concentrated in the intershrub spaces or were equally concentrated under shrubs and in the interspaces. Our results show how vegetation shifts from grassland to shrubland contribute to long-term, widespread change in the structure and function of desert ecosystems.     

Methanogenic and Other Strictly Anaerobic Bacteria in Desert Soil and Other Oxic Soils

Strictly anaerobic bacteria such as methanogenic, sulfate-reducing, and homoacetogenic bacteria could be enriched from all five oxic soils tested. The number of cells was lower than that in typical anoxic habitats. Spores did not always dominate the population of sulfate-reducing bacteria. In all soils, the methanogenic population displayed a long lag phase after anoxic conditions were imposed before methane production began.     

Effects of nitrogen amendment on annual plants in the Chihuahuan Desert

Effects of nitrogen amendments on spring annual plant distribution, primary production, and species diversity in a semi-arid environment were studied. The ecological responses of spring annual plant species to nitrogen differed between species, and between sites. The distribution of each species in a control transect was wider than in a nitrogen-treated transect. Annual plant species diversity at each station in the control transect was higher than that of the nitrogen-treated transect. The lower site of the Lower Basin Slope areas had the highest species diversity (0.94 for the control and 0.84 for the nitrogen-treated), and the Upper Basin Slope area, shrub vegetation zone, had the lowest species diversity (0.27 for the control and 0.05 for the nitrogen-treated) in both transects. Inorganic nitrogen in the nitrogen-treated transect soils was consistently higher than that in the control transect soils; however, the former showed more fluctuation from station to station than the latter. Above-ground biomass of spring annual plants in the nitrogen-treated transect was consistently higher than that in the control at each station. The maximum above-ground biomass in the control and nitrogen-treated transect was 24.4±4.4 gm⁻² and 61.2±10.6 gm⁻², respectively. Variations in above-ground biomass along the transect did not parallel with the variation in inorganic nitrogen in soils and species diversity.     

Polyploidy in Dalea formosa (Fabaceae) on the Chihuahuan Desert

Dalea formosa consists of diploids (n = 7), tetraploids (n = 14), and hexaploids (n = 21), the polyploids restricted to the Chihuahuan Desert region or its immediate borders. There is very little morphological differentiation between the three chromosome races and, therefore, the polyploids are assumed to be primarily autoploid. Tetraploids discovered were few and were very similar to hexaploids; the two ploidy levels were combined as “polyploids” for analyses of geographically and cytologically correlated morphological variation. Pollen length generally was found to be greater in known polyploids than in known diploids. Through the use of pollen length and geographic origin, chromosomally unknown specimens were estimated as to ploidy level. This produced four groups, known diploids and polyploids, and putative diploids and polyploids, which were then subjected to stepwise discriminant analysis (SDA) to search for other morphological characters that might indicate ploidy level, to evaluate the assignments to putative ploidy level in unknown plants, and to assess correlation of these plants of putative ploidy level to geographic regions. SDA also indicated that pollen length, among ten morphological features, is the primary discriminator between ploidy levels, and that putative polyploids are confined primarily to the Chihuahuan Desert. Chromosomally unknown specimens that were originally assigned to one ploidy level, but were classified by SDA as another, are viewed as indicative of areas where further cytological sampling is particularly needed. These areas are southeastern Arizona, where pollen among known diploids is comparatively large, northeastern New Mexico, where polyploids might occur off the Chihuahuan Desert, east edge of the Chihuahuan Desert in Texas, a cytologically poorly sampled contact zone between diploids and polyploids, and central Coahuila, where no cytological sampling has been done. Canonical variate analysis is used to aid in the visualization of the general morphological relationship between diploids and polyploids.     

Effects of Acetic Acid on the Regrowth of Heterotrophic Bacteria in the Drinking Water Distribution System

Summary Three laboratory-scale water pipe systems were set up to study the effects of adding two levels of acetic acid (10 and 50 μg acetate eq-C l⁻¹) on the bacterial regrowth in water pipes. The results of the water pipe test showed that nearly all carbon in the acetic acid could be readily utilized by bacteria and resulted in an increase in biomass concentration. The maximum heterotrophic plate counts in biofilm were equal to 3.5 × 10⁴, 8.9 × 10⁵ and 2.9 × 10⁷ c.f.u. cm⁻² while the maximum heterotrophic plate counts of free bacteria were equal to 1.2 × 10³, 5.0 × 10³ and 6.8 × 10⁴ c.f.u. ml⁻¹ for the blank and with addition of 10 and 50 μg acetate eq-C l⁻¹. These results showed that addition of acetic acid to drinking water has a positive effect on the assimilable organic carbon content of drinking water and bacterial regrowth in the distribution system. This effect is enhanced with addition of high-level acetic acid. Batch tests were also conducted using water samples collected from a Taiwanese drinking water distribution system. The bacterial regrowth potentials of the blank were equal to 4.3 × 10³, 1.5 × 10⁴, 4.9 × 10⁴ and 7.5 × 10⁴ c.f.u. ml⁻¹ for water samples collected from treatment plant effluent, commercial area, mixed area, and residential area, respectively. These results showed that the biological stability of drinking water is the highest in treatment plant effluent, followed by distributed water of the commercial area, distributed water of the mixed area, and then the distributed water of residential area.     

Broad Distribution of Diverse Anaerobic Ammonium-Oxidizing Bacteria in Chinese Agricultural Soils

Anaerobic ammonium-oxidizing (anammox) bacteria have been detected in many marine and freshwater ecosystems. However, little is known about the distribution, diversity, and abundance of anammox bacteria in terrestrial ecosystems. In this study, anammox bacteria were found to be present in various agricultural soils collected from 32 different locations in China. Phylogenetic analysis of the 16S rRNA genes showed “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” in the collected soils, with “Candidatus Brocadia” being the dominant genus. Quantitative PCR showed that the abundance of anammox bacteria ranged from 6.38 × 10⁴ ± 0.42 × 10⁴ to 3.69 × 10⁶ ± 0.25 × 10⁶ copies per gram of dry weight. Different levels of diversity, composition, and abundance of the anammox bacterial communities were observed, and redundancy analysis indicated that the soil organic content and the distribution of anammox communities were correlated in the soils examined. Furthermore, Pearson correlation analysis showed that the diversity of the anammox bacteria was positively correlated with the soil ammonium content and the organic content, while the anammox bacterial abundance was positively correlated with the soil ammonium content. These results demonstrate the broad distribution of diverse anammox bacteria and its correlation with the soil environmental conditions within an extensive range of Chinese agricultural soils.     

A floristic-structural gradient related to land forms in the southern Chihuahuan Desert

Abstract. The purposes of this study were to elucidate the floristic and structural characteristics of the vegetationin the Mapimi subdivision of the Chihuahuan Desert, Mexico, and to relate them to environmental variation. The main question addressed was: How does floristic composition, total species richness and life-form species richness vary in relation to environmental change? 154 sites, randomly selected and stratified over seven landscape units, were analyzed. Results showed the existence of a land form gradient along which vegetation types were ordered. Species richness varied along the gradient, the richest land form was bajada, indicating that the maximum species richness did not occur at one extreme of the water availability gradient but in a moderately poor situation. The lowest species richness was found in the playa land form. Cover-based life form spectra varied significantly with land forms, while presence-absence based life form spectra did not. It is suggested that this may be a consequence of the relatively young age of this desert.     

Aboveground net primary production dynamics in a northern Chihuahuan Desert ecosystem

Aboveground net primary production (ANPP) dynamics are a key element in the understanding of ecosystem processes. For semiarid environments, the pulse-reserve framework links ANPP to variable and unpredictable precipitation events contingent on surficial hydrology, soil moisture dynamics, biodiversity structure, trophic dynamics, and landscape context. Consequently, ANPP may be decoupled periodically from processes such as decomposition and may be subjected to complex feedbacks and thresholds at broader scales. As currently formulated, the pulse-reserve framework may not encompass the breadth of ANPP response to seasonal patterns of precipitation and heat inputs. Accordingly, we examined a 6-year (1999–2004), seasonal record of ANPP with respect to precipitation, soil moisture dynamics, and functional groups in a black grama (Bouteloua eriopoda) grassland and a creosotebush (Larrea tridentata) shrubland in the northern Chihuahuan Desert. Annual ANPP was similar in the grassland (51.1 g/m²) and shrubland (59.2 g/m²) and positively correlated with annual precipitation. ANPP differed among communities with respect to life forms and functional groups and responses to abiotic drivers. In keeping with the pulse-reserve model, ANPP in black grama grassland was dominated by warm-season C₄ grasses and subshrubs that responded to large, transient summer storms and associated soil moisture in the upper 30 cm. In contrast, ANPP in creosotebush shrubland occasionally responded to summer moisture, but the predominant pattern was slower, non-pulsed growth of cool-season C₃ shrubs during spring, in response to winter soil moisture accumulation and the breaking of cold dormancy. Overall, production in this Chihuahuan Desert ecosystem reflected a mix of warm-temperate arid land pulse dynamics during the summer monsoon and non-pulsed dynamics in spring driven by winter soil moisture accumulation similar to that of cool-temperate regions. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Latitudinal Distribution of Ammonia-Oxidizing Bacteria and Archaea in the Agricultural Soils of Eastern China

The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients.     

Metal(loid)-Contaminated Soils as a Source of Culturable Heterotrophic Aerobic Bacteria for Remediation Applications

Heavy metal–contaminated soils are a serious environmental problem. Herein, the culturable heterotrophic bacterial community present on two metal(loid)-contaminated sites in the Northern Portugal was investigated. The bacterial counts ranged from 5.96 to 7.69 and 7.04 to 7.51 (log CFU g^?1 soil) in Sites 1 and 3, respectively. The bacterial population was predominantly composed of Firmicutes, Proteobacteria, and Actinobacteria on both sites. The most represented genera in Site 1 were Bacillus (41%) and Pseudomonas (27%), whereas Arthrobacter (21%) and Pseudomonas (13%) were the most represented genera in Site 3. Several bacterial isolates showed tolerance to high concentrations of metal(loid)s, suggesting that both contaminated sites are a valuable source of metal(loid)-tolerant bacteria, which may be further used in bioremediation and/or phytoremediation processes.     

Metal Distribution and Characterization of Cultivable Lead-Resistant Bacteria in Shooting Range Soils

Shooting ranges represent about 10% of polluted sites in Switzerland. This pollution, mainly consisting of lead (Pb) and antimony (Sb), can spread into the local groundwater, wildlife and plants. In this study, shooting range stop butt soils (elevated soil mount behind the target) of three sites (Versoix, Cartigny and Nyon, Western Switzerland) were investigated for metal contamination and culturable lead-resistant bacteria in contaminated soils. The inductively coupled plasma mass spectrometry analysis of surface stop butt soils (0–5 cm) indicated high metal concentrations especially for Pb and Sb, e.g., the Pb concentration ranging from 61,135 to 395,651, 23,821 to 201,268 and 120 to 27,517 mg kg^?1 in the soil from the sites of Versoix, Cartigny and Nyon, respectively. Molecular analysis of 16S rRNA gene demonstrates the presence of bacteria from diverse classes: Flavobacteriia, α-Proteobacteria, γ-Proteobacteria, Actinobacteria and Bacilli that exhibited high Pb minimum inhibitory concentration value from 1,036 to 2,694 mg kg^?1. The isolated strains could be the subject of further studies to evaluate their role in bioremediation of lead-contaminated soil.