John C. Zak

Functional diversity of microbial communities: A quantitative approach

Abstract Evaluating the biodiversity of microbial communities remains an elusive task because of taxonomic and methodological difficulties. An alternative approach is to examine components of biodiversity for which there exists a reasonable chance of detecting patterns that are biologically meaningful. One such alternative is functional diversity. We propose a procedure based on the Biolog identification system to quickly, effectively, and inexpensively assess aspects of the functional diversity of microbial communities. The numbers and types of substrates utilized by bacterial communities, as well as the levels of activities on various substrates and patterns of temporal development, constitute an information-rich data set from which to assess functional diversity. Data from six plant communities (black grama grassland. Sporobolus grassland, creosotebush bajada, herbaceous bajada, mesquite-playa fringe, and playa grassland) located along an elevational and moisture gradient at the Jornada Long-Term Ecological Research site in the northern Chihuahuan Desert, are analyzed to illustrate the procedure and its relevance to biodiversity. Our analyses demonstrate that the Biolog system can detect considerable variation in the ability of microbial communities to metabolize different carbon compounds. Variation in substrate use was compartmentalized differently along the moisture gradient. Differences in functional diversity were dependent upon the class of carbon sources (guild-specific results). A multifaceted approach to biodiversity that comprises both functional and taxonomic perspectives represents fertile ground for future research endeavors.

Assessing the Response of Terrestrial Ecosystems to Potential Changes in Precipitation

Abstract Changes in Earths surface temperatures caused by anthropogenic emissions of greenhouse gases are expected to affect global and regional precipitation regimes. Interactions between changing precipitation regimes and other aspects of global change are likely to affect natural and managed terrestrial ecosystems as well as human society. Although much recent research has focused on assessing the responses of terrestrial ecosystems to rising carbon dioxide or temperature, relatively little research has focused on understanding how ecosystems respond to changes in precipitation regimes. Here we review predicted changes in global and regional precipitation regimes, outline the consequences of precipitation change for natural ecosystems and human activities, and discuss approaches to improving understanding of ecosystem responses to changing precipitation. Further, we introduce the Precipitation and Ecosystem Change Research Network (PrecipNet), a new interdisciplinary research network assembled to encourage and foster communication and collaboration across research groups with common interests in the impacts of global change on precipitation regimes, ecosystem structure and function, and the human enterprise.

Field response of wheat to arbuscular mycorrhizal fungi and drought stress

Mycorrhizal plants often have greater tolerance to drought than nonmycorrhizal plants. This study was conducted to determine the effects of arbuscular mycorrhizal (AM) fungi inoculation on growth, grain yield and mineral acquisition of two winter wheat (Triticum aestivum L.) cultivars grown in the field under well-watered and water-stressed conditions. Wheat seeds were planted in furrows after treatment with or without the AM fungi Glomus mosseae or G. etunicatum. Roots were sampled at four growth stages (leaf, tillering, heading and grain-filling) to quantify AM fungi. There was negligible AM fungi colonization during winter months following seeding (leaf sampling in February), when soil temperature was low. During the spring, AM fungi colonization increased gradually. Mycorrhizal colonization was higher in well-watered plants colonized with AM fungi isolates than water-stressed plants. Plants inoculated with G. etunicatum generally had higher colonization than plants colonized with G. mosseae under both soil moisture conditions. Biomass and grain yields were higher in mycorrhizal than nonmycorrhizal plots irrespective of soil moisture, and G. etunicatum inoculated plants generally had higher biomass and grain yields than those colonized by G. mosseae under either soil moisture condition. The mycorrhizal plants had higher shoot P and Fe concentrations than nonmycorrhizal plants at all samplings regardless of soil moisture conditions. The improved growth, yield and nutrient uptake in wheat plants reported here demonstrate the potential of mycorrhizal inoculation to reduce the effects of drought stress on wheat grown under field conditions in semiarid areas of the world.

Linking Microbial Community Structure and Function to Seasonal Differences in Soil Moisture and Temperature in a Chihuahuan Desert Grassland

Global and regional climate models predict higher air temperature and less frequent, but larger precipitation events in arid regions within the next century. While many studies have addressed the impact of variable climate in arid ecosystems on plant growth and physiological responses, fewer studies have addressed soil microbial community responses to seasonal shifts in precipitation and temperature in arid ecosystems. This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency of precipitation within any given year. Carbon utilization by fungi in the cooler winter exceeded use in the warmer summer each year suggesting that soil temperature, rather than soil moisture, strongly influenced fungal carbon use and structure and function dynamics. The structure/function relationship for AM fungi and soil bacteria notably changed across season. Moreover, the abundance of Gram-positive bacteria was lower in the winter compared to Gram-negative bacteria. Bacterial carbon use, however, was highest in the summer and lower during the winter. Enzyme activities did not respond to either annual or seasonal differences in the magnitude or timing of precipitation. Specific structural components of the soil microbiota community became uncoupled from total microbial function during different seasons. This change in the microbial structure/function relationship suggests that different components of the soil microbial community may provide similar ecosystem function, but differ in response to seasonal temperature and precipitation. As soil microbes encounter increased soil temperatures and altered precipitation amounts and timing that are predicted for this region, the ability of the soil microbial community to maintain functional resilience across the year may be reduced in this Chihuahuan Desert ecosystem.

Differences in native soil ecology associated with invasion of the exotic annual chenopod, Halogeton glomeratus

Various biotic and abiotic components of soil ecology differed significantly across an area where Halogeton glomeratus is invading a native winterfat, [ Krascheninnikovia (= Ceratoides) lanata] community. Nutrient levels were significantly different among the native, ecotone, and exotic-derived soils. NO3, P, K, and Na all increased as the cover of halogeton increased. Only Ca was highest in the winterfat area. A principal components analysis, conducted separately for water-soluble and exchangeable cations, revealed clear separation between halogeton- and winterfat-derived soils. The diversity of soil bacteria was highest in the exotic, intermediate in the ecotone, and lowest in the native community. Although further studies are necessary, our results offer evidence that invasion by halogeton alters soil chemistry and soil ecology, possibly creating conditions that favor halogeton over native plants.

Choline and osmotic-stress tolerance induced in Arabidopsis by the soil microbe Bacillus subtilis (GB03).

Choline (Cho) is an essential nutrient for humans as well as the precursor of glycine betaine (GlyBet), an important compatible solute in eukaryotes that protects cells from osmotic stress caused by dehydrating conditions. The key enzyme for plant Cho synthesis is phosphoethanolamine N-methyltransferase (PEAMT), which catalyzes all three methylation steps, including the rate-limiting N-methylation of phosphoethanolamine. Herein, we report that the beneficial soil bacterium Bacillus subtilis (strain GB03) enhances Arabidopsis Cho and GlyBet synthesis associated with enhanced plant tolerance to osmotic stress. When stressed with 100 mM exogenous mannitol, GB03-exposed plants exhibit increased transcript level of PEAMT compared with stressed plants without bacterial exposure. Endogenous Cho and GlyBet metabolite pools were elevated by more than two- and fivefold, respectively, by GB03 treatment, consistent with increased stress tolerance. Moreover, in the xipotl mutant line with reduced Cho production, a loss of GB03-induced drought tolerance is observed. Osmotic-stressed plants with or without GB03 exposure show similar levels of abscsisic acid (ABA) accumulation in both shoots and roots, suggesting that GB03-induced osmoprotection is ABA independent. GB03 treatment also improves drought tolerance in soil-grown plants as characterized by phenotypic comparisons, supported by an elevated accumulation of osmoprotectants. These results provide a biological strategy to enhance Cho biosynthesis in plants and, in turn, increase plant tolerance to osmotic stress by elevating osmoprotectant accumulation.

Precipitation timing and magnitude differentially affect aboveground annual net primary productivity in three perennial species in a Chihuahuan Desert grassland

Plant productivity in deserts may be more directly responsive to soil water availability than to precipitation. However, measurement of soil moisture alone may not be enough to elucidate plant responses to precipitation pulses, as edaphic factors may influence productivity when soil moisture is adequate. The first objective of the study was to determine the responses of the aboveground annual net primary productivity (ANPP) of three perennial species (from different functional groups) in a Chihuahuan Desert grassland to variation in natural precipitation (annual and seasonal) and a 25% increase in seasonal precipitation (supplemental watering in summer and winter). Secondly, ANPP responses to other key environmental and soil parameters were explored during dry, average, and wet years over a 5-yr period. ANPP predictors for each species were dynamic. High ANPP in Dasylirion leiophyllum was positively associated with higher soil NH(4)-N and frequent larger precipitation events, while that in Bouteloua curtipendula was positively correlated with frequent small summer precipitation events with short inter-pulse periods and supplemental winter water. Opuntia phaeacantha was responsive to small precipitation events with short inter-pulse periods. Although several studies have shown ANPP increases with increases in precipitation and soil moisture in desert systems, this was not observed here as a universal predictor of ANPP, particularly in dry years.

Effects of water and nitrogen amendment on soil microbial biomass and fine root production in a semi-arid environment in West Texas

Abstract Primary production in semi-arid and arid environments can be water limited and nitrogen regulated. We examined short-term (hourly) and relatively long-term (monthly) responses of soil microbial biomass, soil N mineralization dynamics, fine root production and ectomycorrhizal colonization rates to a single water and N addition in the sand shinnery-oak ecosystem in West Texas. Microbial biomass C and N exhibited rapid response to water and N addition. However, over the short term, water decreased microbial biomass C. A low addition of nitrogen (5 g m−2) had a short-term positive effect on microbial biomass, but no long-term effect. The addition of 50 g N m−2 significantly increased microbial biomass C, N mineralization rates, and root growth over 4 months. Ectomycorrhizal colonization was decreased at the high rates of N addition. The results indicate that in this semi-arid environment, below-ground processes in the sand shinnery-oak ecosystem are strongly limited by N availability, while water regulates the period of activity.

Antimicrobial susceptibilities of Aeromonas spp. isolated from environmental sources.

ABSTRACT Aeromonas spp. are ubiquitous aquatic bacteria that cause serious infections in both poikilothermic and endothermic animals, including humans. Clinical isolates have shown an increasing incidence of antibiotic and antimicrobial drug resistance since the widespread use of antibiotics began. A total of 282 Aeromonas pure cultures were isolated from both urban and rural playa lakes in the vicinity of Lubbock, Texas, and several rivers in West Texas and New Mexico. Of these, at least 104 were subsequently confirmed to be independent isolates. The 104 isolates were identified by Biolog and belonged to 11 different species. The MICs of six metals, one metalloid, five antibiotics, and two antimicrobial drugs were determined. All aeromonads were sensitive to chromate, cobalt, copper, nickel, zinc, cefuroxime, kanamycin, nalidixic acid, ofloxacin, tetracycline, and sulfamethoxazole. Low incidences of trimethoprim resistance, mercury resistance, and arsenite resistance were found. Dual resistances were found in 5 of the 104 Aeromonas isolates. Greater numbers of resistant isolates were obtained from samples taken in March versus July 2002 and from sediment versus water. Plasmids were isolated from selected strains of the arsenite- and mercury-resistant organisms and were transformed into Escherichia coli XL1-Blue MRF′. Acquisition of the resistance phenotypes by the new host showed that these resistance genes were carried on the plasmids. Mercury resistance was found to be encoded on a conjugative plasmid. Despite the low incidence of resistant isolates, the six playa lakes and three rivers that were sampled in this study can be considered a reservoir for antimicrobial resistance genes.

An appraisal of soil fungal biodiversity: the crossroads between taxonomic and functional biodiversity

Attempts at evaluating taxonomic diversity of soil fungi either at the landscape or biome level are just as problematic as current efforts for developing a baseline data set of global biodiversity if the taxonomic information is not integrated into an ecosystem context. That is, attention should be given toward understanding the linkages between taxonomic diversity and functional diversity. Only then can biodiversity data be collected that have some predictive potential rather than simply being descriptive. One aspect of fungal biodiversity that has not been adequately addressed is the impact of the fungal growth form on estimates of biodiversity and the model that is used to express the organization of the fungal mycelium. The indeterminate and mycelial growth form of most fungi allows for ecological properties that have not been well considered in discussions on fungal biodiversity. The aim of this paper is to: (i) expand upon our current discussions on fungal biodiversity by introducing aspects of the biology of fungi that may influence patterns of biodiversity, (ii) to present the discussion of the biodiversity of soil fungi in an ecological framework from which comparisons with other taxonomic groups can be made, and (iii) to introduce new avenues of enquiry that may prove fruitful in the quest towards understanding the mechanisms that account for patterns in fungal biodiversity.