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R D Evans - One of the best experts on this subject based on the ideXlab platform.

  • soil water availability and microsite mediate fungal and bacterial phospholipid fatty acid biomarker abundances in mojave Desert Soils exposed to elevated atmospheric co2
    Journal of Geophysical Research, 2011
    Co-Authors: Sean M Schaeffer, Susan E Ziegler, R D Evans
    Abstract:

    [1] Changes in the rates of nitrogen (N) cycling, microbial carbon (C) substrate use, and extracellular enzyme activities in a Mojave Desert ecosystem exposed to elevated atmospheric CO2 suggest shifts in the size and/or functional characteristics of microbial assemblages in two dominant soil microsites: plant interspaces and under the dominant shrub Larrea tridentata. We used ester-linked phospholipid fatty acid (PLFA) biomarkers as a proxy for microbial biomass to quantify spatial and temporal differences in soil microbial communities from February 2003 to May 2005. Further, we used the 13C signature of the fossil CO2 source for elevated CO2 plots to trace recent plant C inputs into soil organic matter (SOM) and broad microbial groups using δ13C (‰). Differences between individual δ13CPLFA and δ13CSOM for fungal biomarkers indicated active metabolism of newer C in elevated CO2 Soils. Total PLFA-C was greater in shrub microsites compared to plant interspaces, and CO2 treatment differences within microsites increased under higher soil water availability. Total, fungal, and bacterial PLFA-C increased with decreasing soil volumetric water content (VWC) in both microsites, suggesting general adaptations to xeric Desert conditions. Increases in fungal-to-bacterial PLFA-C ratio with decreasing VWC reflected functional group-specific responses to changing soil water availability. While temporal and spatial extremes in resource availability in Desert ecosystems contribute to the difficulty in identifying common trends or mechanisms driving microbial responses in less extreme environments, we found that soil water availability and soil microsite interacted with elevated CO2 to shift fungal and bacterial biomarker abundances in Mojave Desert Soils.

  • microbial 13c utilization patterns via stable isotope probing of phospholipid biomarkers in mojave Desert Soils exposed to ambient and elevated atmospheric co2
    Global Change Biology, 2010
    Co-Authors: R D Evans
    Abstract:

    Changes in plant inputs under changing atmospheric CO 2 can be expected to alter the size and/or functional characteristics of soil microbial communities which can determine whether Soils are a C sink or source. Stable isotope probing was used to trace autotrophically fixed 13 C into phospholipid fatty acid (PLFA) biomarkers in Mojave Desert Soils planted with the Desert shrub, Larrea tridentata. Seedlings were pulse-labeled with 13 CO 2 under ambient and elevated CO 2 in controlled environmental growth chambers. The label was chased into the soil by extracting soil PLFAs after labeling at Days 0, 2, 10, 24, and 49. Eighteen of 29 PLFAs identified showed 13 C enrichment relative to nonlabeled control Soils. Patterns of PLFA enrichment varied temporally and were similar for various PLFAs found within a microbial functional group. Enrichment of PLFA 13 C generally occurred within the first 2 days in general and fungal biomarkers, followed by increasingly greater enrichment in bacterial biomarkers as the study progressed (Gram-negative, Gram-positive, actinobacteria). While treatment CO 2 level did not affect total PLFA-C concentrations, microbial functional group abundances and distribution responded to treatment CO 2 level and these shifts persisted throughout the study. Specifically, ratios of bacterial-to-total PLFA-C decreased and fungal-to-bacterial PLFA-C increased under elevated CO 2 compared with ambient conditions. Differences in the timing of 13 C incorporation into lipid biomarkers coupled with changes in microbial functional groups indicate that microbial community characteristics in Mojave Desert Soils have shifted in response to long-term exposure to increased atmospheric CO 2 .

  • elevated co2 increases microbial carbon substrate use and nitrogen cycling in mojave Desert Soils
    Global Change Biology, 2007
    Co-Authors: R D Evans
    Abstract:

    Identifying soil microbial responses to anthropogenically driven environmental changes is critically important as concerns intensify over the potential degradation of ecosystem function. We assessed the effects of elevated atmospheric CO2 on microbial carbon (C) and nitrogen (N) cycling in Mojave Desert Soils using extracellular enzyme activities (EEAs), community-level physiological profiles (CLPPs), and gross N transformation rates. Soils were collected from unvegetated interspaces between plants and under the dominant shrub (Larrea tridentata) during the 2004–2005 growing season, an above-average rainfall year. Because most measured variables responded strongly to soil water availability, all significant effects of soil water content were used as covariates to remove potential confounding effects of water availability on microbial responses to experimental treatment effects of cover type, CO2, and sampling date. Microbial C and N activities were lower in interspace Soils compared with Soils under Larrea, and responses to date and CO2 treatments were cover specific. Over the growing season, EEAs involved in cellulose (cellobiohydrolase) and orthophosphate (alkaline phosphatase) degradation decreased under ambient CO2, but increased under elevated CO2. Microbial C use and substrate use diversity in CLPPs decreased over time, and elevated CO2 positively affected both. Elevated CO2 also altered microbial C use patterns, suggesting changes in the quantity and/or quality of soil C inputs. In contrast, microbial biomass N was higher in interspace Soils than Soils under Larrea, and was lower in Soils exposed to elevated CO2. Gross rates of NH4+ transformations increased over the growing season, and late-season NH4+ fluxes were negatively affected by elevated CO2. Gross NO3− fluxes decreased over time, with early season interspace Soils positively affected by elevated CO2. General increases in microbial activities under elevated CO2 are likely attributable to greater microbial biomass in interspace Soils, and to increased microbial turnover rates and/or metabolic levels rather than pool size in Soils under Larrea. Because soil water content and plant cover type dominates microbial C and N responses to CO2, the ability of Desert landscapes to mitigate or intensify the impacts of global change will ultimately depend on how changes in precipitation and increasing atmospheric CO2 shift the spatial distribution of Mojave Desert plant communities.

  • trace n gas losses and n mineralization in mojave Desert Soils exposed to elevated co2
    Soil Biology & Biochemistry, 2002
    Co-Authors: Sharon A Billings, Sean M Schaeffer, R D Evans
    Abstract:

    Abstract We examined N cycling processes in Desert Soils exposed to elevated CO 2 to better understand how some features of aridland soil N and C cycling may respond to an altered atmospheric composition. We measured rates of denitrification, potential denitrification, N 2 O fluxes, NH 3 volatilization, and net mineralization in an intact Mojave Desert ecosystem with elevated CO 2 (Free Air Carbon Enrichment technology) over 2 y. All measurements were performed on soil under four different cover types: Larrea tridentata ; Lycium spp.; Pleuraphis rigida ; and plant interspaces. The mean rate of denitrification was 161±96 μg N m −2  d −1 . Field fluxes of N 2 O occurred sporadically, with a mean of 30±20 μg N m −2  d −1 . Rates of NH 3 volatilization experienced less variability than did N 2 O fluxes, with a mean of 120±45 μg N m −2  d −1 . Mean potential denitrification enzyme activity (DEA) was 146±8 mg N m −2  d −1 . Rates of net mineralization were highest in soil under L. tridentata and Lycium spp. (398±108 mg N m −2  d −1 ) and lowest in the plant interspaces (129±28 mg N m −2  d −1 ). There was no effect of elevated CO 2 on N 2 O fluxes or mineralization rates. There was a 39% increase in NH 3 volatilization with elevated CO 2 during March 2000. Potential DEA increased by 193% with elevated CO 2 in October 1999 and decreased by 45% in March 2001. These results suggest that NH 3 volatilization may be a more important component of aridland gaseous N emissions than previously thought, and that the potential for high DEA does not necessarily induce large fluxes of N 2 O under natural conditions, especially in aridlands where rainfall primarily occurs in winter when soil temperatures can limit microbial activity. This study also suggests that the effects of elevated CO 2 on soil microbial activity may not be consistent for all seasons.

Jason P. Kaye - One of the best experts on this subject based on the ideXlab platform.

  • Decomposition of urban atmospheric carbon in Sonoran Desert Soils
    Urban Ecosystems, 2011
    Co-Authors: Jason P. Kaye, Sara E. Eckert, Daniel A. Gonzales, Jonathan O. Allen, Sharon J. Hall, Ryan A. Sponseller, Nancy B Grimm
    Abstract:

    Urban atmospheres can have high concentrations of particulate organic carbon (oC) but the rate and fate oC deposition in near-urban ecosystems are rarely quantified. We collected atmospheric particulate matter in Phoenix, AZ and applied these samples to Sonoran Desert Soils in a series of laboratory incubation experiments. The addition of fine particulate matter (2.5 μm aerodynamic diameter) was added to interspace Soils, suggesting that coarse particulate oC is recalcitrant to microbial decomposition. Due to comparatively higher background levels of C mineralization, we rarely detected changes in microbial respiration when fine or coarse particulate oC was added to Soils collected beneath shrub canopies. We measured total atmospheric C concentrations within and surrounding Phoenix and, using inferential methods, estimated rates of deposition that ranged from 0.02 to 0.58 mg C m−2 d−1 for fine particles and from 0 to 6.15 mg C m−2 d−1 for coarse particles. Results show that fine atmospheric particulate matter deposited at low rates downwind of Phoenix is a labile oC substrate for soil heterotrophs. In contrast, oC deposited at higher rates as coarse particulate matter may accumulate in Soils due to slow microbial decomposition rates.

  • responses of soil microorganisms to resource availability in urban Desert Soils
    Biogeochemistry, 2008
    Co-Authors: Michelle L Mccrackin, Nancy B Grimm, Sharon J. Hall, Tamara K Harms, Jason P. Kaye
    Abstract:

    Terrestrial Desert ecosystems are strongly structured by the distribution of plants, which concentrate resources and create islands of fertility relative to interplant spaces. Atmospheric nitrogen (N) deposition resulting from urbanization has the potential to change those spatial patterns via resource inputs, resulting in more homogeneous soil resource availability. We sampled Soils at 12 Desert remnant sites around Phoenix, Arizona along a model-predicted gradient in N deposition to determine the degree to which deposition has altered spatial patterns in soil resource availability and microbial activity. Soil microbial biomass and abundance were not influenced by atmospheric N deposition. Instead, plant islands remained strong organizers of soil microbial processes. These islands of fertility exhibited elevated pools of resources, microbial abundance, and activity relative to interspaces. In both plant islands and interspaces, soil moisture and soil N concentrations predicted microbial biomass and abundance. Following experimental wetting, carbon dioxide (CO2) flux from soil of interspaces was positively correlated with N deposition, whereas in plant islands, soil CO2 flux was positively correlated with soil moisture content and soil organic matter. Soil CO2 flux in both patch types showed rapid and short-lived responses to precipitation, demonstrating the brief time scales during which soil biota may process deposited materials. Although we observed patterns consistent with N limitation of microbes in interspaces, we conclude that atmospheric N deposition likely accumulates in Soils because microbes are primarily limited by water and secondarily by carbon or nitrogen. Soil microbial uptake of atmospherically deposited N likely occurs only during sparse and infrequent rainfall.

Nancy B Grimm - One of the best experts on this subject based on the ideXlab platform.

  • Decomposition of urban atmospheric carbon in Sonoran Desert Soils
    Urban Ecosystems, 2011
    Co-Authors: Jason P. Kaye, Sara E. Eckert, Daniel A. Gonzales, Jonathan O. Allen, Sharon J. Hall, Ryan A. Sponseller, Nancy B Grimm
    Abstract:

    Urban atmospheres can have high concentrations of particulate organic carbon (oC) but the rate and fate oC deposition in near-urban ecosystems are rarely quantified. We collected atmospheric particulate matter in Phoenix, AZ and applied these samples to Sonoran Desert Soils in a series of laboratory incubation experiments. The addition of fine particulate matter (2.5 μm aerodynamic diameter) was added to interspace Soils, suggesting that coarse particulate oC is recalcitrant to microbial decomposition. Due to comparatively higher background levels of C mineralization, we rarely detected changes in microbial respiration when fine or coarse particulate oC was added to Soils collected beneath shrub canopies. We measured total atmospheric C concentrations within and surrounding Phoenix and, using inferential methods, estimated rates of deposition that ranged from 0.02 to 0.58 mg C m−2 d−1 for fine particles and from 0 to 6.15 mg C m−2 d−1 for coarse particles. Results show that fine atmospheric particulate matter deposited at low rates downwind of Phoenix is a labile oC substrate for soil heterotrophs. In contrast, oC deposited at higher rates as coarse particulate matter may accumulate in Soils due to slow microbial decomposition rates.

  • responses of soil microorganisms to resource availability in urban Desert Soils
    Biogeochemistry, 2008
    Co-Authors: Michelle L Mccrackin, Nancy B Grimm, Sharon J. Hall, Tamara K Harms, Jason P. Kaye
    Abstract:

    Terrestrial Desert ecosystems are strongly structured by the distribution of plants, which concentrate resources and create islands of fertility relative to interplant spaces. Atmospheric nitrogen (N) deposition resulting from urbanization has the potential to change those spatial patterns via resource inputs, resulting in more homogeneous soil resource availability. We sampled Soils at 12 Desert remnant sites around Phoenix, Arizona along a model-predicted gradient in N deposition to determine the degree to which deposition has altered spatial patterns in soil resource availability and microbial activity. Soil microbial biomass and abundance were not influenced by atmospheric N deposition. Instead, plant islands remained strong organizers of soil microbial processes. These islands of fertility exhibited elevated pools of resources, microbial abundance, and activity relative to interspaces. In both plant islands and interspaces, soil moisture and soil N concentrations predicted microbial biomass and abundance. Following experimental wetting, carbon dioxide (CO2) flux from soil of interspaces was positively correlated with N deposition, whereas in plant islands, soil CO2 flux was positively correlated with soil moisture content and soil organic matter. Soil CO2 flux in both patch types showed rapid and short-lived responses to precipitation, demonstrating the brief time scales during which soil biota may process deposited materials. Although we observed patterns consistent with N limitation of microbes in interspaces, we conclude that atmospheric N deposition likely accumulates in Soils because microbes are primarily limited by water and secondarily by carbon or nitrogen. Soil microbial uptake of atmospherically deposited N likely occurs only during sparse and infrequent rainfall.

Sharon J. Hall - One of the best experts on this subject based on the ideXlab platform.

  • ammonia oxidizing archaea respond positively to inorganic nitrogen addition in Desert Soils
    FEMS Microbiology Ecology, 2015
    Co-Authors: Yevgeniy Marusenko, Ferran Garciapichel, Sharon J. Hall
    Abstract:

    In Soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land Soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top Soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these Desert Soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera ), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.

  • Decomposition of urban atmospheric carbon in Sonoran Desert Soils
    Urban Ecosystems, 2011
    Co-Authors: Jason P. Kaye, Sara E. Eckert, Daniel A. Gonzales, Jonathan O. Allen, Sharon J. Hall, Ryan A. Sponseller, Nancy B Grimm
    Abstract:

    Urban atmospheres can have high concentrations of particulate organic carbon (oC) but the rate and fate oC deposition in near-urban ecosystems are rarely quantified. We collected atmospheric particulate matter in Phoenix, AZ and applied these samples to Sonoran Desert Soils in a series of laboratory incubation experiments. The addition of fine particulate matter (2.5 μm aerodynamic diameter) was added to interspace Soils, suggesting that coarse particulate oC is recalcitrant to microbial decomposition. Due to comparatively higher background levels of C mineralization, we rarely detected changes in microbial respiration when fine or coarse particulate oC was added to Soils collected beneath shrub canopies. We measured total atmospheric C concentrations within and surrounding Phoenix and, using inferential methods, estimated rates of deposition that ranged from 0.02 to 0.58 mg C m−2 d−1 for fine particles and from 0 to 6.15 mg C m−2 d−1 for coarse particles. Results show that fine atmospheric particulate matter deposited at low rates downwind of Phoenix is a labile oC substrate for soil heterotrophs. In contrast, oC deposited at higher rates as coarse particulate matter may accumulate in Soils due to slow microbial decomposition rates.

  • responses of soil microorganisms to resource availability in urban Desert Soils
    Biogeochemistry, 2008
    Co-Authors: Michelle L Mccrackin, Nancy B Grimm, Sharon J. Hall, Tamara K Harms, Jason P. Kaye
    Abstract:

    Terrestrial Desert ecosystems are strongly structured by the distribution of plants, which concentrate resources and create islands of fertility relative to interplant spaces. Atmospheric nitrogen (N) deposition resulting from urbanization has the potential to change those spatial patterns via resource inputs, resulting in more homogeneous soil resource availability. We sampled Soils at 12 Desert remnant sites around Phoenix, Arizona along a model-predicted gradient in N deposition to determine the degree to which deposition has altered spatial patterns in soil resource availability and microbial activity. Soil microbial biomass and abundance were not influenced by atmospheric N deposition. Instead, plant islands remained strong organizers of soil microbial processes. These islands of fertility exhibited elevated pools of resources, microbial abundance, and activity relative to interspaces. In both plant islands and interspaces, soil moisture and soil N concentrations predicted microbial biomass and abundance. Following experimental wetting, carbon dioxide (CO2) flux from soil of interspaces was positively correlated with N deposition, whereas in plant islands, soil CO2 flux was positively correlated with soil moisture content and soil organic matter. Soil CO2 flux in both patch types showed rapid and short-lived responses to precipitation, demonstrating the brief time scales during which soil biota may process deposited materials. Although we observed patterns consistent with N limitation of microbes in interspaces, we conclude that atmospheric N deposition likely accumulates in Soils because microbes are primarily limited by water and secondarily by carbon or nitrogen. Soil microbial uptake of atmospherically deposited N likely occurs only during sparse and infrequent rainfall.

Michael Goodfellow - One of the best experts on this subject based on the ideXlab platform.

  • rare taxa and dark microbial matter novel bioactive actinobacteria abound in atacama Desert Soils
    Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2018
    Co-Authors: Michael Goodfellow, Imen Nouioui, Roy A Sanderson, Alan T Bull
    Abstract:

    An “in house” taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert Soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the Soils encompassed an astonishing degree of actinobacterial ‘dark matter’, while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.

  • streptomyces asenjonii sp nov isolated from hyper arid atacama Desert Soils and emended description of streptomyces viridosporus pridham et al 1958
    Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2017
    Co-Authors: Michael Goodfellow, Imen Nouioui, Kanungnid Busarakam, Hamidah Idris, David P Labeda, Roselyn Brown, Maria Del Carmen Monterocalasanz, Barbara A Andrews, Alan T Bull
    Abstract:

    A polyphasic study was undertaken to establish the taxonomic status of Streptomyces strains isolated from hyper-arid Atacama Desert Soils. Analysis of the 16S rRNA gene sequences of the isolates showed that they formed a well-defined lineage that was loosely associated with the type strains of several Streptomyces species. Multi-locus sequence analysis based on five housekeeping gene alleles showed that the strains form a homogeneous taxon that is closely related to the type strains of Streptomyces ghanaensis and Streptomyces viridosporus. Representative isolates were shown to have chemotaxonomic and morphological properties consistent with their classification in the genus Streptomyces. The isolates have many phenotypic features in common, some of which distinguish them from S. ghanaensis NRRL B-12104T, their near phylogenetic neighbour. On the basis of these genotypic and phenotypic data it is proposed that the isolates be recognised as a new species within the genus Streptomyces, named Streptomyces asenjonii sp. nov. The type strain of the species is KNN35.1bT (NCIMB 15082T = NRRL B-65050T). Some of the isolates, including the type strain, showed antibacterial activity in standard plug assays. In addition, MLSA, average nucleotide identity and phenotypic data show that the type strains of S. ghanaensis and S. viridosporus belong to the same species. Consequently, it is proposed that the former be recognised as a heterotypic synonym of the latter and an emended description is given for S. viridosporus.

  • modestobacter caceresii sp nov novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper arid atacama Desert Soils
    Systematic and Applied Microbiology, 2016
    Co-Authors: Kanungnid Busarakam, Alan T Bull, Martha E Trujillo, Raul Riesco, Vartul Sangal, Gilles P Van Wezel, Michael Goodfellow
    Abstract:

    A polyphasic study was designed to determine the taxonomic provenance of three Modestobacter strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates KNN 45-1a, KNN 45-2b(T) and KNN 45-3b, were shown to have chemotaxonomic and morphological properties in line with their classification in the genus Modestobacter. The isolates had identical 16S rRNA gene sequences and formed a branch in the Modestobacter gene tree that was most closely related to the type strain of Modestobacter marinus (99.6% similarity). All three isolates were distinguished readily from Modestobacter type strains by a broad range of phenotypic properties, by qualitative and quantitative differences in fatty acid profiles and by BOX fingerprint patterns. The whole genome sequence of isolate KNN 45-2b(T) showed 89.3% average nucleotide identity, 90.1% (SD: 10.97%) average amino acid identity and a digital DNA-DNA hybridization value of 42.4±3.1 against the genome sequence of M. marinus DSM 45201(T), values consistent with its assignment to a separate species. On the basis of all of these data, it is proposed that the isolates be assigned to the genus Modestobacter as Modestobacter caceresii sp. nov. with isolate KNN 45-2b(T) (CECT 9023(T)=DSM 101691(T)) as the type strain. Analysis of the whole-genome sequence of M. caceresii KNN 45-2b(T), with 4683 open reading frames and a genome size of ∽4.96Mb, revealed the presence of genes and gene-clusters that encode for properties relevant to its adaptability to harsh environmental conditions prevalent in extreme hyper arid Atacama Desert Soils.