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Egbert Schwartz

Bio: Egbert Schwartz is an academic researcher from Northern Arizona University. The author has contributed to research in topics: Stable-isotope probing & Soil water. The author has an hindex of 32, co-authored 95 publications receiving 3342 citations. Previous affiliations of Egbert Schwartz include University of Michigan & University of California, Davis.


Papers
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Journal ArticleDOI
TL;DR: In this paper, a new approach was developed to determine the natural abundance C and N isotope composition of the microbial biomass across a broad range of soil types, vegetation, and climates.
Abstract: Stable isotope analysis is a powerful tool in the study of soil organic matter formation. It is often observed that more decomposed soil organic matter is 13 C, and especially 15 N-enriched relative to fresh litter and recent organic matter. We investigated whether this shift in isotope composition relates to the isotope composition of the microbial biomass, an important source for soil organic matter. We developed a new approach to determine the natural abundance C and N isotope composition of the microbial biomass across a broad range of soil types, vegetation, and climates. We found consistently that the soil microbial biomass was 15 N-enriched relative to the total (3.2 %) and extractable N pools (3.7 %), and 13 C-enriched relative to the extractable C pool (2.5 %). The microbial biomass was also 13 C-enriched relative to total C for soils that exhibited a C3-plant signature (1.6 %), but 13 C-depleted for soils with a C4 signature (� 1.1 %). The latter was probably associated with an increase of annual C3 forbs in C4 grasslands after an extreme drought. These findings are in agreement with the proposed contribution of microbial products to the stabilized soil organic matter and may help explain the shift in isotope composition during soil organic matter formation. r 2006 Elsevier Ltd. All rights reserved.

246 citations

Journal ArticleDOI
TL;DR: Research now shows that microbial growth efficiency is insensitive to temperature change and that the response of microbial respiration to warming is driven by accelerated microbial turnover and enzyme kinetics.
Abstract: Whether rising temperatures will reduce global soil carbon stocks and enhance climate warming remains uncertain, in part because of a poor understanding of the mechanisms of soil microbial response to warming. Research now shows that microbial growth efficiency is insensitive to temperature change and that the response of microbial respiration to warming is driven by accelerated microbial turnover and enzyme kinetics.

226 citations

Journal ArticleDOI
TL;DR: qSIP is demonstrated using soil incubations, in which soil bacteria exhibited strong taxonomic variations in 18O and 13C composition after exposure to [18O]water or [13C]glucose, demonstrating the benefit of a quantitative approach to stable isotope probing.
Abstract: Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.

190 citations

Journal ArticleDOI
TL;DR: In response to temperature, communities behave biochemically similarly to single species and the understanding of temperature effects on CUE, energy production and use for maintenance and growth processes is still incomplete.
Abstract: We used metabolic tracers and modeling to analyze the response of soil metabolism to a sudden change in temperature from 4 to 20 °C. We hypothesized that intact soil microbial communities would exhibit shifts in pentose phosphate pathway and glycolysis activity in the same way as is regularly observed for individual microorganisms in pure culture. We also hypothesized that increased maintenance respiration at higher temperature would result in greater energy production and reduced carbon use efficiency (CUE). Two hours after temperature increase, respiration increased almost 10-fold. Although all metabolic processes were increased, the relative activity of metabolic processes, biosynthesis, and energy production changed. Pentose phosphate pathway was reduced (17–20%), while activities of specific steps in glycolysis (51%) and Krebs cycle (7–13%) were increased. In contrast, only small but significant changes in biosynthesis (+2%), ATP production (−3%) and CUE (+2%) were observed. In a second experiment, we compared the metabolic responses to temperature increases in soils from high and low elevation. The shift in activity from pentose phosphate pathway to glycolysis with higher temperature was confirmed in both soils, but the responses of Krebs cycle, biosynthesis, ATP production, and CUE were site dependent. Our results indicate that 1) in response to temperature, communities behave biochemically similarly to single species and, 2) our understanding of temperature effects on CUE, energy production and use for maintenance and growth processes is still incomplete.

190 citations

Journal ArticleDOI
TL;DR: The results suggest that in semiarid soils, archaea may be the primary ammonia oxidizers, and that ammonia-oxidizing archaea and ammonia-Oxidizing bacteria occupy different niches.
Abstract: Autotrophic ammonia-oxidizing communities, which are responsible for the rate-limiting step of nitrification in most soils, have not been studied extensively in semiarid ecosystems. Abundances of soil archaeal and bacterial amoA were measured with real-time polymerase chain reaction along an elevation gradient in northern Arizona. Archaeal amoA was the predominant form of amoA at all sites; however, ratios of archaeal to bacterial amoA ranged from 17 to more than 1,600. Although size of ammonia-oxidizing bacteria populations was correlated with precipitation, temperature, percent sand, and soil C/N, there were no significant relationships between ammonia-oxidizing archaea populations and any of the environmental parameters evaluated in this study. Our results suggest that in these soils, archaea may be the primary ammonia oxidizers, and that ammonia-oxidizing archaea and ammonia-oxidizing bacteria occupy different niches.

180 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

01 Jan 1980
TL;DR: In this article, the influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition and found that the variability of the relationship between the δ^(15)N values of animals and their diets is greater for different individuals raised on the same diet than for the same species raised on different diets.
Abstract: The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

5,548 citations

Journal ArticleDOI
TL;DR: It is proposed that labile plant constituents are the dominant source of microbial products, relative to input rates, because they are utilized more efficiently by microbes, and become the main precursors of stable SOM by promoting aggregation and through strong chemical bonding to the mineral soil matrix.
Abstract: The decomposition and transformation of above- and below-ground plant detritus (litter) is the main process by which soil organic matter (SOM) is formed. Yet, research on litter decay and SOM formation has been largely uncoupled, failing to provide an effective nexus between these two fundamental processes for carbon (C) and nitrogen (N) cycling and storage. We present the current understanding of the importance of microbial substrate use efficiency and C and N allocation in controlling the proportion of plant-derived C and N that is incorporated into SOM, and of soil matrix interactions in controlling SOM stabilization. We synthesize this understanding into the Microbial Efficiency-Matrix Stabilization (MEMS) framework. This framework leads to the hypothesis that labile plant constituents are the dominant source of microbial products, relative to input rates, because they are utilized more efficiently by microbes. These microbial products of decomposition would thus become the main precursors of stable SOM by promoting aggregation and through strong chemical bonding to the mineral soil matrix.

1,851 citations

Journal ArticleDOI
TL;DR: Although most soil microorganisms remain undescribed, the field is now poised to identify how to manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve the understanding of how terrestrial ecosystems will respond to environmental change.
Abstract: Soil microorganisms are clearly a key component of both natural and managed ecosystems. Despite the challenges of surviving in soil, a gram of soil can contain thousands of individual microbial taxa, including viruses and members of all three domains of life. Recent advances in marker gene, genomic and metagenomic analyses have greatly expanded our ability to characterize the soil microbiome and identify the factors that shape soil microbial communities across space and time. However, although most soil microorganisms remain undescribed, we can begin to categorize soil microorganisms on the basis of their ecological strategies. This is an approach that should prove fruitful for leveraging genomic information to predict the functional attributes of individual taxa. The field is now poised to identify how we can manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve our understanding of how terrestrial ecosystems will respond to environmental change.

1,720 citations

Journal ArticleDOI
01 Dec 1992-Genetics
TL;DR: Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.
Abstract: High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.

1,636 citations