Michael Weintraub | The University of Toledo (original) (raw)

Papers by Michael Weintraub

Research in Microbiology, 2005

Cultivation-independent molecular phylogenetic techniques are now widely employed to examine envi... more Cultivation-independent molecular phylogenetic techniques are now widely employed to examine environmental microbial diversity; however, the relationship between microbial community structure and ecosystem function is unclear. This review synthesizes cultivationindependent views of microbiological diversity with our current understanding of nutrient dynamics in alpine and arctic soils. Recently, we have begun to explore connections between microbial community structure and function in soils from the alpine Niwot Ridge LTER site in Colorado, USA, whose ecology has been extensively investigated for over 50 years. We examined the diversity of bacterial, eucaryal, and archaeal small subunit rRNA genes in tundra and talus soils across seasons in the alpine. This work has provided support for spatial and seasonal shifts in specific microbial groups, which correlate well with previously documented transitions in microbial processes. In addition, these preliminary results suggest that the physiologies of certain groups of organisms may scale up to the ecosystem level, providing the basis for testable hypotheses about the function of specific microbes in this system. These studies have also expanded on the known diversity of life, as these soils harbor bacterial and eucaryotic lineages that are distantly related to other known organisms. In contrast to the alpine, microbial diversity in the arctic has been little explored; only three published studies have used molecular techniques to examine these soils. Because of the importance of these systems, particularly to the global C cycle, and their vulnerability to current and impending climate change, the microbial diversity of these soils needs to be further investigated.  2005 Elsevier SAS. All rights reserved.

Journal of Plant Physiology, 2014

Global warming will increase heat waves, but effects of abrupt heat stress on shoot-root interact... more Global warming will increase heat waves, but effects of abrupt heat stress on shoot-root interactions have rarely been studied in heat-tolerant species, and abrupt heat-stress effects on root N uptake and shoot C flux to roots and soil remains uncertain. We investigated effects of a high-temperature event on shoot vs. root growth and function, including transfer of shoot C to roots and soil and uptake and translocation of soil N by roots in the warm-season drought-tolerant C 4 prairie grass, Andropogon gerardii. We heated plants in the lab and field (lab = 5.5 days at daytime of 30 + 5 or 10 • C; field = 5 days at ambient (up to 32 • C daytime) vs. ambient +10 • C). Heating had small or no effects on photosynthesis, stomatal conductance, leaf water potential, and shoot mass, but increased root mass and decreased root respiration and exudation per g. 13 C-labeling indicated that heating increased transfer of recently-fixed C from shoot to roots and soil (the latter likely via increased fine-root turnover). Heating decreased efficiency of N uptake by roots (uptake/g root), but did not affect total N uptake or the transfer of labeled soil 15 N to shoots. Though heating increased soil temperature in the lab, it did not do so in the field (10 cm depth); yet results were similar for lab and field. Hence, acute heating affected roots more than shoots in this stress-tolerant species, increasing root mass and C loss to soil, but decreasing function per g root, and some of these effects were likely independent of direct effects from soil heating.

Global Biogeochemical Cycles, 2006

Environmental Microbiology, 2008

Many studies have shown that changes in nitrogen (N) availability affect primary productivity in ... more Many studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0-5 cm) samples from five control and five long-term N-amended plots established and maintained at the Niwot Ridge Longterm Ecological Research (LTER) site. Samples were bulked by treatment and all analyses were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N-amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N-amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G-lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function.

Ecosystems, 2003

We used long-term laboratory incubations and chemical fractionation to characterize the mineraliz... more We used long-term laboratory incubations and chemical fractionation to characterize the mineralization dynamics of organic soils from tussock, shrub, and wet meadow tundra communities, to determine the relationship between soil organic matter (SOM) decomposition and chemistry, and to quantify the relative proportions of carbon (C) and nitrogen (N) in tundra SOM that are biologically available for decomposition. In all soils

Ecology Letters, 2008

Extracellular enzymes are the proximate agents of organic matter decomposition and measures of th... more Extracellular enzymes are the proximate agents of organic matter decomposition and measures of these activities can be used as indicators of microbial nutrient demand. We conducted a global-scale meta-analysis of the seven-most widely measured soil enzyme activities, using data from 40 ecosystems. The activities of b-1,4-glucosidase, cellobiohydrolase, b-1,4-N-acetylglucosaminidase and phosphatase g )1 soil increased with organic matter concentration; leucine aminopeptidase, phenol oxidase and peroxidase activities showed no relationship. All activities were significantly related to soil pH. Specific activities, i.e. activity g )1 soil organic matter, also varied in relation to soil pH for all enzymes. Relationships with mean annual temperature (MAT) and precipitation (MAP) were generally weak. For hydrolases, ratios of specific C, N and P acquisition activities converged on 1 : 1 : 1 but across ecosystems, the ratio of C : P acquisition was inversely related to MAP and MAT while the ratio of C : N acquisition increased with MAP. Oxidative activities were more variable than hydrolytic activities and increased with soil pH. Our analyses indicate that the enzymatic potential for hydrolyzing the labile components of soil organic matter is tied to substrate availability, soil pH and the stoichiometry of microbial nutrient demand. The enzymatic potential for oxidizing the recalcitrant fractions of soil organic material, which is a proximate control on soil organic matter accumulation, is most strongly related to soil pH. These trends provide insight into the biogeochemical processes that create global patterns in ecological stoichiometry and organic matter storage.

Biogeochemistry, 2005

Past research strongly indicates the importance of amino acids in the N economy of the Arctic tun... more Past research strongly indicates the importance of amino acids in the N economy of the Arctic tundra, but little is known about the seasonal dynamics of amino acids in tundra soils. We repeatedly sampled soils from tussock, shrub, and wet sedge tundra communities in the summers of 2000 and 2001 and extracted them with water (H 2 O) and potassium sulfate (K 2 SO 4 ) to determine the seasonal dynamics of soil amino acids, ammonium (NH 4 + ), nitrate (NO 3 À ), dissolved organic nitrogen (DON), dissolved organic carbon (DOC), and phosphate (PO 4 2À Abbreviations: TFAA -Total free amino acids; DOC -Dissolved organic carbon; DON -Dissolved organic nitrogen; NH 4 + -Ammonium; NO 3 À -Nitrate; PO 4 2À -Phosphate; DIN -Dissolved inorganic nitrogen: ammonium + nitrate; N -Nitrogen; C -Carbon Biogeochemistry (2005) 73: 359-380 Ó Springer 2005

In the Arctic and around the world, earlier plant growth is an indication that warmer temperature... more In the Arctic and around the world, earlier plant growth is an indication that warmer temperatures or other global changes are changing the seasonality of the Earth's ecosystems. To determine how changes in seasonality affect plant life histories and biogeochemical cycles in tussock tundra, we established a factorial experiment that includes two approaches to changing the seasonality of this ecosystem.

Soil Science Society of America Journal, 2004

Doyle and Schimel, 1998). Persulfate oxidation has been developed for soil extract DON (Cabrera a... more Doyle and Schimel, 1998). Persulfate oxidation has been developed for soil extract DON (Cabrera and Persulfate digestions have been used for analyzing dissolved or- Beare, 1993) and for fresh water DOC (McDowell et ganic carbon (DOC) and nitrogen (DON), but most existing methods do not simultaneously analyze the same digest. Persulfate oxidizes al., 1987). It is conveniently run in an

Soil Biology and Biochemistry, 2011

Microbial digestive enzymes in soil and litter have been studied for over a half century, yet the... more Microbial digestive enzymes in soil and litter have been studied for over a half century, yet the understanding of microbial enzymes as drivers of ecosystem processes remains hindered by methodological differences among researchers and laboratories. Modern techniques enable the comparison of enzyme activities from different sites and experiments, but most researchers do not optimize enzyme assay methods for their study sites, and thus may not properly assay potential enzyme activity. In this review, we characterize important procedural details of enzyme assays, and define the steps necessary to properly assay potential enzyme activities in environmental samples. We make the following recommendations to investigators measuring soil enzyme activities: 1) run enzyme assays at the environmental pH and temperature; 2) run proper standards, and if using fluorescent substrates with NaOH addition, use a standard time of 1 min between the addition of NaOH and reading in a fluorometer; 3) run enzyme assays under saturating substrate concentrations to ensure V max is being measured; 4) confirm that product is produced linearly over the duration of the assay; 5) examine whether mixing during the reaction is necessary to properly measure enzyme activity; 6) find the balance between dilution of soil homogenate and assay variation; and 7) ensure that enzyme activity values are properly calculated. These steps should help develop a unified understanding of enzyme activities in ecosystem ecology.

Soil Biology and Biochemistry, 2008

Current soil enzyme methods measure potential enzyme activities, which are indicative of overall ... more Current soil enzyme methods measure potential enzyme activities, which are indicative of overall enzyme concentrations. However, they do not provide insight in the actual rates of enzymatically catalyzed reactions under natural in situ conditions. The objectives of this review are to (1) clarify what is being measured by current standard soil enzymology methods; (2) present an overview of the factors that control in situ activities of soil enzymes; and (3) evaluate how emerging technologies and modeling approaches could enhance our understanding of in situ extracellular enzyme activity (EEA). Genomic studies targeting functional genes coding for extracellular enzymes can identify the genetic potential of microbial communities to produce enzymes. Microbial regulation of enzyme production can be assessed with transcriptomic studies of mRNA. Emerging proteomic tools could be used assess the pool sizes, diversity, and microbial source of soil enzymes. New mass-spectrometry approaches can be used to quantify the products of enzymatic degradation. The insights gathered from these approaches will foster improved models of decomposition that explicitly include enzymes and microbial species or functional groups. A comprehensive approach to measuring in situ activity and elucidating the regulation of enzyme production and stabilization is required to advance our understanding of the biochemistry of decomposition.

Soil Biology and Biochemistry, 2005

In the arctic tundra of Alaska, plant growth is limited by N supply, especially in tussock tundra... more In the arctic tundra of Alaska, plant growth is limited by N supply, especially in tussock tundra. Because proteins are the predominant form of soil organic N, proteolysis is considered to be the rate-limiting step in both the release of amino acids and in N mineralization. To help understand the controls on N availability in tundra soils, and to determine whether proteolysis is controlled by enzyme activity or by substrate availability, we measured soil protein concentrations, and proteolysis rates with and without added protein, every 1-2 weeks through the summer of 2000 and twice in the summer of 2001. Protease activity with added protein ('potential') was higher than without added protein ('actual'). However, differences between the two tended to be driven by relatively brief peaks in potential protease activity. In fact, actual and potential rates were usually similar, suggesting that much of the time proteolysis was not limited by substrate availability, but rather by enzyme activity. Our data suggest that protease activity was actually only substrate limited at the times when it was highest. Potential rates peaked at the same times that soluble proteins were also high. These increases in protease activity and soluble protein concentrations occurred when soil amino acid and NH 4 C concentrations were at their lowest, drawn down by the seasonal peaks in root growth. The fact that the peaks in protease activity coincided with the peak in soil amino acid and NH 4 C demand strongly suggests that proteolysis was stimulated by high soil amino acid demand, and resulted in increases in soluble protein concentrations caused by the solubilization of larger proteins. q (J.P. Schimel). 1 Tel.: C1 805 893 7688.

Proceedings of the Royal Society B: Biological Sciences, 2008

Global climate change has accelerated the pace of glacial retreat in high-latitude and high-eleva... more Global climate change has accelerated the pace of glacial retreat in high-latitude and high-elevation environments, exposing lands that remain devoid of vegetation for many years. The exposure of 'new' soil is particularly apparent at high elevations (5000 metres above sea level) in the Peruvian Andes, where extreme environmental conditions hinder plant colonization. Nonetheless, these seemingly barren soils contain a diverse microbial community; yet the biogeochemical role of micro-organisms at these extreme elevations remains unknown. Using biogeochemical and molecular techniques, we investigated the biological community structure and ecosystem functioning of the pre-plant stages of primary succession in soils along a high-Andean chronosequence. We found that recently glaciated soils were colonized by a diverse community of cyanobacteria during the first 4-5 years following glacial retreat. This significant increase in cyanobacterial diversity corresponded with equally dramatic increases in soil stability, heterotrophic microbial biomass, soil enzyme activity and the presence and abundance of photosynthetic and photoprotective pigments. Furthermore, we found that soil nitrogen-fixation rates increased almost two orders of magnitude during the first 4-5 years of succession, many years before the establishment of mosses, lichens or vascular plants. Carbon analyses (pyrolysis-gas chromatography/mass spectroscopy) of soil organic matter suggested that soil carbon along the chronosequence was of microbial origin. This indicates that inputs of nutrients and organic matter during early ecosystem development at these sites are dominated by microbial carbon and nitrogen fixation. Overall, our results indicate that photosynthetic and nitrogen-fixing bacteria play important roles in acquiring nutrients and facilitating ecological succession in soils near some of the highest elevation receding glaciers on the Earth.

Oecologia, 2007

Previous studies have found that root carbon inputs to the soil can stimulate the mineralization ... more Previous studies have found that root carbon inputs to the soil can stimulate the mineralization of existing soil carbon (C) pools. It is still uncertain, however, whether this ''primed'' C is derived from elevated rates of soil organic matter (SOM) decomposition, greater C release from microbial pools, or both. The goal of this research was to determine how the activities of the microbial exoenzymes that control SOM decomposition are affected by root C inputs. This was done by manipulating rhizodeposition with tree girdling in a coniferous subalpine forest in the Rocky Mountains of Colorado, USA, and following changes in the activities of nine exoenzymes involved in decomposition, as well as soil dissolved organic C, dissolved organic and inorganic nitrogen (N), and microbial biomass C and N. We found that rhizodeposition is high in the spring, when the soils are still snow-covered, and that there are large ephemeral populations of microorganisms dependent upon this C. Microbial N acquisition from peptide degradation increased with increases in microbial biomass when rhizodeposition was highest. However, our data indicate that the breakdown of cellulose, lignin, chitin, and organic phosphorus are not affected by springtime increases in soil microbial biomass associated with increases in rhizodeposition. We conclude that the priming of soil C mineralization by rhizodeposition is due to growth of the microbial biomass and an increase in the breakdown of N-rich proteins, but not due to increases in the degradation of plant litter constituents such as cellulose and lignin.

Soil Biology and Biochemistry, 2003

Traditional models of soil organic matter (SOM) decomposition are all based on first order kineti... more Traditional models of soil organic matter (SOM) decomposition are all based on first order kinetics in which the decomposition rate of a particular C pool is proportional to the size of the pool and a simple decomposition constant ðdC=dt ¼ kCÞ: In fact, SOM decomposition is catalyzed by extracellular enzymes that are produced by microorganisms. We built a simple theoretical model to explore the behavior of the decomposition -microbial growth system when the fundamental kinetic assumption is changed from first order kinetics to exoenzymes catalyzed decomposition ðdC=dt ¼ KC £ EnzymesÞ: An analysis of the enzyme kinetics showed that there must be some mechanism to produce a non-linear response of decomposition rates to enzyme concentration-the most likely is competition for enzyme binding on solid substrates as predicted by Langmuir adsorption isotherm theory. This non-linearity also induces C limitation, regardless of the potential supply of C. The linked C and N version of the model showed that actual polymer breakdown and microbial use of the released monomers can be disconnected, and that it requires relatively little N to maintain the maximal rate of decomposition, regardless of the microbial biomass' ability to use the breakdown products. In this model, adding a pulse of C to an N limited system increases respiration, while adding N actually decreases respiration (as C is redirected from waste respiration to microbial growth). For many years, researchers have argued that the lack of a respiratory response by soil microbes to added N indicates that they are not N limited. This model suggests that conclusion may be wrong. While total C flow may be limited by the functioning of the exoenzyme system, actual microbial growth may be N limited. q