Evolutionary-Economic Principles as Regulators of Soil Enzyme Production and Ecosystem Function

Allison, Steven D.; Weintraub, Michael N.; Gartner, Tracy B.; Waldrop, Mark P.

doi:10.1007/978-3-642-14225-3_12

Cited by 232 publications

(241 citation statements)

References 75 publications

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“…In support of our hypothesis, we found a significant association between the ability to hydrolyze chitin and use the end products of hydrolysis, regardless of whether we corrected for shared evolutionary history. Allocation to extracellular enzymes represents a significant investment of carbon and nitrogen, and cells should be under selection to regulate production and maximize substrate use (Allison et al, 2007(Allison et al, , 2011. Most of the Vibrio genomes in our data set were capable of complete chitin hydrolysis, which is consistent with their known ecology.…”

Section: Discussionsupporting

confidence: 63%

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

2013

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Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and b-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzymeproducing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.

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Section: Discussionsupporting

confidence: 63%

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

2013

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“…Soil enzyme activities reflect the cumulative effects of substrate availability, microbial activity and environmental conditions (Allison et al, 2011). In this regard, Chu et al (2016) demonstrated that enzymes activities, such as DHA, are suitable indicators of soil quality due to their sensitivity to environmental factors.…”

Section: Microbial Respiration and Soil Enzyme Activitiesmentioning

confidence: 99%

Soil microbial functionality in response to the inclusion of cover crop mixtures in agricultural systems

Chavarría

Verdenelli

Muñoz

et al. 2016

Span. j. agric. res.

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Agricultural systems where monoculture prevails are characterized by fertility losses and reduced contribution to ecosystem services. Including cover crops (CC) as part of an agricultural system is a promising choice in sustainable intensification of those demanding systems. We evaluated soil microbial functionality in cash crops in response to the inclusion of CC by analyzing soil microbial functions at two different periods of the agricultural year (cash crop harvest and CC desiccation) during 2013 and 2014. Three plant species were used as CC: oat (Avena sativa L.), vetch (Vicia sativa L.) and radish (Raphanus sativus L.) which were sown in two different mixtures of species: oat and radish mix (CC1) and oat, radish and vetch mix (CC2), with soybean monoculture and soybean/corn being the cash crops. The study of community level physiological profiles showed statistical differences in respiration of specific C sources indicating an improvement of catabolic diversity in CC treatments. Soil enzyme activities were also increased with the inclusion of CC mixtures, with values of dehydrogenase activity and fluorescein diacetate hydrolysis up to 38.1% and 35.3% higher than those of the control treatment, respectively. This research evidenced that CC inclusion promotes soil biological quality through a contribution of soil organic carbon, improving the sustainability of agrosystems. The use of a CC mixture of three plant species including the legume vetch increased soil biological processes and catabolic diversity, with no adverse effects on cash crop grain yield.

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“…Soil EEA's are commonly studied to relate shifts in microbial function to soil nutrient cycling; useful indicators to assess microbial nutrient demands in response to climate change, plant community shifts, and more broadly ecosystem functioning [31][32][33] . EEA stoichiometry has been more recently adopted as an index to assess soil biochemical nutrient cycling by intersecting ecological stoichiometric theory and metabolic theory of ecology to assess potential microbial nutrient imbalances corresponding to environmental conditions 5 .…”

Section: Introductionmentioning

confidence: 99%

High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities

Bell

Fricks

Rocca

et al. 2013

JoVE

271

224

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Microbes in soils and other environments produce extracellular enzymes to depolymerize and hydrolyze organic macromolecules so that they can be assimilated for energy and nutrients. Measuring soil microbial enzyme activity is crucial in understanding soil ecosystem functional dynamics. The general concept of the fluorescence enzyme assay is that synthetic C-, N-, or P-rich substrates bound with a fluorescent dye are added to soil samples. When intact, the labeled substrates do not fluoresce. Enzyme activity is measured as the increase in fluorescence as the fluorescent dyes are cleaved from their substrates, which allows them to fluoresce. Enzyme measurements can be expressed in units of molarity or activity. To perform this assay, soil slurries are prepared by combining soil with a pH buffer. The pH buffer (typically a 50 mM sodium acetate or 50 mM Tris buffer), is chosen for the buffer's particular acid dissociation constant (pKa) to best match the soil sample pH. The soil slurries are inoculated with a nonlimiting amount of fluorescently labeled (i.e. C-, N-, or P-rich) substrate. Using soil slurries in the assay serves to minimize limitations on enzyme and substrate diffusion. Therefore, this assay controls for differences in substrate limitation, diffusion rates, and soil pH conditions; thus detecting potential enzyme activity rates as a function of the difference in enzyme concentrations (per sample).Fluorescence enzyme assays are typically more sensitive than spectrophotometric (i.e. colorimetric) assays, but can suffer from interference caused by impurities and the instability of many fluorescent compounds when exposed to light; so caution is required when handling fluorescent substrates. Likewise, this method only assesses potential enzyme activities under laboratory conditions when substrates are not limiting. Caution should be used when interpreting the data representing cross-site comparisons with differing temperatures or soil types, as in situ soil type and temperature can influence enzyme kinetics.

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Evolutionary-Economic Principles as Regulators of Soil Enzyme Production and Ecosystem Function

Cited by 232 publications

References 75 publications

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Soil microbial functionality in response to the inclusion of cover crop mixtures in agricultural systems

High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities

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