Soil Enzymes: Linking Proteomics and Ecological Processes

Allison, Steven D.; Gartner, Tracy B.; Holland, Keri; Weintraub, Michael N.; Sinsabaugh, Robert L.

doi:10.1128/9781555815882.ch58

Cited by 82 publications

(62 citation statements)

References 90 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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“…Microbes produce extracellular enzymes that target all essential macronutrients, including C, N, P, and S (enzymes from plant roots target only P and possibly N) (Burns 1978;Allison et al 2007a). The availability of these nutrients fluctuates in space and time, and nutrient supply does not necessarily match microbial or plant nutrient requirements.…”

Section: Microbial Demandmentioning

confidence: 99%

“…Extracellular enzymes target nearly every macromolecule on earth, including proteins (proteases), carbohydrates (amylases, cellulases), amino sugar polymers (chitinases), organic phosphates (phosphatases), and lignins (oxidases, peroxidases) (Burns 1978;Allison et al 2007a). The costs of enzyme production include the metabolic energy required for protein synthesis and excretion, as well as the C and nutrient content of the enzymes themselves.…”

mentioning

confidence: 99%

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

et al. 2010

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“…Additionally, enzymes are well suited to studying inter-seasonal dynamics as they persist in the soil [28] and are assayed for enzyme potential (at controlled temperature, moisture, and pH) rather than in situ enzyme activity. Enzyme potential assays, such as those completed in the lab, may therefore reflect successional dynamics rather than seasonal ones where variable in situ temperature, pH, and moisture can strongly affect enzymatic activity.…”

Section: Discussionmentioning

confidence: 99%

“…As such, we assessed the activities of these enzymes alongside nutrient pools, pH, and moisture. Enzyme potential and soil nutrient pools are well suited for examining successional patterns as they may broadly persist over inter-seasonal time scales [28] and thus reflect successional patterns beyond seasonal variability.…”

Section: Introductionmentioning

confidence: 99%

Rapid Shifts in Soil Nutrients and Decomposition Enzyme Activity in Early Succession Following Forest Fire

Knelman

Graham

Ferrenberg

et al. 2017

Forests

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While past research has studied forest succession on decadal timescales, ecosystem responses to rapid shifts in nutrient dynamics within the first months to years of succession after fire (e.g., carbon (C) burn-off, a pulse in inorganic nitrogen (N), accumulation of organic matter, etc.) have been less well documented. This work reveals how rapid shifts in nutrient availability associated with fire disturbance may drive changes in soil enzyme activity on short timescales in forest secondary succession. In this study, we evaluate soil chemistry and decomposition extracellular enzyme activity (EEA) across time to determine whether rapid shifts in nutrient availability (1-29 months after fire) might control microbial enzyme activity. We found that, with advancing succession, soil nutrients correlate with C-targeting β-1,4-glucosidase (BG) EEA four months after the fire, and with N-targeting β-1,4-N-acetylglucosaminidase (NAG) EEA at 29 months after the fire, indicating shifting nutrient limitation and decomposition dynamics. We also observed increases in BG:NAG ratios over 29 months in these recently burned soils, suggesting relative increases in microbial activity around C-cycling and C-acquisition. These successional dynamics were unique from seasonal changes we observed in unburned, forested reference soils. Our work demonstrates how EEA may shift even within the first months to years of ecosystem succession alongside common patterns of post-fire nutrient availability. Thus, this work emphasizes that nutrient dynamics in the earliest stages of forest secondary succession are important for understanding rates of C and N cycling and ecosystem development.

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Soil Enzymes: Linking Proteomics and Ecological Processes

Cited by 82 publications

References 90 publications

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

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

Rapid Shifts in Soil Nutrients and Decomposition Enzyme Activity in Early Succession Following Forest Fire

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