Enzyme activity as a method for soil biochemistry and microbiology research has a long history of more than 100 years that is not widely acknowledged in terms of adherence to strict assay protocols ...and the interpretation of results. However, in the recent past, there is a growing lack of recognition of the historic advancements among researchers that use soil enzymology. Today, many papers are being published that use methods that either do not follow exact protocols as originally vetted in the research literature or individual labs use their own method that has not been optimized for pH, co-factors, substrate concentrations, or other conditions. This is of particular concern for fluorogenic substrates and microplate methods. Furthermore, there is a lack of understanding of the origin and location of a given enzyme being studied. Notably, regardless of the enzyme, it is too often assumed that enzyme activity equals microbial activity—which is not the case for most hydrolytic enzyme assays. Because as established by Douglas McLaren in the 1950s, a considerable amount of activity can come from catalytic enzymes stabilized in the soil matrix but that are no longer associated with viable cells (known as abiontic enzymes). In summary, today, many papers are using imperfect methods and/or misinterpret enzyme activity data that at a minimum confounds cross paper studies and meta-analysis. However, most importantly, lack of historical perspectives and ignoring strict protocols cause redundancy and fundamentally undermine the discipline and understanding of soil microbiology/biochemistry when enzymology methods are used.
Congenital zika virus syndrome (CZS) has become a significant worldwide concern since the sudden rise of microcephaly related to zika virus (ZIKV) in Brazil. Primarily transmitted by Aedes ...mosquitoes, ZIKV shares serologic similarities with dengue virus (DENV), complicating the diagnosis and/or clinical management. The Angiotensin I-Converting Enzyme (ACE) was associated with either neuroprotective or anti-inflammatory properties in the central nervous system (CNS). The possible role(s) of ACE in these two flaviviruses infection remain largely unexplored. In this study, we evaluate ACE activity in the brain of ZIKV- or DENV-infected mice, both compared to MOCK, showing about 30 % increased ACE activity only in ZIKV-infected mice (p = 0.024), while no change was noticed in brain from DENV-infected animals (p = 0.888). In addition, the treatment with interferon beta (IFNβ), under conditions previously demonstrated to rescue the normal size of microcephalic brains determined by ZIKV infection, also restored ACE activity in ZIKV-infected animals to levels close to that of the MOCK control group. Although inflammatory responses expected for either ZIKV or DENV infections, only ZIKV was associated with microcephaly, as well as with increased ACE activity and reversion by treatment with IFNβ. Furthermore, this increase in ACE activity was observed only after intracerebroventricular (ICV) injection (F (2, 16) = 7.907, p = 0.004), but not for intraperitoneal (IP) administration of ZIKV (F (2, 26) = 1.996, p = 0.156), suggesting that the observed central ACE activity modulation may be associated with the presence of this specific flavivirus in the brain.
•ACE activity increased in the brain of mice infected by zika virus.•No change was noticed in brain from DENV-infected animals.•IFNβ treatment restored ACE activity increased by zika virus.•ICV but not IP administration of zika virus increased ACE activity in brain.
Plant invasion can significantly alter soil nutrient cycling of ecosystems. How these changes are linked to soil enzyme activities is still unknown, however, even though these are proximate agents of ...organic matter decomposition and nutrient release. We performed a meta-analysis of 60 case studies examining responses of 10 unique soil enzymes to plant invasion, and tested whether invaded soils differed in their enzyme activities from uninvaded soils. We also examined whether increases in soil nutrient-releasing enzyme activity were paralleled by enhanced soil nutrient availability after plant invasion. Overall, we found that plant invasion had significant impacts on the activities of seven types of soil enzymes. Plant invasion had inconsistent impacts on C-decomposing enzymes, but invaded sites had significantly higher activities of soil enzymes related to N- and P-release than noninvaded sites. Increases in nutrient- releasing enzyme activity after plant invasion ranged from +23% to +69%, which potentially results in a linear increase of soil nutrient availability in response to enhanced enzyme activities. Invaded soils also had higher nutrient stocks and soil microbial biomass than uninvaded soils. Our results suggest that enhanced activity of soil nutrient-releasing enzymes after plant invasion may accelerate nutrient cycling, potentially creating a nutrient-rich soil environment that benefits invaders and promotes their persistence, as invasive plants often appear to be more resource-demanding and competitive than native species.
The effects of short‐term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two ...continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought‐induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant–microbial interactions and a greater incidence of certain soil‐borne diseases.
Direct and indirect effects of drought and environmental conditions on bacterial community composition and microbial activity.
Agronomic practices such as crop residue return and additional nutrient supply are recommended to increase soil organic carbon (SOC) in arable farmlands. However, changes in the priming effect (PE) ...on native SOC mineralization in response to integrated inputs of residue and nutrients are not fully known. This knowledge gap along with a lack of understanding of microbial mechanisms hinders the ability to constrain models and to reduce the uncertainty to predict carbon (C) sequestration potential. Using a 13C‐labeled wheat residue, this 126‐day incubation study examined the dominant microbial mechanisms that underpin the PE response to inputs of wheat residue and nutrients (nitrogen, phosphorus and sulfur) in two contrasting soils. The residue input caused positive PE through “co‐metabolism,” supported by increased microbial biomass, C and nitrogen (N) extracellular enzyme activities (EEAs), and gene abundance of certain microbial taxa (Eubacteria, β‐Proteobacteria, Acidobacteria, and Fungi). The residue input could have induced nutrient limitation, causing an increase in the PE via “microbial nutrient mining” of native soil organic matter, as suggested by the low C‐to‐nutrient stoichiometry of EEAs. At the high residue, exogenous nutrient supply (cf. no‐nutrient) initially decreased positive PE by alleviating nutrient mining, which was supported by the low gene abundance of Eubacteria and Fungi. However, after an initial decrease in PE at the high residue with nutrients, the PE increased to the same magnitude as without nutrients over time. This suggests the dominance of “microbial stoichiometry decomposition,” supported by higher microbial biomass and EEAs, while Eubacteria and Fungi increased over time, at the high residue with nutrients cf. no‐nutrient in both soils. Our study provides novel evidence that different microbial mechanisms operate simultaneously depending on organic C and nutrient availability in a residue‐amended soil. Our results have consequences for SOC modeling and integrated nutrient management employed to increase SOC in arable farmlands.
This study examined the dynamics of priming effect (PE), controlled by the interaction of crop residue input and balanced supply of nutrients (N, P, and S), and the underlying mechanisms in relation to microbial community growth and extracellular enzyme activity. The results showed that the “microbial nutrient mining” and “microbial stoichiometry decomposition” mechanisms relating to nutrient availability mainly operated at high residue input. The image presents a conceptualized model based on key findings on the dominant occurrence of microbial mechanisms relating to PE, with implications to underpin soil organic carbon (SOC) modeling and guide integrated residue–nutrient management in croplands for SOC sequestration.
Conversion of forestland to intensively managed agricultural land occurs worldwide and can increase soil nitrous oxide (N2O) emissions by altering the transformation processes of nitrogen (N) cycling ...related microbes and environmental conditions. However, little research has been conducted to assess the relationships between nitrifying and denitrifying functional genes and enzyme activities, the altered soil environment and N2O emissions under forest conversion in subtropical China. Here, we investigated the long-term (two decades) effect of converting natural forests to intensively managed tea (Camellia sinensis L.) plantations on soil potential N2O emissions, inorganic N concentrations, functional gene abundances of nitrifying and denitrifying bacteria, as well as nitrifying and denitrifying enzyme activities in subtropical China. The conversion significantly increased soil potential N2O emissions, which were regulated directly by increased denitrifying enzyme activity (52 %) and nirS + nirK gene abundance (38 %) as shown by structural equation modeling, and indirectly by AOB-amoA gene abundance and inorganic N concentration. Our results indicate that converting natural forests to tea plantations directly increases soil inorganic N concentration, resulting in increases in the abundance of soil nitrifying and denitrifying microorganisms and the associated N2O emissions. These findings are crucial for disentangling the factors that directly and indirectly affect soil potential N2O emissions respond to the conversion of forest to tea plantation.
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•Converting natural forest to tea plantation increased soil potential N2O emissions.•Forest conversion increased the concentration of soil inorganic nitrogen.•Land-use change increased soil denitrifying enzyme activity (DEA).•Forest conversion increased the abundance of soil AOB-amoA and nirK genes.•Soil N2O emissions were regulated directly by increased DEA and nirS + nirK gene abundance.
Plastics accumulating in the environment, especially microplastics (defined as particles <5 mm), can lead to a range of problems and potential loss of ecosystem services. Polyhydroxyalkanoates (PHAs) ...are biodegradable plastics used in mulch films, and in packaging material to minimize plastic waste and to reduce soil pollution. Little is known, however, about the effect of microbioplastics on soil-plant interactions, especially soil microbial community structure and functioning in agroecosystems. For the first time, we combined zymography (to localize enzyme activity hotspots) with substrate-induced growth respiration to investigate the effect of PHAs addition on soil microbial community structure, growth, and exoenzyme kinetics in the microplastisphere (i.e. interface between soil and microplastic particles) compared to the rhizosphere and bulk soil. We used a common PHAs biopolymer, poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and showed that PHBV was readily used by the microbial community as a source of carbon (C) resulting in an increased specific microbial growth rate and a more active microbial biomass in the microplastisphere in comparison to the bulk soil. Higher β-glucosidase and leucine aminopeptidase activities (0.6–5.0 times higher Vmax) and lower enzyme affinities (1.5–2.0 times higher Km) were also detected in the microplastisphere relative to the rhizosphere. Furthermore, the PHBV addition changed the soil bacterial community at different taxonomical levels and increased the alpha diversity, as well as the relative abundance of Acidobacteria and Verrucomicrobia phyla, compared to the untreated soils. Overall, PHBV addition created soil hotspots where C and nutrient turnover is greatly enhanced, mainly driven by the accelerated microbial biomass and activity. In conclusion, microbioplastics have the potential to alter soil ecological functioning and biogeochemical cycling (e.g., SOM decomposition).
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•Microplastisphere (soil-MPs interface) is localized and visualized by zymography.•MPs stimulates microbial turnover and nutrient efficiency in microplastisphere.•MPs increases soil enzyme activity and shifts bacterial community to K-strategy.•MPs have the potential to alter soil functioning and biogeochemical cycling.
Ecoenzymatic stoichiometry links microbial decomposition with nutrient mineralization and improves our understanding of nutrient cycling in terrestrial ecosystems. Microbial C:N:P acquisition in the ...topsoil converged at a ratio of 1:1:1 in global ecosystems. However, whether the ratio of microbial acquisition is stable in forest soils, and is applicable among different soil depths remain unknown.
Based on large‐scale soil sampling in China's forests, we examined the patterns and environmental drivers of the eight most‐widely measured enzyme activities and the relevant stoichiometry.
We found that the ratio of C:N:P acquisition significantly deviated from 1:1:1. The specific enzyme activities (normalized by SOC) did not change significantly with latitude except those for xylosidase and acid phosphatase. Similarly, only the C:P acquisition ratio increased with latitude. Vertically, the specific activities of C‐acquiring enzymes mainly increased, N‐acquiring enzymes decreased and P‐acquiring enzymes did not change with soil depth. Moreover, all ratios of microbial acquisition decreased, and the percentage of recalcitrant C increased significantly with increasing depth. Our study also showed that temperature and soil C:N ratio were the important factors in explaining the variations in specific enzyme activities and microbial nutrient acquisition, respectively.
Our results indicated that no constant microbial C:N:P acquisition ratio can be widely recognized, and that SOC quality changed from labile to recalcitrant with depth. We highlight that depth‐dependent enzymatic processes should be considered in future SOC dynamic models.
A free Plain Language Summary can be found within the Supporting Information of this article.
A free Plain Language Summary can be found within the Supporting Information of this article.
Herein, we report a bottom-up approach to assemble a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the bio–nano interface. We systematically investigated the ...impact of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic behaviors at the interfaces of spherical nucleic acids. Our mechanistic study has revealed critical roles of various interfacial factors that significantly alter molecular binding and enzymatic behaviors from bulk solutions. The improved understanding of the bio–nano interface may facilitate better design and operation of nanoparticle-based biosensors and/or functional devices. We successfully demonstrate how improved understanding of the bio–nano interface help rationalize the design of amplifiable biosensors for nucleic acids and antibodies.
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