Diversifying and perennializing plants in agroecosystems alters retention of new C and N from crop residues.

Managing soils to retain new plant inputs is key to moving toward a sustainable and regenerative agriculture. Management practices, like diversifying and perennializing agroecosystems, may affect the decomposer organisms that regulate how new residue is converted to persistent soil organic matter. Here we tested whether 12 years of diversifying/perennializing plants in agroecosystems through extended rotations or grassland restoration would decrease losses of new plant residue inputs and, thus, increase retention of carbon (C) and nitrogen (N) in soil. We tracked dual-labeled (13 C and 15 N), isotopically enriched wheat (Triticum aestivum) residue in situ for 2 years as it decomposed in three agroecosystems: maize-soybean (CS) rotation, maize-soybean-wheat plus red clover and cereal rye cover crops (CSW2), and spring fallow management with regeneration of natural grassland species (seven to 10 species; SF). We measured losses of wheat residue (Cwheat and Nwheat ) in leached soil solution and greenhouse gas fluxes, as well as how much was recovered in microbial biomass and bulk soil at 5-cm increments down to 20 cm. CSW2 and SF both had unique, significant effects on residue decomposition and retention dynamics that were clear only when using nuanced metrics that able to tease apart subtle differences. For example, SF retained a greater portion of Cwheat in 0-5 cm surface soils (155%, p = 0.035) and narrowed the Cwheat to Nwheat ratio (p < 0.030) compared to CS. CSW2 increased an index of carbon-retention efficiency, Cwheat retained in the mesocosm divided by total measured, from 0.18 to 0.27 (49%, p = 0.001), compared to CS. Overall, we found that diversifying and extending the duration of living plants in agroecosystems can lead to greater retention of new residue inputs in subtle ways that require further investigation to fully understand.

Inexpensive Near-Infrared Fluorimeters: Enabling Translation of nIR-Based Assays to the Field.

The practical impact of analytical probes that transduce in the near-infrared (nIR) has been dampened by the lack of cost-effective and portable nIR fluorimeters. Herein, we demonstrate straightforward designs for an inexpensive microplate reader and a portable fluorimeter. These instruments require minimally complex machining and fabrication and operate with an open-source programming language (Python). Complete wiring diagrams, assembly diagrams, and scripts are provided. To demonstrate the utility of these two instruments, we performed high-throughput and field-side measurements of soil samples to evaluate the effect of soil management strategies on extracellular proteolytic, cellulolytic, and lignin-modifying activities. This was accomplished with fluorescent enzyme probes that utilized uniquely sensitive transducers exclusive to the nIR spectrum, single-walled carbon nanotubes. We also used the portable fluorimeter to evaluate spatial variations of proteolytic activity within individual field plots, while minimizing the effects of soil storage and handling. These demonstrations indicate the utility of these fluorimeters for translating analytical probes that operate in the nIR beyond the laboratory and into actual use.

Prescribed fire alters nematode communities in an old-field grassland.

Fire is a common disturbance in many biomes, with both beneficial and detrimental effects on soil biology, which largely depend on fire intensity. However, little is known about the impact of fire on soil nematode communities in terrestrial ecosystem. In the present study, we investigated the effects of short-term prescribed fire on soil nematode communities and soil properties in an old-field grassland in Northern China. The results showed that burning significantly increased soil nematode abundance by 77% and genus richness by 49% compared to the control. Burning also decreased taxon dominance by 45% (Simpson's D) and increased nematode diversity by 31% (Shannon-Weaver H'). However, burning increased plant parasites (particularly genera Cephalenchus and Pratylenchus) and shifted community to more bacterial-feeding genera (i.e., decreased Channel Index). Generally, burning increased soil bio-available nitrogen (NH4 +-N and NO3 --N) content, which would be the main drivers causing nematode community to flourish via a "bottom-up" effect. These results suggest that prescribed fire increases nematode diversity and alters community composition toward more plant parasites and bacterial feeders. Our findings highlight the importance of prescribed fire management in shaping short-term nematode community structure and function, but the long-term effects and impacts of these changes on soil nutrient and carbon cycling remain unknown.

Disproportionate CH4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community.

Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil-vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil/vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO2) and CH4 fluxes and their production/consumption at 5 cm intervals to a depth of 30 cm. All soils were sources of CO2, ranging from 49 to 93 mg CO2 m-2 h-1. Forest soils were strong net sinks for CH4, at rates of up to -413 µg CH4 m-2 h-1. Grassland soils varied, with some soils acting as sources and some as sinks, but overall averaged -97 µg CH4 m-2 h-1. Bog soils were net sources of CH4 (+340 µg CH4 m-2 h-1). Methanotrophs were dominated by USCα in forest and grassland soils, and Candidatus Methylomirabilis in the bog soils. Methylocystis were also detected at relatively low abundance in all soils. Our study suggests that there is a disproportionately large contribution of these ecosystems to the global soil CH4 sink, which highlights our dependence on soil ecosystem services in remote locations driven by unique populations of soil microbes. It is paramount to explore and understand these remote, hard-to-reach ecosystems to better understand biogeochemical cycles that underpin global sustainability.

Sediment phosphorus buffering in streams at baseflow: A meta-analysis.

Phosphorus (P) pollution of surface waters remains a challenge for protecting and improving water quality. Central to the challenge is understanding what regulates P concentrations in streams. This quantitative review synthesizes the literature on a major control of P concentrations in streams at baseflow-the sediment P buffer-to better understand streamwater-sediment P interactions. We conducted a global meta-analysis of sediment equilibrium phosphate concentrations at net zero sorption (EPC0 ), which is the dissolved reactive P (DRP) concentration toward which sediments buffer solution DRP. Our analysis of 45 studies and >900 paired observations of DRP and EPC0 showed that sediments often have potential to remove or release P to the streamwater (83% of observations), meaning that "equilibrium" between sediment and streamwater is rare. This potential for P exchange is moderated by sediment and stream characteristics, including sorption affinity, stream pH, exchangeable P concentration, and particle sizes. The potential for sediments to modify streamwater DRP concentrations is often not realized owing to other factors (e.g., hydrologic interactions). Sediment surface chemistry, hyporheic exchange, and biota can also influence the potential exchange of P between sediments and the streamwater. Methodological choices significantly influenced EPC0 determination and thus the estimated potential for P exchange; we therefore discuss how to measure and report EPC0 to best suit research objectives and aid in interstudy comparison. Our results enhance understanding of the sediment P buffer and inform how EPC0 can be effectively applied to improve management of aquatic P pollution and eutrophication.

MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes.

Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably. IMPORTANCE Amplification-based gene characterization allows for sensitive and specific quantification of functional genes. There is often a large diversity of genes represented for functional gene groups, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high-throughput primer design for various genes of interest and also allows for ranking gene targets by their presence and abundance in environmental data sets. Primers designed by this tool improve the characterization and quantification of functional genes in broad gene amplification platforms and can be powerful with high-throughput qPCR approaches.

Relationships between benthic sediments and water column phosphorus in Illinois streams.

Sediments can be important in regulating stream water P concentrations, and this has implications for establishing nutrient standards that have not been fully investigated. We evaluated abiotic and biotic processes to better understand the role of sediments in determining stream water dissolved P concentrations. Sediment and stream water samples were collected during low discharge from 105 streams across Illinois and analyzed for equilibrium P concentration at zero release or retention (EPC(0)), P sorption characteristics, stream water P concentration, and sediment particle size. In addition, four east-central Illinois streams were repeatedly sampled to examine temporal patterns in sediment P retention and biotic processing of P. Median dissolved reactive P (DRP) and total P concentrations across the state were 0.081 and 0.168 mg L(-1), respectively. Sediment EPC(0) concentrations were related to stream water DRP concentrations (r(s) = 0.75). Sediment silt+clay (and co-correlated organic matter) was related to sorbed P (r(s) = -0.49) and the reactive sediment pool of P (r(s) = 0.76). However, for most sites this pool was small given the coarse textures present (median silt+clay was 5.7%). Repeated sampling at the four intensive sites showed little variation in EPC(0) values or alkaline phosphatase activity, suggesting overall stream conditions regulated the biotic processing. Biotic retention of P was 32% of short-term P removal. We conclude that sediments in Illinois streams are a reflection of and partially affected by stream water P concentrations through both abiotic and biotic processes. Sediments seem unlikely to alter annual stream P loads, but may affect concentrations at low discharge.

Resonant Sensors for Low-Cost, Contact-Free Measurement of Hydrolytic Enzyme Activity in Closed Systems.

A passive, resonant sensor was developed that can be embedded in closed systems for wireless monitoring of hydrolytic enzyme activity. The resonators are rapidly prototyped from copper coated polyimide substrates that are masked using an indelible marker with an XY plotter and subsequently etched. The resonator's frequency response window is designed by the Archimedean coil length and pitch and is tuned for the 1-100 MHz range for better penetration through soil, water, and tissue. The resonant frequency is measured up to 5 cm stand-off distance by a coplanar, two-loop coil reader antenna attached to a vector network analyzer monitoring the S21 scattering parameter. The resonant frequency is modulated (up to 50 MHz redshift) by changing the relative permittivity of the medium in contact with the resonator (e.g., air to water). The resonant sensors are coated by an enzyme substrate, which, when degraded, causes a change in dielectric and a shift in resonant frequency (up to 7 MHz redshift). The activity (turnover rate, or kcat) of the enzyme is calculated by fitting the measured data via a custom transport and reaction model which simulates the radial digestion profile. This is used to test purified Subtilisin A and unpurified bacterial protease samples at concentrations of 30 mg/mL to 200 mg/mL with kcat ranges of 0.003-0.002 and 0.008-0.004 gsubstrate/ genzyme per second. The sensor response rate can be tuned by substrate composition (e.g., gelatin and glycerol plasticizer weight percentage). Finally, the utility of these sensors is demonstrated by wirelessly measuring the proteolytic activity of farm soil with a measured kcat of 0.00152 gsubstrate/( gsoil·s).