Maize, switchgrass, and ponderosa pine biochar added to soil increased herbicide sorption and decreased herbicide efficacy.

Biochar, a by-product of pyrolysis made from a wide array of plant biomass when producing biofuels, is a proposed soil amendment to improve soil health. This study measured herbicide sorption and efficacy when soils were treated with low (1% w/w) or high (10% w/w) amounts of biochar manufactured from different feedstocks [maize (Zea mays) stover, switchgrass (Panicum vigatum), and ponderosa pine (Pinus ponderosa)], and treated with different post-processing techniques. Twenty-four hour batch equilibration measured sorption of (14)C-labelled atrazine or 2,4-D to two soil types with and without biochar amendments. Herbicide efficacy was measured with and without biochar using speed of seed germination tests of sensitive species. Biochar amended soils sorbed more herbicide than untreated soils, with major differences due to biochar application rate but minor differences due to biochar type or post-process handling technique. Biochar presence increased the speed of seed germination compared with herbicide alone addition. These data indicate that biochar addition to soil can increase herbicide sorption and reduce efficacy. Evaluation for site-specific biochar applications may be warranted to obtain maximal benefits without compromising other agronomic practices.

RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.

Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in Arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest that the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.

Tillage and corn residue harvesting impact surface and subsurface carbon sequestration.

Corn stover harvesting is a common practice in the western U.S. Corn Belt. This 5-yr study used isotopic source tracking to quantify the influence of two tillage systems, two corn ( L.) surface residue removal rates, and two yield zones on soil organic C (SOC) gains and losses at three soil depths. Soil samples collected in 2008 and 2012 were used to determine C enrichment during SOC mineralization, the amount of initial SOC mineralized (SOC), and plant C retained in the soil (PCR) and sequestered C (PCR - SOC). The 30% residue soil cover after planting was achieved by the no-till and residue returned treatments and was not achieved by the chisel plow, residue removed treatment. In the 0- to 15-cm soil depth, the high yield zone had lower SOC (1.49 Mg ha) than the moderate yield zone (2.18 Mg ha), whereas in the 15- to 30-cm soil depth, SOC was higher in the 60% (1.38 Mg ha) than the 0% (0.82 Mg ha) residue removal treatment. When the 0- to 15- and 15- to 30-cm soil depths were combined, (i) 0.91 and 3.62 Mg SOC ha were sequestered in the 60 and 0% residue removal treatments; (ii) 2.51 and 0.36 Mg SOC ha were sequestered in the no-till and chisel plow treatments, and (iii) 1.16 and 1.65 Mg SOC ha were sequestered in the moderate and high yield zone treatments, respectively. The surface treatments influenced C cycling in the 0- to 15- and 15- to 30-cm depths but did not influence SOC turnover in the 30- to 60-cm depth.

An affinity-effect relationship for microbial communities in plant-soil feedback loops.

Feedback loops involving soil microorganisms can regulate plant populations. Here, we hypothesize that microorganisms are most likely to play a role in plant-soil feedback loops when they possess an affinity for a particular plant and the capacity to consistently affect the growth of that plant for good or ill. We characterized microbial communities using whole-community DNA fingerprinting from multiple "home-and-away" experiments involving giant ragweed (Ambrosia trifida L.) and common sunflower (Helianthus annuus L.), and we looked for affinity-effect relationships in these microbial communities. Using canonical ordination and partial least squares regression, we developed indices expressing each microorganism's affinity for ragweed or sunflower and its putative effect on plant biomass, and we used linear regression to analyze the relationship between microbial affinity and effect. Significant linear affinity-effect relationships were found in 75 % of cases. Affinity-effect relationships were stronger for ragweed than for sunflower, and ragweed affinity-effect relationships showed consistent potential for negative feedback loops. The ragweed feedback relationships indicated the potential involvement of multiple microbial taxa, resulting in strong, consistent affinity-effect relationships in spite of large-scale microbial variability between trials. In contrast, sunflower plant-soil feedback may involve just a few key players, making it more sensitive to underlying microbial variation. We propose that affinity-effect relationship can be used to determine key microbial players in plant-soil feedback against a low "signal-to-noise" background of complex microbial datasets.

Weed-induced crop yield loss: a new paradigm and new challenges.

Direct competition for resources is generally considered the primary mechanism for weed-induced yield loss. A re-evaluation of physiological evidence suggests weeds initially impact crop growth and development through resource-independent interference. We suggest weed perception by crops induce a shift in crop development, before resources become limited, which ultimately reduce crop yield, even if weeds are subsequently removed. We present the mechanisms by which crops perceive and respond to weeds and discuss the technologies used to identify these mechanisms. These data lead to a fundamental paradigm shift in our understanding of how weeds reduce crop yield and suggest new research directions and opportunities to manipulate or engineer crops and cropping systems to reduce weed-induced yield losses.

Land application of tylosin and chlortetracycline swine manure: Impacts to soil nutrients and soil microbial community structure.

The land application of aged chortetracycle (CTC) and tylosin-containing swine manure was investigated to determine associated impacts to soil microbial respiration, nutrient (phosphorus, ammonium, nitrate) cycling, and soil microbial community structure under laboratory conditions. Two silty clay loam soils common to southeastern South Dakota were used. Aerobic soil respiration results using batch reactors containing a soil-manure mixture showed that interactions between soil, native soil microbial populations, and antimicrobials influenced CO(2) generation. The aged tylosin treatment resulted in the greatest degree of CO(2) inhibition, while the aged CTC treatment was similar to the no-antimicrobial treatment. For soil columns in which manure was applied at a one-time agronomic loading rate, there was no significant difference in soil-P behavior between either aged CTC or tylosin and the no-antimicrobial treatment. For soil-nitrogen (ammonium and nitrate), the aged CTC treatment resulted in rapid ammonium accumulation at the deeper 40cm soil column depth, while nitrate production was minimal. The aged CTC treatment microbial community structure was different than the no-antimicrobial treatment, where amines/amide and carbohydrate chemical guilds utilization profile were low. The aged tylosin treatment also resulted in ammonium accumulation at 40 cm column depth, however nitrate accumulation also occurred concurrently at 10 cm. The microbial community structure for the aged tylosin was also significantly different than the no-antimicrobial treatment, with a higher degree of amines/amides and carbohydrate chemical guild utilization compared to the no-antimicrobial treatment. Study results suggest that land application of CTC and tylosin-containing manure appears to fundamentally change microbial-mediated nitrogen behavior within soil A horizons.

CO2 and N2 O emissions and microbial community structure from fields that include salt-affected soils.

Although salinity and sodicity are worldwide problems, information on greenhouse gas (GHG) emissions from agricultural salt-affected soils is scarce. The CO2 -C and N2 O-N emissions were quantified from three zones intertwined within a single U.S. northern Great Plains field: a highly productive zone (electrical conductivity with 1:1 soil/water mass ratio [EC1:1 ] = 0.4 dS m-1 ; sodium adsorption ratio [SAR] = 1.8), a transition zone (moderately salt-affected; EC1:1  = 1.6 dS m-1 ; SAR = 4.99), and a saline/sodic zone (EC1:1  = 3.9 dS m-1 ; SAR = 22). In each zone, emissions were measured every 4 h for 7 d in four randomly placed chambers that were treated with two N rates (0 and 224 kg N ha-1 ). The experiment was conducted in 2018 and 2019 during similar seasonal periods. Soil samples taken from treatments after GHG measurement were analyzed for soil inorganic N, and microbial biomass from different communities was quantified using phospholipid fatty acid analysis. Real-time polymerase chain reaction was used to quantify the number of copies of some specific denitrification functional genes. The productive zone had the highest CO2 -C, the lowest N2 O-N emissions, and the greatest microbial biomass, whereas the saline/sodic zone had the lowest CO2 -C, the highest N2 O-N emissions, and the lowest microbial biomass. Within a zone, urea application did not influence CO2 -C emissions; however, N2 O-N emissions from the urea-treated saline/sodic zone were 84 and 57% higher than from the urea-treated productive zone in 2018 and 2019, respectively. The copy number of the nitrite reductase gene, nirS, was 42-fold higher in the saline/sodic zone than in the productive soil, suggesting that the saline/sodic soil had a high potential for denitrification. These findings suggest N2 O-N emissions could be reduced by not applying N to saline/sodic zones.

Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States.

Tamarix spp. (saltcedar) were introduced from Asia to the southern United States as windbreak and ornamental plants and have spread into natural areas. This study determined differential gene expression responses to water deficit (WD) in seedlings of T. chinensis and T. ramosissima from established invasive stands in New Mexico and Montana, respectively. A reference de novo transcriptome was developed using RNA sequences from WD and well-watered samples. Blast2GO analysis of the resulting 271,872 transcripts yielded 89,389 homologs. The reference Tamarix (Tamaricaceae, Carophyllales order) transcriptome showed homology with 14,247 predicted genes of the Beta vulgaris subsp. vulgaris (Amaranthaceae, Carophyllales order) genome assembly. T. ramosissima took longer to show water stress symptoms than T. chinensis. There were 2068 and 669 differentially expressed genes (DEG) in T. chinensis and T. ramosissima, respectively; 332 were DEG in common between the two species. Network analysis showed large biological process networks of similar gene content for each of the species under water deficit. Two distinct molecular function gene ontology networks (binding and transcription factor-related) encompassing multiple up-regulated transcription factors (MYB, NAC, and WRKY) and a cellular components network containing many down-regulated photosynthesis-related genes were identified in T. chinensis, in contrast to one small molecular function network in T. ramosissima.

Alteration of the ileal microbiota of weanling piglets by the growth-promoting antibiotic chlortetracycline.

Antibiotics such as chlortetracycline (CTC) have been used to promote growth of pigs for decades, but concerns over increased antibiotic-resistant infections in humans have prompted the development of alternative strategies. Developing alternatives to antibiotic growth promoters (AGPs) could be informed by information on the mechanisms of growth promotion, notably, how AGPs affect the microbial populations of the gastrointestinal tract. Pigs from three sows were aseptically delivered by cesarean section. Six piglets were distributed to each of two foster mothers until weaning, when piglets were fed a diet with or without 50 mg/kg CTC for 2 weeks. The ileal bacterial microbiota was characterized by using a cultivation-independent approach based on DNA extraction, PCR amplification, cloning, and sequencing of the 16S rRNA gene pool. The ileal and mucosal communities of these growing pigs were dominated by Lactobacillus bacteria, various members of the family Clostridiaceae, and members of the poorly known genus Turicibacter. Overall, CTC treatment resulted in three shifts: a decrease in Lactobacillus johnsonii, an increase in L. amylovorus, and a decrease in Turicibacter phylotypes. The composition of the microbiota varied considerably between individual pigs, as revealed by shared operational taxonomic units (OTUs) and similarity (SONS) analysis (theta(YC) values). While the observed variation between untreated pigs obscured the possible effect of CTC, integral-LIBSHUFF and SONS analyses of pooled libraries indicated a significant shift due to CTC in both the lumen and the mucosa, with some OTUs unique to either treated or control ileum. DOTUR analysis revealed little overlap between control and treated communities at the 3% difference level, indicating unique ileal communities in the presence of CTC.

Varying Weed Densities Alter the Corn Transcriptome, Highlighting a Core Set of Weed-Induced Genes and Processes with Potential for Manipulating Weed Tolerance.

CORE IDEAS: Corn increases the number of differentially expressed genes and the intensity of differential gene expression in response to increasing weed density. Genes associated with kinase signaling and transport functions are upregulated by weeds. Genes associated with protein production are downregulated by weeds. A sugar transporter (PMT5) and NUCLEOREDOXIN 1 are upregulated by weeds under diverse conditions. The phenological responses of corn (Zea mays L.) to competition with increasing densities of winter canola (Brassica napus L.) as the weedy competitor were investigated. Changes in the corn transcriptome resulting from varying weed densities were used to identify genes and processes responsive to competition under controlled conditions where light, nutrients, and water were not limited. Increasing densities of weeds resulted in decreased corn growth and development and increased the number and expression intensity of competition-responsive genes. The physiological processes identified in corn that were consistently induced by competition with weeds included protein synthesis and various transport functions. Likewise, numerous genes involved in these processes, as well as several genes implicated in phytochrome signaling and defense responses, were noted as differentially expressed. The results obtained in this study, conducted under controlled (greenhouse) conditions, were compared with a previously published study where the response of corn to competition with other species was evaluated under field conditions. Approximately one-third of the genes were differentially expressed in response to competition under both field and controlled conditions. These competition-responsive genes represent a resource for investigating the signaling processes by which corn recognizes and responds to competition. These results also highlight specific physiological processes that might be targets for mitigating the response of crops to weeds or other competitive plants under field conditions.

Weed presence altered biotic stress and light signaling in maize even when weeds were removed early in the critical weed-free period.

Weed presence early in the life cycle of maize (typically, from emergence through the 8 to 12 leaf growth stage) can reduce crop growth and yield and is known as the critical weed-free period (CWFP). Even if weeds are removed during or just after the CWFP, crop growth and yield often are not recoverable. We compared transcriptome responses of field-grown hybrid maize at V8 in two consecutive years among plants grown under weed-free and two weed-stressed conditions (weeds removed at V4 or present through V8) using RNAseq analysis techniques. Compared with weed-free plant responses, physiological differences at V8 were identified in all weed-stressed plants and were most often associated with altered photosynthetic processes, hormone signaling, nitrogen use and transport, and biotic stress responses. Even when weeds were removed at V4 and tissues sampled at V8, carbon: nitrogen supply imbalance, salicylic acid signals, and growth responses differed between the weed-stressed and weed-free plants. These underlying processes and a small number of developmentally important genes are potential targets for decreasing the maize response to weed pressure. Expression differences of several novel, long noncoding RNAs resulting from exposure of maize to weeds during the CWFP were also observed and could open new avenues for investigation into the function of these transcription units.

Enhanced atrazine degradation is widespread across the United States.

BACKGROUND: Atrazine (ATZ) has been a key herbicide for annual weed control in corn, with both a soil and post-emergence vegetation application period. Although enhanced ATZ degradation in soil with a history of ATZ use has been reported, the extent and rate of degradation in the US Corn Belt is uncertain. We show that enhanced ATZ degradation exists across much of the country. RESULTS: Soils from 15 of 16 surveyed states had enhanced ATZ degradation. The average ATZ half-life was only 2.3 days in ATZ history soils, compared with an average 14.5 days in soils with no previous ATZ use, meaning that ATZ degrades an average 6 times faster in soils with previous ATZ use. CONCLUSION: When ATZ is used for several years, enhanced degradation will undoubtedly change the way ATZ is used in agronomic crops and also its ultimate environmental fate. © 2017 Society of Chemical Industry.

Sorption-desorption of imidacloprid and its metabolites in soil and vadose zone materials.

Sorption-desorption is one of the most important processes affecting the leaching of pesticides through soil because it controls the amount of pesticide available for transport. Subsurface soil properties can significantly affect pesticide transport and the potential for groundwater contamination. This research characterized the sorption-desorption of imidacloprid (1-[(6-chloro-3-pyridinyl)-methyl]-N-nitro-2-imidazolidinimine) and three of its metabolites, 1-[(6-chloro-3-pyridinyl)methyl]-2-imidazolidinone (imidacloprid-urea), 1-[(6-chloro-3-pyridinyl)methyl]-4,5-dihydro-1H-imidazol-2-amine (imidacloprid-guanidine), and 1-[(6-chloro-3-pyridinyl)methyl]-1H-imidazol-2-amine (imidacloprid-guanidine-olefin), as a function of changing soil properties with depth in two profiles extending from the surface to a depth of 1.8 or 8 m. Sorption of each compound was highly variable and hysteretic in all cases. Normalizing the sorption coefficients (K(f)) to the organic carbon or the clay content of the soil did not reduce the variability in sorption coefficients for any compound. These results illustrate the importance of evaluation of the sorption data used to predict potential mobility. Understanding the variability of soil properties and processes as a function of depth is necessary for accurate prediction of pesticide dissipation.

Effects of chlortetracycline amended feed on anaerobic sequencing batch reactor performance of swine manure digestion.

The effects of antimicrobial chlortetracycline (CTC) on the anaerobic digestion (AD) of swine manure slurry using anaerobic sequencing batch reactors (ASBRs) was investigated. Reactors were loaded with manure collected from pigs receiving CTC and no-antimicrobial amended diets at 2.5 g/L/d. The slurry was intermittently fed to four 9.5L lab-scale anaerobic sequencing batch reactors, two with no-antimicrobial manure, and two with CTC-amended manure, and four 28 day ASBR cycles were completed. The CTC concentration within the manure was 2 8 mg/L immediately after collection and 1.02 mg/L after dilution and 250 days of storage. CTC did not inhibit ASBR biogas production extent, however the volumetric composition of methane was significantly less (approximately 13% and 15% for cycles 1 and 2, respectively) than the no-antimicrobial through 56 d. CTC decreased soluble chemical oxygen demand and acetic acid utilization through 56 d, after which acclimation to CTC was apparent for the duration of the experiment.

Impact of chlortetracycline on sequencing batch reactor performance for swine manure treatment.

Treatment of aged (500 day, 4°C stored) chlortetracycline (CTC; 0, 20, 40, 80 mg/L CTC)-amended swine manure using two cycle, 22 day stage anaerobic sequencing batch reactors (SBR) was assessed. Eighty milligrams per liter CTC treatment inhibited SBR treatment efficiencies, although total gas production was enhanced compared to the no-CTC treatment. The 20 and 40 mg/L CTC treatments resulted in either slight or no differences to SBR treatment efficiencies and microbial diversities compared to the no-CTC treatment, and were generally similar to no-CTC treatments upon completion of the first 22 day SBR cycle. All CTC treatments enhanced SBR gas generation, however CH(4) yields were lowest for the 80 mg/L CTC treatment (0.111L CH(4)/g tCOD) upon completion of the second SBR react cycle. After a 22 day acclimation period, the 80 mg/L CTC treatment inhibited methanogenesis due to acetate accumulation, and decreased microbial diversity and CH(4) yield compared to the no-CTC treatment.

GC-clamp primer batches yield 16S rRNA gene amplicon pools with variable GC clamps, affecting denaturing gradient gel electrophoresis profiles.

Fingerprinting methods such as denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene pools have become a popular tool for comparisons between microbial communities. The GC-clamp portion of primers for DGGE amplicon preparation provides a key component in resolving fragments of similar size but different sequence. We hypothesized that repeat syntheses of identical 40-base GC-clamp primers lead to different DGGE profiles. Three repeat syntheses of the same GC-clamp primer and two different GC-clamp primers directed at the V3-5 region of the 16S rRNA gene were compared. Genomic DNA of two separate soil bacterial communities and three bacterial species was amplified and resolved by DGGE. The DGGE profiles obtained with repeat-synthesized primers differed among each other as much as with alternate primers, for both soil DNA and pure single species. The GC-clamp portion of members of amplicon pools varied among each other, deviating from the design sequence, and was the likely cause for multiple bands derived from a single 16S rRNA gene sequence. We recommend procuring an oligonucleotide batch large enough to conduct an entire project. This should help to avoid any DGGE profile variations due to performance differences between repeat syntheses of GC-clamp oligonucleotide primers.

Tylosin and chlortetracycline effects during swine manure digestion: influence of sodium azide.

The antibiotics tylosin and chlortetracycline (CTC), which are commonly used in pig production, were studied to determine their effects on swine manure digestion in the presence and absence of biocide sodium azide. CTC enhanced initial hydrolysis reactions through volatile suspended solids production, while inhibiting methane and carbon dioxide production. Tylosin did not affect methane and carbon dioxide production; however, the relative abundance of both hydrogen utilizing and acetate-only utilizing microbial populations was significantly compromised. Sodium azide in the absence of antibiotics enhanced metabolic output and initial biomass production, and this observation suggests that populations of Methanobacteriales and Methanosaetaceae spp. appeared to contain sufficient periplasmic bound reductase to effectively utilize acetate and hydrogen in the presence of sodium azide. However, the combination of sodium azide and either CTC or tylosin was a very effective metabolic inhibitor, inhibiting methane and carbon dioxide production and VSS consumption compared to their no-azide counterpart.

Effect of antimicrobial compounds tylosin and chlortetracycline during batch anaerobic swine manure digestion.

Tylosin and chlortetracycline (CTC) are antimicrobial chemicals that are fed to >45% of the US swine herds at therapeutic and sub-therapeutic dosages to enhance growth rates and treat swine health problems. These compounds are poorly absorbed during digestion so that the bioactive compound or metabolites are excreted. This study investigated the degradation and stabilization of swine manure that contained no additives and compared the observed processes with those of manure containing either tylosin or CTC. The batch anaerobic incubation lasted 216 days. The breakdown of insoluble organic matter through anaerobic hydrolysis reactions was faster for manure containing CTC compared with tylosin or no-antimicrobial treatments. Volatile fatty acid (VFA) accumulation, including acetate, butyrate, and propionate, was greater for CTC-containing manure compared to tylosin and no-antimicrobial treatments. The relative abundance of two aceticlastic methanogens, Methanosaetaceae and Methanosarcinaceae spp., were less for CTC manure than manure with no-antimicrobial treatment. In addition, generation of methane and carbon dioxide was inhibited by 27.8% and 28.4%, respectively, due to the presence of CTC. Tylosin effects on manure degradation were limited, however the relative abundance of Methanosarcinaceae spp. was greater than found in the CTC or no-antimicrobial manures. These data suggest that acetate and other C-1 VFA compounds would be effectively utilized during methanogenesis in the presence of tylosin.