Cropping system characteristics such as tillage intensity, crop identity, crop-livestock integration and the application of off-farm synthetic inputs influence weed abundance, plant community composition and crop-weed competition. The resulting plant community, in turn, has species-specific effects on soil microbial communities which can impact the growth and competitive ability of subsequent plants, completing a plant–soil feedback (PSF) loop. Farming systems that minimize the negative impacts of PSFs on subsequent crop growth can increase the sustainability of the farming enterprise. This study sought to assess the individual and combined impact of the cropping system (certified organic-grazed, certified organic till and conventional no-till) and crop sequence [pairwise rotations with safflower (Carthamus tinctorius), yellow sweet clover (Melilotus officinalis) and winter wheat (Triticum aestivum)] on the PSF magnitude and direction. All cropping systems followed the same 5-year rotation and had completed one full rotation before soil was sampled. In a greenhouse setting, a sterile soil mix was inoculated with field soil collected from all systems and three crops. The PSF study consisted of two stages (conditioning and response phases) that mimicked the rotation stages occurring in the field. PSFs were calculated by comparing the biomass of the response phase plants grown in inoculated and uninoculated soils. The farm management system affected PSFs, inferring that tillage reduction can encourage more positive PSFs. Crop sequence did not affect PSF but interacted strongly with the farm system. As such, the effects of the farming system on PSFs are best illustrated when taken into account with the identity of the previous and current crops of a cropping sequence.

The effect of soil disinfestation with methyl bromide (MB) or by soil solarization (solar heating) and the fungicides TMTD (tetramethylthiuram disulfide) and fentin acetate (triphenyltin acetate) on the degradation of terbutryn [2-(tert-butylamino)-4-(ethylamino)-6-methylthio)-s-triazine] and atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-s-triazine] were investigated. The degradation of terbutryn appeared to follow first-order kinetics with a half-life of about 2 weeks and was much slower in MB-treated or solarized soils, i.e. half-life of about 11 weeks. Suppression of terbutryn degradation in the MB-treated soil was still evident 8 months after soil fumigation, similar to that found in autoclaved soil. TMTD and fentin acetate at 20 μg/g soil strongly inhibited degradation of terbutryn in soil. Degradation of atrazine was affected to a lesser extent by soil disinfestation. Results from the present study suggest that biocidal soil treatments may slow herbicide degradation. Thus, herbicide dosages in disinfested soil should be adjusted in order to avoid phytotoxicity. Moreover, lower dosages might be sufficient to attain weed control, and combined disinfestation or fungicides with herbicide treatments might be intentionally used to extend herbicide activity.

Herbicide effects on vesicular-arbuscular mycorrhizal fungi were studied in greenhouse and field tests. In field plots treated with a bromacil (5-bromo-3-sec-butyl-6-methyluracil) and diuron (3-[3,4-dichlorophenyl]-1,1-dimethylurea) mixture, fungus infection was similar to levels present in cultivated plots. A slight reduction of infection occurred in roots of grove trees in a simazine (2-chloro-4,6-bis [ethylamino]-s-triazine) plus paraquat (1,1′-dimethyl-4,4′-bipyridinium ion)-treated plot compared to a cultivated plot. In the greenhouse studies, diuron, bromacil, and trifluralin (α,α,α-trifluoro-2,6-dinitro-N,N-dipropyl-p-toluidine) had no apparent effect on Glomus etunicatus Becker and Gerd. and plant growth. Paraquat, PPG 844 {1-(carboethoxy) ethyl 5-[2′-chloro-4′-(trifluoromethyl) phenoxy]-2-nitrobenzoate} and simazine adversely affected plant growth and the fungus.

In a previous study, glyphosate-susceptible and -resistant giant ragweed biotypes grown in sterile field soil survived a higher rate of glyphosate than those grown in unsterile field soil, and the roots of the susceptible biotype were colonized by a larger number of soil microorganisms than those of the resistant biotype when treated with 1.6 kg ae ha−1 glyphosate. Thus, we concluded that soil-borne microbes play a role in glyphosate activity and now hypothesize that the ability of the resistant biotype to tolerate glyphosate may involve microbial interactions in the rhizosphere. The objective of this study was to evaluate differences in the rhizosphere microbial communities of glyphosate-susceptible and -resistant giant ragweed biotypes 3 d after a glyphosate treatment. Giant ragweed biotypes were grown in the greenhouse in unsterile field soil and glyphosate was applied at either 0 or 1.6 kg ha−1. Rhizosphere soil was sampled 3 d after the glyphosate treatment, and DNA was extracted, purified, and sequenced with the use of Illumina Genome Analyzer next-generation sequencing. The taxonomic distribution of the microbial community, diversity, genera abundance, and community structure within the rhizosphere of the two giant ragweed biotypes in response to a glyphosate application was evaluated by metagenomics analysis. Bacteria comprised approximately 96% of the total microbial community in both biotypes, and differences in the distribution of some microbes at the phyla level were observed. Select soil-borne plant pathogens (Verticillium and Xanthomonas) and plant-growth–promoting rhizobacteria (Burkholderia) present in the rhizosphere were influenced by either biotype or glyphosate application. We did not, however, observe large differences in the diversity or structure of soil microbial communities among our treatments. The results of this study indicate that challenging giant ragweed biotypes with glyphosate causes perturbations in rhizosphere microbial communities and that the perturbations differ between the susceptible and resistant biotypes. However, biological relevance of the rhizosphere microbial community data that we obtained by next-generation sequencing remains unclear.

Greenhouse and laboratory experiments were conducted on common waterhemp and soil collected from 131 soybean fields in Missouri that contained late-season common waterhemp escapes. The objectives of these experiments were to determine the effects of soil sterilization on glyphosate-resistant (GR) and -susceptible (GS) common waterhemp survival, to determine the effects of soil sterilization and glyphosate treatment on infection of GR and GS common waterhemp biotypes by Fusarium spp., and to determine the soil microbial abundance and diversity in soils collected from soybean fields with differences in common waterhemp biotypes and herbicide and crop rotation histories. Common waterhemp biotypes were treated with 1.7 kg glyphosate ae ha−1 or left untreated once plants reached approximately 15 cm in height. Common waterhemp survival was visually assessed at 21 d after glyphosate treatment (21 DAT). To determine Fusarium infection frequency, a single intact common waterhemp root was harvested from each treatment at 0, 3, 7, 14, and 21 DAT and surface sterilized, and 10 to 15–mm common waterhemp root sections were plated on Komada culture medium. After 14 d incubation, fungal colonies were selected from colonized roots and maintained on potato dextrose agar medium amended with antibiotics before identification. Speciation of Fusarium isolates was conducted through microscopic examination of fungal characters and confirmed by sequencing and analysis of ribosomal DNA. Soil samples from 131 different collections were subjected to phospholipid fatty acid (PLFA) analysis and were conducted utilizing gas chromatography to determine the soil microbial community abundance and structure. Common waterhemp plants grown in sterile soils had the highest common waterhemp survival, regardless of biotype. After treatment with glyphosate, survival of GS common waterhemp grown in nonsterile soil was only 29% 21 DAT, whereas survival of GS common waterhemp grown in nonsterile soil was only 10%. Similarly, GR common waterhemp survival was reduced from 83 to 61% following treatment with glyphosate when grown in nonsterile compared to sterile soil. Fusarium spp. were recovered from only 12% of the assayed roots (223 treatments with Fusarium out of a total 1,920 treatments). The greatest occurrence of Fusarium root infection in both GR and GS common waterhemp occurred in nonsterile soils following a glyphosate treatment. Few differences in total PLFA were observed in field soil collected from locations with either GR or GS common waterhemp, and regardless of herbicide or crop history. This research supports previous findings that plant species are more sensitive to glyphosate in nonsterile than sterile soils and indicates glyphosate may predispose plants to soil-borne phytopathogens. This research also suggests that continuous use of glyphosate does not significantly affect soil microbial abundance or diversity.

Rhizobacteria isolated from the rhizospheres of dominant weed species in six representative cropping systems and one native prairie ecosystem in mid-Missouri were screened for phytotoxicity on Lactuca sativa seedlings and their host plants in the laboratory. The proportions of deleterious rhizobacteria (DRB) were compared among different cropping systems to determine possible effects of crop management practices on the occurrence of DRB. Phytotoxicity screening on L. sativa seedlings revealed that an integrated crop management system with a Zea mays–Glycine max–Triticum aestivum cover crop rotation under no-tillage had the highest proportion of DRB at 25.3%, followed by an organic farming system with continuous Fragaria virginiana (strawberry) and organic amendments under minimum tillage at 22.9%. A continuous cool-season grass–legume meadow with no agrochemical inputs had the lowest proportion of DRB at 13%. Crop management practices that maintained high soil organic matter had higher proportions of DRB compared to cropping systems with lower organic matter. Phytotoxicity screening on host plants greatly reduced the proportion of rhizobacteria characterized as DRB, likely because of the high sensitivity of L. sativa seedlings to phytotoxins. Although screening on L. sativa is an effective method to detect phytotoxic rhizobacteria, our research indicates that it is essential to test selected cultures on their host weed species for accurate assessment of their occurrence in the field. Using this approach, we found that crop management practices influence the occurrence of DRB naturally associated with weed seedlings. Results suggest that crop production systems can be developed to favor soil microorganisms such as DRB that affect weed growth and thereby become important considerations in overall weed management.

Our study examines the effect of seasonal rains on soil organic C dynamics in a tropical deciduous forest ecosystem in Western Mexico. At the end of the wet season, an accumulation of labile nutrient forms developed and was maintained during the dry season. This accumulation enhances microbial activity in the first rains of the wet season. For example, the litter samples of the dry season had a higher C and N mineralization than those of the wet season. Similarly, the January soil samples had higher C mineralization than October soil samples (55 and 34 μg C g-1 d-1, respectively). These results suggest that the quality of C is strongly affected by the seasonality of rains, which in turn influences microbial activity. This seasonality also influences nutrient redistribution between soil aggregate fractions. Chemical changes across seasons suggest that soil organic matter associated with macro-aggregates represents the main source of energy for microbial activity at the beginning of the wet season, while micro-aggregates protect the labile nutrient forms during the growing season.

There is considerable uncertainty about how rates of soil carbon (C) and nitrogen (N) cycling will change as CO2 accumulates in the Earth's atmosphere. We summarized data from 47 published reports on soil C and N cycling under elevated CO2 in an attempt to generalize whether rates will increase, decrease, or not change. Our synthesis centres on changes in soil respiration, microbial respiration, microbial biomass, gross N mineralization, microbial immobilization and net N mineralization, because these pools and processes represent important control points for the below-ground flow of C and N. To determine whether differences in C allocation between plant life forms influence soil C and N cycling in a predictable manner, we summarized responses beneath graminoid, herbaceous and woody plants grown under ambient and elevated atmospheric CO2. The below-ground pools and processes that we summarized are characterized by a high degree of variability (coefficient of variation 80–800%), making generalizations within and between plant life forms difficult. With few exceptions, rates of soil and microbial respiration were more rapid under elevated CO2, indicating that (1) greater plant growth under elevated CO2 enhanced the amount of C entering the soil, and (2) additional substrate was being metabolized by soil microorganisms. However, microbial biomass, gross N mineralization, microbial immobilization and net N mineralization are characterized by large increases and declines under elevated CO2, contributing to a high degree of variability within and between plant life forms. From this analysis we conclude that there are insufficient data to predict how microbial activity and rates of soil C and N cycling will change as the atmospheric CO2 concentration continues to rise. We argue that current gaps in our understanding of fine-root biology limit our ability to predict the response of soil microorganisms to rising atmospheric CO2, and that understanding differences in fine-root longevity and biochemistry between plant species are necessary for developing a predictive model of soil C and N cycling under elevated CO2.