In California, invasive grasses have displaced native plants, transforming much of the endemic coastal sage scrub (CSS) to nonnative grasslands. This has occurred for several reasons, including increased competitive ability of invasive grasses and long-term alterations to the soil environment, called legacy effects. Despite the magnitude of this problem, however, it is not well understood how these legacy effects have altered the soil microbial community and, indirectly, native plant restoration. We assessed the microbial composition of soils collected from an uninvaded CSS community (uninvaded soil) and a nearby 10-ha site from which the invasive grass Harding grass (Phalaris aquatica L.) was removed after 11 yr of growth (postinvasive soil). We also measured the survival rate, biomass, and length of three CSS species and P. aquatica grown in both soil types (uninvaded and postinvasive). Our findings indicate that P. aquatica may create microbial legacy effects in the soil that likely cause soil conditions inhibitory to the survival rate, biomass, and length of coastal sagebrush, but not the other two native plant species. Specifically, coastal sagebrush growth was lower in the postinvasive soil, which had more Bacteroidetes, Proteobacteria, Agrobacterium, Bradyrhizobium, Rhizobium (R. leguminosarum), Candidatus koribacter, Candidatus solibacter, and rhizophilic arbuscular mycorrhizal fungi, and fewer Planctomycetes, Acidobacteria, Nitrospira, and Rubrobacter compared with the uninvaded soil. Shifts in soil microbial community composition such as these can have important implications for restoration strategies in postinvasive sites.

Soil microbial community structure and activity are linked to plant communities. Weeds may alter their soil environment, selecting for specific rhizosphere microbial communities. Rhizosphere modification occurs for many crop and horticultural plants. However, impacts of weeds in agroecosystems on soil biology and ecology have received less attention because effective weed management practices were developed to minimize their impacts on crop production. The recent development of herbicide resistance (HR) in several economically important weeds leading to widespread infestations in crop fields treated with a single herbicide has prompted a re-evaluation of the effects of weed growth on soil biology and ecology. The objective of this article is to review the potential impacts of herbicide-resistant weeds on soil biological and ecological properties based on reports for crops, weeds, and invasive plants. Persistent weed infestations likely establish extensive root systems and release various plant metabolites through root exudation. Many exudates are selective for specific soil microbial groups mediating biochemical and nutrient acquisition processes. Exudates may stimulate development of microbial groups beneficial to weed but detrimental to crop growth or beneficial to both. Changes in symbiotic and associative microbial interactions occur, especially for arbuscular mycorrhizal fungi (AMF) that are important in plant uptake of nutrients and water, and protecting from phytopathogens. Mechanisms used by weeds to disrupt symbioses in crops are not clearly described. Many herbicide-resistant weeds including Amaranthus and Chenopodium do not support AMF symbioses, potentially reducing AMF propagule density and establishment with crop plants. Herbicides applied to control HR weeds may compound effects of weeds on soil microorganisms. Systemic herbicides released through weed roots may select microbial groups that mediate detrimental processes such as nutrient immobilization or serve as opportunistic pathogens. Understanding complex interactions of weeds with soil microorganisms under extensive infestations is important in developing effective management of herbicide-resistant weeds.

It has been proposed that cropping systems can be managed to promote the development of soil microbial communities that accelerate weed seed mortality. We examined soil fungal and bacterial communities, soil C:N ratio, soil particle size fractions, and weed seed mortality in soil from fields with over 10 yr of five contrasting management histories with the objective of determining if seed mortality could be explained by differences in soil properties. Seed mortality of giant foxtail and velvetleaf were greatest in soil from the conventionally managed systems and lowest in soil from a reduced input system. Principal-components analysis of soil microbial communities, as determined through denaturing gradient gel electrophoresis of polymerase chain reaction–amplified ribosomal RNA genes (PCR-DGGE), showed distinct differences in the composition of fungal and bacterial communities among the study soils. The first principal component of the 18S rDNA PCR-DGGE analysis of fungal community composition showed a strong negative correlation with both giant foxtail (− 0.52, P < 0.05) and velvetleaf (− 0.57, P < 0.01) seed mortality, as did ordination with nonmetric multidimensional scaling (NMS) [giant foxtail (− 0.54, P < 0.01) and velvetleaf (− 0.60, P < 0.01)], suggesting that seeds of the two species were affected similarly by changes in the soil fungal community. For giant foxtail, weed seed mortality was also positively correlated (r = 0.48, P < 0.05) with the first NMS axis of the bacterial 16S rDNA analysis. None of the other measured soil properties were significantly correlated with weed seed mortality. Thus, for the soils tested here, management history, microbial community composition, and weed seed mortality were linked. To extend these results to the field, more work is needed to identify components of the fungal and bacterial communities that are active in seed degradation, and to develop conservation biocontrol recommendations for these species.

Recently, we conducted a case study that showed a no-till, diverse cropping system increasing corn yields in a semiarid climate compared with a tilled, corn–soybean rotation. Further analysis showed that the no-till system improved resource-use-efficiency of corn; inputs were reduced 42% averaged across five resources. The largest reduction with inputs involved nitrogen fertilizer and fuel. Reduced fertilizer input was attributed to greater soil microbial activity. A surprising trend was that cost of weed management in corn was 45% lower in the no-till system, due to resistant weeds being present only in the tilled, corn–soybean system. Crop diversity in the no-till system suppressed development of weed resistance. Integrating a diversity of crops with no-till can improve efficient use of resources.

No-till practices have improved crop yields in the semiarid Great Plains. However, a recent assessment of research studies across the globe indicated that crop yields are often reduced by no-till. To understand this contrast, we examined corn yields across time in a no-till cropping system of one producer in central South Dakota to identify factors associated with increased yield. The producer started no-till in 1990; by 2013, corn yield increased 116%. In comparison, corn increased only 32% during this interval with a conventional, tillage-based system in a neighboring county. With no-till, corn yields increased in increments due to changes in management. For example, corn yield increased 52% when crop diversity in the rotation was expanded from 2 to 5 crops. A further 18% gain in yield occurred when dry pea was grown before corn in sequence. Nitrogen (N) requirement for corn is 25% lower in no-till compared with a tillage-based rotation. Furthermore, phosphorus (P) fertilizer input also has been reduced 30% after 20 yr of no-till, even with higher yields. Our case study shows that integrating no-till with crop diversity and soil microbial changes improves corn yield considerably. This integration also reduces need for inputs such as water, N and P.

We utilized an automated ribosomal intergenic spacer analysis (ARISA) method as a more rapid alternative to classical morphological/nutritional identification and a less expensive alternative to sequencing for identification and grouping of isolates in culture-based fungal abundance studies. This method is well suited for the study of culturable Antarctic soil fungal communities where both abundance and diversity are relatively low. We optimized template concentration and verified the effect of primer selection from eight commonly used fungal polymerase chain reaction primers on ARISA chromatographs for 46 fungal species commonly isolated from south Victoria Land. A database of Antarctic fungal electropherograms was produced containing each of the species and was used as the first step in a tiered system for species identification. In addition, isolates containing more than one species were identified, allowing isolates not in the database to be sequenced for further analysis. This method unambiguously identified 78% of the fungal taxa in this study and we were able to rapidly determine which isolates should be subjected to further analysis by DNA sequencing. Using this approach, the cost of analysis for abundance studies can be greatly reduced compared to DNA sequencing of each isolate.