Response of benthic macroinvertebrates to dam removal in the restoration of the Boardman River, Michigan, USA.

Dam removal is an increasingly important method of stream restoration, but most removal efforts are under-studied in their effects. In order to better understand the effects of such removals on the stream ecosystem, we examined changes in stream macroinvertebrate communities from 2011-2016. Comparisons were focused above, below, and before and after the October 2012 removal of the Brown Bridge Dam on the Boardman River in Michigan (USA), as well as to new channel sites created in its former reservoir (2013-2015). Using linear mixed-effect models on the percent abundance of ecologically sensitive taxa (% Ephemeroptera, Plecoptera, Trichoptera (EPT)), total density of all macroinvertebrates, overall taxa richness, and Functional Feeding Groups, along with multivariate analyses on the community matrix, we examined differences in community composition among sites and years. EPT declined downstream of the dam immediately after dam removal, but recovered in the second year, becoming dominant within 2-4 years. Downstream sites before removal had different community composition than upstream sites and downstream sites after removal (p<0.001), while upstream and downstream sites after removal converged towards similarity. New channel (restored) %EPT, density, and taxa richness were not different from upstream sites in any year following removal, but new channel sites were the most distinct in community composition, possessing multiple indicator taxa characteristic of unique new conditions. The invasive New Zealand mud snail (Potamopyrgus antipodarum) was absent from all sites prior to dam removal, but appeared at low densities in upstream sites in 2013, had spread to all sites by 2015, and showed large increases at all sites by 2016. Managers employing dam removal for stream restoration should include post-removal monitoring for multiple years following removal and conduct risk analysis regarding potential effects on colonization of invasive invertebrate species.

Dividing the pie: A quantitative review on plant density responses.

Plant population density is an important variable in agronomy and forestry and offers an experimental way to better understand plant-plant competition. We made a meta-analysis of responses of even-aged mono-specific stands to population density by quantifying for 3 stand and 33 individual plant variables in 334 experiments how much both plant biomass and phenotypic traits change with a doubling in density. Increasing density increases standing crop per area, but decreases the mean size of its individuals, mostly through reduced tillering and branching. Among the phenotypic traits, stem diameter is negatively affected, but plant height remains remarkably similar, partly due to an increased stem length-to-mass ratio and partly by increased allocation to stems. The reduction in biomass is caused by a lower photosynthetic rate, mainly due to shading of part of the foliage. Total seed mass per plant is also strongly reduced, marginally by lower mass per seed, but mainly because of lower seed numbers. Plants generally have fewer shoot-born roots, but their overall rooting depth seems hardly affected. The phenotypic plasticity responses to high densities correlate strongly with those to low light, and less with those to low nutrients, suggesting that at high density, shading affects plants more than nutrient depletion.

An Analysis of Soil Coring Strategies to Estimate Root Depth in Maize (Zea mays) and Common Bean (Phaseolus vulgaris).

A soil coring protocol was developed to cooptimize the estimation of root length distribution (RLD) by depth and detection of functionally important variation in root system architecture (RSA) of maize and bean. The functional-structural model OpenSimRoot was used to perform in silico soil coring at six locations on three different maize and bean RSA phenotypes. Results were compared to two seasons of field soil coring and one trench. Two one-sided T-test (TOST) analysis of in silico data suggests a between-row location 5 cm from plant base (location 3), best estimates whole-plot RLD/D of deep, intermediate, and shallow RSA phenotypes, for both maize and bean. Quadratic discriminant analysis indicates location 3 has ~70% categorization accuracy for bean, while an in-row location next to the plant base (location 6) has ~85% categorization accuracy in maize. Analysis of field data suggests the more representative sampling locations vary by year and species. In silico and field studies suggest location 3 is most robust, although variation is significant among seasons, among replications within a field season, and among field soil coring, trench, and simulations. We propose that the characterization of the RLD profile as a dynamic rhizo canopy effectively describes how the RLD profile arises from interactions among an individual plant, its neighbors, and the pedosphere.

Genetic control of root architectural plasticity in maize.

Root phenotypes regulate soil resource acquisition; however, their genetic control and phenotypic plasticity are poorly understood. We hypothesized that the responses of root architectural phenes to water deficit (stress plasticity) and different environments (environmental plasticity) are under genetic control and that these loci are distinct. Root architectural phenes were phenotyped in the field using a large maize association panel with and without water deficit stress for three seasons in Arizona and without water deficit stress for four seasons in South Africa. All root phenes were plastic and varied in their plastic response. We identified candidate genes associated with stress and environmental plasticity and candidate genes associated with phenes in well-watered conditions in South Africa and in well-watered and water-stress conditions in Arizona. Few candidate genes for plasticity overlapped with those for phenes expressed under each condition. Our results suggest that phenotypic plasticity is highly quantitative, and plasticity loci are distinct from loci that control phene expression in stress and non-stress, which poses a challenge for breeding programs. To make these loci more accessible to the wider research community, we developed a public online resource that will allow for further experimental validation towards understanding the genetic control underlying phenotypic plasticity.

A Behavioral Survey of the Effects of Kavalactones on Caenorhabditis elegans Neuromuscular Transmission.

Kava is a plant root extract that is widely consumed by Pacific Islanders. Kava contains a class of lactone compounds called kavalactones. The sedative and anxiolytic effects of kava are likely attributed to the efficacies of kavalactones on the nervous system. Although some studies have implicated the potencies of certain kavalactone species on γ-aminobutyric acid transmission, evidence supporting the action of kavalactones on the eukaryotic neuromuscular junction (NMJ) and acetylcholine (ACh) transmission is scant. Here, we used behavioral assays to demonstrate the effects of kavalactones at the Caenorhabditis elegans NMJ. Our results suggest that kavalactones disrupt the inhibitory-excitatory balance at the NMJ. Such perturbation of NMJ activity is likely due to excess or prolonged ACh transmission. In addition, we found that kavain, a major constituent of kava, induced worm paralysis but not convulsions. Hence, the modulatory action of kavain could be distinct from the other kavalactone species.

Phosphorylation-specific status of RNAi triggers in pharmacokinetic and biodistribution analyses.

The RNA interference (RNAi)-based therapeutic ARC-520 for chronic hepatitis B virus (HBV) infection consists of a melittin-derived peptide conjugated to N-acetylgalactosamine for hepatocyte targeting and endosomal escape, and cholesterol-conjugated RNAi triggers, which together result in HBV gene silencing. To characterize the kinetics of RNAi trigger delivery and 5΄-phosphorylation of guide strands correlating with gene knockdown, we employed a peptide-nucleic acid (PNA) hybridization assay. A fluorescent sense strand PNA probe binding to RNAi duplex guide strands was coupled with anion exchange high performance liquid chromatography to quantitate guide strands and metabolites. Compared to PCR- or ELISA-based methods, this assay enables separate quantitation of non-phosphorylated full-length guide strands from 5΄-phosphorylated forms that may associate with RNA-induced silencing complexes (RISC). Biodistribution studies in mice indicated that ARC-520 guide strands predominantly accumulated in liver. 5΄-phosphorylation of guide strands was observed within 5 min after ARC-520 injection, and was detected for at least 4 weeks corresponding to the duration of HBV mRNA silencing. Guide strands detected in RISC by AGO2 immuno-isolation represented 16% of total 5΄-phosphorylated guide strands in liver, correlating with a 2.7 log10 reduction of HBsAg. The PNA method enables pharmacokinetic analysis of RNAi triggers, elucidates potential metabolic processing events and defines pharmacokinetic-pharmacodynamic relationships.

Response to elevated CO2 in the temperate C3 grass Festuca arundinaceae across a wide range of soils.

Soils vary widely in mineral nutrient availability and physical characteristics, but the influence of this variability on plant responses to elevated CO2 remains poorly understood. As a first approximation of the effect of global soil variability on plant growth response to CO2, we evaluated the effect of CO2 on tall fescue (Festuca arundinacea) grown in soils representing 10 of the 12 global soil orders plus a high-fertility control. Plants were grown in small pots in continuously stirred reactor tanks in a greenhouse. Elevated CO2 (800 ppm) increased plant biomass in the high-fertility control and in two of the more fertile soils. Elevated CO2 had variable effects on foliar mineral concentration-nitrogen was not altered by elevated CO2, and phosphorus and potassium were only affected by CO2 in a small number of soils. While leaf photosynthesis was stimulated by elevated CO2 in six soils, canopy photosynthesis was not stimulated. Four principle components were identified; the first was associated with foliar minerals and soil clay, and the second with soil acidity and foliar manganese concentration. The third principle component was associated with gas exchange, and the fourth with plant biomass and soil minerals. Soils in which tall fescue did not respond to elevated CO2 account for 83% of global land area. These results show that variation in soil physical and chemical properties have important implications for plant responses to global change, and highlight the need to consider soil variability in models of vegetation response to global change.

Image-based high-throughput field phenotyping of crop roots.

Current plant phenotyping technologies to characterize agriculturally relevant traits have been primarily developed for use in laboratory and/or greenhouse conditions. In the case of root architectural traits, this limits phenotyping efforts, largely, to young plants grown in specialized containers and growth media. Hence, novel approaches are required to characterize mature root systems of older plants grown under actual soil conditions in the field. Imaging methods able to address the challenges associated with characterizing mature root systems are rare due, in part, to the greater complexity of mature root systems, including the larger size, overlap, and diversity of root components. Our imaging solution combines a field-imaging protocol and algorithmic approach to analyze mature root systems grown in the field. Via two case studies, we demonstrate how image analysis can be utilized to estimate localized root traits that reliably capture heritable architectural diversity as well as environmentally induced architectural variation of both monocot and dicot plants. In the first study, we show that our algorithms and traits (including 13 novel traits inaccessible to manual estimation) can differentiate nine maize (Zea mays) genotypes 8 weeks after planting. The second study focuses on a diversity panel of 188 cowpea (Vigna unguiculata) genotypes to identify which traits are sufficient to differentiate genotypes even when comparing plants whose harvesting date differs up to 14 d. Overall, we find that automatically derived traits can increase both the speed and reproducibility of the trait estimation pipeline under field conditions.

Root cortical aerenchyma enhances nitrogen acquisition from low-nitrogen soils in maize.

Suboptimal nitrogen (N) availability is a primary constraint for crop production in developing nations, while in rich nations, intensive N fertilization carries substantial environmental and economic costs. Therefore, understanding root phenes that enhance N acquisition is of considerable importance. Structural-functional modeling predicts that root cortical aerenchyma (RCA) could improve N acquisition in maize (Zea mays). We evaluated the utility of RCA for N acquisition by physiological comparison of maize recombinant inbred lines contrasting in RCA grown under suboptimal and adequate N availability in greenhouse mesocosms and in the field in the United States and South Africa. N stress increased RCA formation by 200% in mesocosms and by 90% to 100% in the field. RCA formation substantially reduced root respiration and root N content. Under low-N conditions, RCA formation increased rooting depth by 15% to 31%, increased leaf N content by 28% to 81%, increased leaf chlorophyll content by 22%, increased leaf CO2 assimilation by 22%, increased vegetative biomass by 31% to 66%, and increased grain yield by 58%. Our results are consistent with the hypothesis that RCA improves plant growth under N-limiting conditions by decreasing root metabolic costs, thereby enhancing soil exploration and N acquisition in deep soil strata. Although potential fitness tradeoffs of RCA formation are poorly understood, increased RCA formation appears be a promising breeding target for enhancing crop N acquisition.

Integration of root phenes for soil resource acquisition.

Suboptimal availability of water and nutrients is a primary limitation to plant growth in terrestrial ecosystems. The acquisition of soil resources by plant roots is therefore an important component of plant fitness and agricultural productivity. Plant root systems comprise a set of phenes, or traits, that interact. Phenes are the units of the plant phenotype, and phene states represent the variation in form and function a particular phene may take. Root phenes can be classified as affecting resource acquisition or utilization, influencing acquisition through exploration or exploitation, and in being metabolically influential or neutral. These classifications determine how one phene will interact with another phene, whether through foraging mechanisms or metabolic economics. Phenes that influence one another through foraging mechanisms are likely to operate within a phene module, a group of interacting phenes, that may be co-selected. Examples of root phene interactions discussed are: (1) root hair length × root hair density, (2) lateral branching × root cortical aerenchyma (RCA), (3) adventitious root number × adventitious root respiration and basal root growth angle (BRGA), (4) nodal root number × RCA, and (5) BRGA × root hair length and density. Progress in the study of phenes and phene interactions will be facilitated by employing simulation modeling and near-isophenic lines that allow the study of specific phenes and phene combinations within a common phenotypic background. Developing a robust understanding of the phenome at the organismal level will require new lines of inquiry into how phenotypic integration influences plant function in diverse environments. A better understanding of how root phenes interact to affect soil resource acquisition will be an important tool in the breeding of crops with superior stress tolerance and reduced dependence on intensive use of inputs.

Root cortical burden influences drought tolerance in maize.

BACKGROUND AND AIMS: Root cortical aerenchyma (RCA) increases water and nutrient acquisition by reducing the metabolic costs of soil exploration. In this study the hypothesis was tested that living cortical area (LCA; transversal root cortical area minus aerenchyma area and intercellular air space) is a better predictor of root respiration, soil exploration and, therefore, drought tolerance than RCA formation or root diameter. METHODS: RCA, LCA, root respiration, root length and biomass loss in response to drought were evaluated in maize (Zea mays) recombinant inbred lines grown with adequate and suboptimal irrigation in soil mesocosms. KEY RESULTS: Root respiration was highly correlated with LCA. LCA was a better predictor of root respiration than either RCA or root diameter. RCA reduced respiration of large-diameter roots. Since RCA and LCA varied in different parts of the root system, the effects of RCA and LCA on root length were complex. Greater crown-root LCA was associated with reduced crown-root length relative to total root length. Reduced LCA was associated with improved drought tolerance. CONCLUSIONS: The results are consistent with the hypothesis that LCA is a driver of root metabolic costs and may therefore have adaptive significance for water acquisition in drying soil.

Optimizing reproductive phenology in a two-resource world: a dynamic allocation model of plant growth predicts later reproduction in phosphorus-limited plants.

BACKGROUND AND AIMS: Timing of reproduction is a key life-history trait that is regulated by resource availability. Delayed reproduction in soils with low phosphorus availability is common among annuals, in contrast to the accelerated reproduction typical of other low-nutrient environments. It is hypothesized that this anomalous response arises from the high marginal value of additional allocation to root growth caused by the low mobility of phosphorus in soils. METHODS: To better understand the benefits and costs of such delayed reproduction, a two-resource dynamic allocation model of plant growth and reproduction is presented. The model incorporates growth, respiration, and carbon and phosphorus acquisition of both root and shoot tissue, and considers the reallocation of resources from senescent leaves. The model is parameterized with data from Arabidopsis and the optimal reproductive phenology is explored in a range of environments. KEY RESULTS: The model predicts delayed reproduction in low-phosphorus environments. Reproductive timing in low-phosphorus environments is quite sensitive to phosphorus mobility, but is less sensitive to the temporal distribution of mortality risks. In low-phosphorus environments, the relative metabolic cost of roots was greater, and reproductive allocation reduced, compared with high-phosphorus conditions. The model suggests that delayed reproduction in response to low phosphorus availability may be reduced in plants adapted to environments where phosphorus mobility is greater. CONCLUSIONS: Delayed reproduction in low-phosphorus soils can be a beneficial response allowing for increased acquisition and utilization of phosphorus. This finding has implications both for efforts to breed crops for low-phosphorus soils, and for efforts to understand how climate change may impact plant growth and productivity in low-phosphorus environments.

Root responses to neighbouring plants in common bean are mediated by nutrient concentration rather than self/non-self recognition.

Plants are reported to over-proliferate roots in response to belowground competition, thereby reducing reproductive biomass. This has been cited as an instance of the 'tragedy of the commons'. Many of the studies that report this response suggest that plants can sense neighbours and discriminate between 'self' and 'non-self' roots. To test the alternate hypothesis that root responses to a neighbouring plant are mediated by resource depletion, common bean plants were supplied with the same phosphorus (P) fertiliser dose in varying rooting volumes, or with neighbouring plants separated by plastic film, nylon mesh, or no barrier to vary access to a neighbour. Phosphorus concentration, but not the presence of a neighbour or rooting volume, strongly influenced biomass allocation to roots. Root architecture was significantly altered by both neighbours and P availability. When exposed to the roots of a neighbour, plants altered the vertical and horizontal distribution of roots, placing fewer roots in soil domains occupied by roots of a neighbour. These results support the hypothesis that root responses to neighbouring plants are mediated by resource depletion by the neighbour rather than sensing of 'non-self' roots and show that the presence of a neighbour may affect root architecture without affecting biomass allocation to roots.

Plant phenology: a critical controller of soil resource acquisition.

Plant phenology, the timing of plant growth and development, is changing in response to global climate change. Changing temperature, soil moisture, nitrogen availability, light, and elevated CO(2) are all likely to affect plant phenology. Alteration of plant phenology by global climate change may alter the ability of plants to acquire soil resources (water and nutrients) by altering the timing and duration of the deployment of roots and leaves, which drive resource acquisition. The potential importance of phenologically-driven changes in soil resource acquisition for plant fitness and productivity have received little attention. General hypotheses are proposed for how plant acquisition of soil resources may be affected by the alteration of phenology. It is expected that the acquisition of mobile resources will be approximately proportional to total transpiration. Alteration of phenology that increases total transpiration should increase, while changes in phenology that reduce transpiration should decrease the acquisition of mobile resources. The acquisition of immobile resources will be approximately proportional to root length duration, thus changes in phenology that increase growth duration should increase the acquisition of immobile resources and vice versa. For both groups of resources, longer growing seasons would tend to increase resource acquisition, and shorter growing seasons would tend to decrease resource acquisition. In the case of resources that exhibit seasonal variability in availability, the synchrony of resource availability and acquisition capacity is important, and subject to disturbance by the alteration of phenology.

Delayed reproduction in Arabidopsis thaliana improves fitness in soil with suboptimal phosphorus availability.

Low phosphorus availability (low P) often delays flowering and maturity in annual plants, while abiotic stress generally accelerates flowering and maturity. The utility of this response is unknown. We hypothesize that phenological delay in low P is beneficial by permitting more time for phosphorus acquisition and utilization. We grew seven genotypes of Arabidopsis thaliana with contrasting phenology in high and low P. Low P delayed bolting and maturity in all genotypes. Low P decreased root length, but not root-length duration (the integral of root length over time), because phenological delay allowed low-P plants to compensate for shorter root length. Root-length duration was correlated with phosphorus accumulation. Leaf phosphorus duration (the integral of leaf phosphorus over time) was correlated with reproductive biomass, indicating the utility of increased phosphorus utilization. Phenological delays accounted for up to 30% of biomass production when low-P plants were compared to models of plants with no delays. These results support the hypothesis that phenological delay in low P is adaptive and leads to increased phosphorus acquisition and utilization. Because low P conditions are prevalent, understanding the utility of this response could be useful in crop breeding and in predicting plant responses to global climate change.