Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high‐throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co‐occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field‐collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population‐level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives.     

高寒草甸主要植物地上地下生物量分布及退化对根冠比和根系表面积的影响

研究高寒草甸主要植物地上地下生物量的分布及其对退化的响应有利于了解高寒草甸的退化过程。该研究首先在西藏那曲生态环境综合观测研究站小嵩草围栏内(2009年围封)选择原生植被较好的地点随机选择小嵩草(Kobresia pygmaea)、矮嵩草(K.humilis)、紫花针茅(Stipa purpurea)、二裂委陵菜(Potentila bifurca)和青藏苔草(Carex moorcroftii)等5种植物斑块,选择退化斑块上(与原生植被相比)的二裂委陵菜和青藏苔草;然后用烘箱烘至恒重并称重,用扫描仪对根系进行扫描用于估算根系表面积;最后利用2因子方差分析检验不同物种个体、不同取样层次对地上和地下生物量的影响,利用物种和退化状态2因子方差分析检验对地上生物量的影响,以及利用物种、取样层次和退化状态3因子方差分析检验对二裂委陵菜和青藏苔草地下生物量、根冠比和根系表面积的影响。结果表明:在未退化条件下,小嵩草、矮嵩草和紫花针茅0~10cml地下生物量占0~30cm地下生物量的70%以上,0~30cm地下生物量占其地上地下总生物量的96%以上;二裂委陵菜(Potentilla bifurca)和青藏苔草(Carex moorcroftii)0~10cm地下生物量占0~30cml地下生物量的50%以上,其中二裂委陵菜0~30cm地下生物量占其地上地下总生物量的57%,青藏苔草0~30cm地下生物量占其地上地下总生物量的87%;对于退化草甸的主要植物,退化显著降低了二裂委陵菜的地上生物量、地下生物量和根冠比,对其根系表面积影响不大,但显著增加了青藏苔草的地上生物量,降低了其根冠比,对其地下生物量和根系表面积影响不大。     

On the significance of belowground overyielding in temperate mixed forests: separating species identity and species diversity effects

Complementary soil exploration by the root systems of coexisting tree species has been hypothesised to result in a higher root biomass of mixed forests than of monocultures but the existing evidence for a belowground diversity effect in forests is scarce and not conclusive. In a species‐rich temperate broad‐leaved forest, we analysed the fine root biomass (roots ≤ 2 mm) and necromass in 100 plots differing in tree species diversity (one to three species) and species composition (all possible combinations of five species of the genera Acer, Carpinus, Fagus, Fraxinus and Tilia) which allowed us to separate possible species diversity and species identity effects on fine root biomass. We found no evidence of a positive diversity effect on standing fine root biomass and thus of overyielding in terms of root biomass. Root necromass decreased with increasing species diversity at marginal significance. Various lines of evidence indicate significant species identity effects on fine root biomass (10–20% higher fine root biomass in plots with presence of maple and beech than in plots with hornbeam; 100% higher fine root biomass in monospecific beech and ash plots than in hornbeam plots; differences significant). Ash fine roots tended to be over‐represented in the 2‐ and 3‐species mixed plots compared to monospecific ash plots pointing at apparent belowground competitive superiority of Fraxinus in this mixed forest. Our results indicate that belowground overyielding and spatial complementarity of root systems may be the exception rather than the rule in temperate mixed forests.     

Specific impacts of two root herbivores and soil nutrients on plant performance and insect–insect interactions

Soil‐dwelling insects commonly co‐occur and feed simultaneously on belowground plant parts, yet patterns of damage and consequences for plant and insect performance remain poorly characterized. We tested how two species of root‐feeding insects affect the performance of a perennial plant and the mass and survival of both conspecific and heterospecific insects. Because root damage is expected to impair roots’ ability to take up nutrients, we also evaluated how soil fertility alters belowground plant–insect and insect–insect interactions. Specifically, we grew common milkweed Asclepias syriaca in low or high nutrient soil and added seven densities of milkweed beetles Tetraopes tetraophthalmus, wireworms (mainly Hypnoides abbreviatus), or both species. The location and severity of root damage was species‐specific: Tetraopes caused 59% more damage to main roots than wireworms, and wireworms caused almost seven times more damage to fine roots than Tetraopes. Tetraopes damage decreased shoot, main root and fine root biomass, however substantial damage by wireworms did not decrease any component of plant biomass. With the addition of soil nutrients, main root biomass increased three times more, and fine root biomass increased five times more when wireworms were present than when Tetraopes were present. We detected an interactive effect of insect identity and nutrient availability on insect mass. Under high nutrients, wireworm mass decreased 19% overall and was unaffected by the presence of Tetraopes. In contrast, Tetraopes mass increased 114% overall and was significantly higher when wireworms were also present. Survival of wireworms decreased in the presence of Tetraopes, and both species’ survival was negatively correlated with conspecific density. We conclude that insect identity, density and soil nutrients are important in mediating the patterns and consequences of root damage, and suggest that these factors may account for some of the contradictory plant responses to belowground herbivory reported in the literature.     

Low‐abundant species facilitates specific spatial organization that promotes multispecies biofilm formation

Microorganisms frequently co‐exist in matrix‐embedded multispecies biofilms. Within biofilms, interspecies interactions influence the spatial organization of member species, which likely play an important role in shaping the development, structure and function of these communities. Here, a reproducible four‐species biofilm, composed of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus, was established to study the importance of individual species spatial organization during multispecies biofilm development. We found that the growth of species that are poor biofilm formers, M. oxydans and P. amylolyticus, were highly enhanced when residing in the four‐species biofilm. Interestingly, the presence of the low‐abundant M. oxydans (0.5% of biomass volume) was observed to trigger changes in the composition of the four‐species community. The other three species were crucially needed for the successful inclusion of M. oxydans in the four‐species biofilm, where X. retroflexus was consistently positioned in the top layer of the mature four‐species biofilm. These findings suggest that low abundance key species can significantly impact the spatial organization and hereby stabilize the function and composition of complex microbiomes.     

Tree species diversity interacts with elevated CO2 to induce a greater root system response

As a consequence of land‐use change and the burning of fossil fuels, atmospheric concentrations of CO₂ are increasing and altering the dynamics of the carbon cycle in forest ecosystems. In a number of studies using single tree species, fine root biomass has been shown to be strongly increased by elevated CO₂. However, natural forests are often intimate mixtures of a number of co‐occurring species. To investigate the interaction between tree mixture and elevated CO₂, Alnus glutinosa, Betula pendula and Fagus sylvatica were planted in areas of single species and a three species polyculture in a free‐air CO₂ enrichment study (BangorFACE). The trees were exposed to ambient or elevated CO₂ (580 μmol mol^?1) for 4 years. Fine and coarse root biomass, together with fine root turnover and fine root morphological characteristics were measured. Fine root biomass and morphology responded differentially to the elevated CO₂ at different soil depths in the three species when grown in monocultures. In polyculture, a greater response to elevated CO₂ was observed in coarse roots to a depth of 20 cm, and fine root area index to a depth of 30 cm. Total fine root biomass was positively affected by elevated CO₂ at the end of the experiment, but not by species diversity. Our data suggest that existing biogeochemical cycling models parameterized with data from species grown in monoculture may be underestimating the belowground response to global change.     

Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures

Pollen DNA metabarcoding—marker‐based genetic identification of potentially mixed‐species pollen samples—has applications across a variety of fields. While basic species‐level pollen identification using standard DNA barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities to mixes (qualitative matching) and (b) generates sequence reads proportionally to their relative abundance in a sample (quantitative matching) is unclear, as these have not been assessed relative to known standards. We tested the quantitative and qualitative robustness of metabarcoding in constructed pollen mixtures varying in species richness (1–9 species), taxonomic relatedness (within genera to across class) and rarity (5%–100% of grains), using Illumina MiSeq with the markers rbcL and ITS2. Qualitatively, species composition determinations were largely correct, but false positives and negatives occurred. False negatives were typically driven by lack of a barcode gap or rarity in a sample. Species richness and taxonomic relatedness, however, did not strongly impact correct determinations. False positives were likely driven by contamination, chimeric sequences and/or misidentification by the bioinformatics pipeline. Quantitatively, the proportion of reads for each species was only weakly correlated with its relative abundance, in contrast to suggestions from some other studies. Quantitative mismatches are not correctable by consistent scaling factors, but instead are context‐dependent on the other species present in a sample. Together, our results show that metabarcoding is largely robust for determining pollen presence/absence but that sequence reads should not be used to infer relative abundance of pollen grains.     

Assessment of Root System Dynamics of Species Grown in Mixtures under Field Conditions using Herbicide Injection and 15N Natural Abundance Methods: A Case Study with Pea, Barley and Mustard

Two methods were developed and used to study the root system dynamics of two species grown together or separately under field conditions. The first method, based on herbicide injection at different soil depths, was used to determine the rooting depth penetration rate of each species in pea–barley and pea–mustard mixtures. The roots absorbed the herbicide when they reached the treated zone leading to visible symptoms on the leaves which could be readily monitored. The second method used differences in ¹⁵N natural abundance and N concentration between legume and non-legume species to quantify the contribution of each species to root biomass of a pea–barley mixture. Each contribution was calculated using ¹⁵N abundance and N concentration of root mixtures and of subsamples of roots of individual species within mixtures. Both methods can indeed be used to distinguish roots of species in mixtures and thus to study belowground competition between associated species. The use of these methods demonstrated species differences in root system dynamics between species but also significant effects of interactions between species in mixtures. The rooting depth penetration rate was mainly species specific whereas root biomass was dependant on plant growth, allocation of dry matter between shoot and root components and growth factors such as N fertilization. Root biomass of each species may vary therefore with the level of competition between species.     

基于生物量回归方程估算黔中喀斯特常绿落叶阔叶混交林木本植物的根系生物量

常规根系生物量研究方法在我国西南喀斯特森林地区实施困难,根系挖掘法所得研究结果不确定性高,导致目前根系生物量数据匮乏。选择贵州中部喀斯特常绿落叶阔叶混交林为对象,建立常规的根系生物量回归方程,结合群落调查数据,以期研究该森林木本植物的根系生物量特征及其空间分布格局。利用106株乔木、34株灌木和34株藤本标准木根系数据,构建了5种优势乔木(安顺润楠Machilus cavaleriei、化香树Platycarya strobilacea、云贵鹅耳枥Carpinus pubescens、云南鼠刺Itea yunnanensis和窄叶石栎Lithocarpus confinis)、3种优势灌木(刺异叶花椒Zanthoxylum dimorphophyllum、倒卵叶旌节花Stachyurus obovatus和异叶鼠李Rhamnus heterophylla)和2种优势藤本(藤黄檀Dalbergia hancai Benth和小果蔷薇Rosa cymosa)以及乔木通用、灌木通用和藤本通用共13个根系生物量回归方程。利用这些方程计算得到该喀斯特森林木本植物总根系生物量为22.72Mg/hm2。乔木根系生物量(22.57 Mg/hm2)远高于灌木和藤本,占森林总根系生物量的99.30%。5个优势乔木树种的根系生物量(19.67 Mg/hm2)占森林总根系生物量的86.54%。物种根系发达程度是影响根系生物量空间分布格局的重要因素。研究可为喀斯特地区植被地下生物量与碳储量的全面估算提供一个新途径。     

Community composition of root‐associated fungi in a Quercus‐dominated temperate forest: “codominance” of mycorrhizal and root‐endophytic fungi

In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak‐dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. In total, 345 operational taxonomic units (OTUs) of fungi were found from 159 terminal‐root samples from 12 plant species occurring in the forest. Due to the dominance of an oak species (Quercus serrata), diverse ectomycorrhizal clades such as Russula, Lactarius, Cortinarius, Tomentella, Amanita, Boletus, and Cenococcum were observed. Unexpectedly, the root‐associated fungal community was dominated by root‐endophytic ascomycetes in Helotiales, Chaetothyriales, and Rhytismatales. Overall, 55.3% of root samples were colonized by both the commonly observed ascomycetes and ectomycorrhizal fungi; 75.0% of the root samples of the dominant Q. serrata were so cocolonized. Overall, this study revealed that root‐associated fungal communities of oak‐dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities.     

N fertilizer and harvest impacts on bioenergy crop contributions to SOC

Belowground root biomass is infrequently measured and simply represented in models that predict landscape‐level changes to soil carbon stocks and greenhouse gas balances. Yet, crop‐specific responses to N fertilizer and harvest treatments are known to impact both plant allocation and tissue chemistry, potentially altering decomposition rates and the direction and magnitude of soil C stock changes and greenhouse gas fluxes. We examined switchgrass (Panicum virgatum L.) and corn (Zea mays L.,) yields, belowground root biomass, C, N and soil particulate organic matter‐C (POM‐C) in a 9‐year rainfed study of N fertilizer rate (0, 60, 120 and 180 kg N ha^?1) and harvest management near Mead, NE, USA. Switchgrass was harvested with one pass in either August or postfrost, and for no‐till (NT) corn, either 50% or no stover was removed. Switchgrass had greater belowground root biomass C and N (6.39, 0.10 Mg ha^?1) throughout the soil profile compared to NT‐corn (1.30, 0.06 Mg ha^?1) and a higher belowground root biomass C:N ratio, indicating greater recalcitrant belowground root biomass C input beneath switchgrass. There was little difference between the two crops in soil POM‐C indicating substantially slower decomposition and incorporation into SOC under switchgrass, despite much greater root C. The highest N rate decreased POM‐C under both NT‐corn and switchgrass, indicating faster decomposition rates with added fertilizer. Residue removal reduced corn belowground root biomass C by 37% and N by 48% and subsequently reduced POM‐C by 22% compared to no‐residue removal. Developing productive bioenergy systems that also conserve the soil resource will require balancing fertilization that maximizes aboveground productivity but potentially reduces SOC sequestration by reducing belowground root biomass and increasing root and soil C decomposition.     

Responses of High Arctic wet sedge tundra to climate warming since 1980

The global climate is changing rapidly and Arctic regions are showing responses to recent warming. Responses of tundra ecosystems to climate change have been examined primarily through short‐term experimental manipulations, with few studies of long‐term ambient change. We investigated changes in above‐ and belowground biomass of wet sedge tundra to the warming climate of the Canadian High Arctic over the past 25 years. Aboveground standing crop was harvested from five sedge meadow sites and belowground biomass was sampled from one of the sites in the early 1980s and in 2005 using the same methods. Aboveground biomass was on average 158% greater in 2005 than in the early 1980s. The belowground biomass was also much greater in 2005: root biomass increased by 67% and rhizome biomass by 139% since the early 1980s. Dominant species from each functional group (graminoids, shrubs and forbs) showed significant increases in aboveground biomass. Responsive species included the dominant sedge species Carex aquatilis stans, C. membranacea, and Eriophorum angustifolium, as well as the dwarf shrub Salix arctica and the forb Polygonum viviparum. However, diversity measures were not different between the sample years. The greater biomass correlated strongly with increased annual and summer temperatures over the same time period, and was significantly greater than the annual variation in biomass measured in 1980–1983. Increased decomposition and mineralization rates, stimulated by warmer soils, were likely a major cause of the elevated productivity, as no differences in the mass of litter were found between sample periods. Our results are corroborated by published short‐term experimental studies, conducted in other wet sedge tundra communities which link warming and fertilization with elevated decomposition, mineralization and tundra productivity. We believe that this is the first study to show responses in High Arctic wet sedge tundra to recent climate change.     

Effect of plant root symbionts on performance of native woody species in competition with an invasive grass in multispecies microcosms

The majority of terrestrial plants form mutualistic associations with arbuscular mycorrhizal fungi (AMF) and rhizobia (i.e., nitrogen‐fixing bacteria). Understanding these associations has important implications for ecological theory and for restoration practice. Here, we tested whether the presence of AMF and rhizobia influences the performance of native woody plants invaded by a non‐native grass in experimental microcosms. We planted eight plant species (i.e., Acacia acuminata, A. microbotrya, Eucalyptus loxophleba subsp. loxophleba, E. astringens, Calothamnus quadrifidus, Callistemon phoeniceus, Hakea lissocarpha and H. prostrata) in microcosms of field‐conditioned soil with and without addition of AMF and rhizobia in a fully factorial experimental design. After seedling establishment, we seeded half the microcosms with an invasive grass Bromus diandrus. We measured shoot and root biomass of native plants and Bromus, and on roots, the percentage colonization by AMF, number of rhizobia‐forming nodules and number of proteaceous root clusters. We found no effect of plant root symbionts or Bromus addition on performance of myrtaceous, and as predicted, proteaceous species as they rely little or not at all on AMF and rhizobia. Soil treatments with AMF and rhizobia had a strong positive effect (i.e., larger biomass) on native legumes (A. microbotrya and A. acuminata). However, the beneficial effect of root symbionts on legumes became negative (i.e., lower biomass and less nodules) if Bromus was present, especially for one legume, i.e., A. acuminata, suggesting a disruptive effect of the invader on the mutualism. We also found a stimulating effect of Bromus on root nodule production in A. microbotrya and AMF colonization in A. acuminata which could be indicative of legumes’ increased resource acquisition requirement, i.e., for nitrogen and phosphorus, respectively, in response to the Bromus addition. We have demonstrated the importance of measuring belowground effects because the aboveground effects gave limited indication of the effects occurring belowground.     

Diet preferences based on sequence read count: The role of species interaction in tissue bias correction

High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator–prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In this study, we propose two categories of tissue bias correction indices: sequence read count number per unit tissue (SCN) and its ratio form (SCN ratio). By constructing plant mock communities with different numbers of co-occurring species in metabarcoding mixtures and conducting feeding trails on captive sika deer (Cervus nippon), we demonstrate the features of the SCN and SCN ratio, evaluate their correction effects and assess the role of species interactions during tissue bias correction. Tissue differences between species are defined as the differential ability to generate sequence counts. Our study suggests that pure tissue differences among species without a species interaction is not an optimal correction index for many biomes with limited tissue differences among species. Species interactions in mixtures may amplify tissue differences, which is beneficial for tissue bias correction. However, caution must be taken because varied species interactions among communities may increase the risk of worse correction. Correction effects based on the SCN and SCN ratio are comparable, but the SCN is less influenced by control species than the SCN ratio. Based on our study, several suggestions are provided for future animal diet studies or other high-throughput sequencing studies containing tissue bias.     

Above- and belowground biomass allocation and its regulation by plant density in six common grassland species in China

Above- and belowground biomass allocation is an essential plant functional trait that reflects plant survival strategies and affects belowground carbon pool estimation in grasslands. However, due to the difficulty of distinguishing living and dead roots, estimation of biomass allocation from field-based studies currently show large uncertainties. In addition, the dependence of biomass allocation on plant species, functional type as well as plant density remains poorly addressed. Here, we conducted greenhouse manipulation experiments to study above- and belowground biomass allocation and its density regulation for six common grassland species with different functional types (i.e., C₃ vs C₄; annuals vs perennials) from temperate China. To explore the density regulation on the biomass allocation, we used five density levels: 25, 100, 225, 400, and 625 plant m^?2. We found that mean root to shoot ratio (R/S) values ranged from 0.04 to 0.92 across the six species, much lower than those obtained in previous field studies. We also found much lower R/S values in annuals than in perennials (C. glaucum and S. viridis vs C. squarrosa, L. chinensis, M. sativa and S. grandis) and in C₄ plants than in C₃ plants (C. squarrosa vs L. chinensis, M. sativa and S. grandis). In addition to S. grandis, plant density had significant effects on the shoot and root biomass fraction and R/S for the other five species. Plant density also affected the allometric relationships between above- and belowground biomass significantly. Our results suggest that R/S values obtained from field investigations may be severely overestimated and that R/S values vary largely across species with different functional types. Our findings provide novel insights into approximating the difficult-to-measure belowground living biomass in grasslands, and highlight that species composition and intraspecific competition will regulate belowground carbon estimation.

     

The relation between above- and belowground biomass allocation patterns and competitive ability

Summary In a 2-year experiment, the evergreen shrubsErica tetralix andCalluna vulgaris (dominant on nutrient-poor heathland soils) and the perennial deciduous grassMolinia caerulea (dominant on nutrient-rich heathland soils) were grown in replacement series in a factorial combination of four competition types (no competition, only aboveground competition, only belowground competition, full competition) and two levels of nutrient supply (no nutrients and 10 g N+2 g P+10 g K m⁻² yr⁻¹). Both in the unfertilized and in the fertilized treatmentsMolinia allocated about twice as much biomass to its root system than didErica andCalluna. In all three species the relative amount of biomass allocated to the roots was lower at high than at low nutrient supply. The relative decrease was larger forMolinia than forErica andCalluna. In the fertilized monocultures biomass of all three species exceeded that in the unfertilized series.Molinia showed the greatest biomass increase. In the unfertilized series no effects of interspecific competition on the biomass of each species were observed in either of the competition treatments. In the fertilized mixtures where only belowground competition was possibleMolinia increased its biomass at the expense of bothErica andCalluna. When only aboveground competition was possible no effects of interspecific competition on the biomass of the competing species were observed. However, in contrast with the evergreens,Molinia responded by positioning its leaf layers relatively higher in the canopy. The effects of full competition were similar to those of only belowground competition, so in the fertilized series belowground competition determined the outcome of competition. The high competitive ability ofMolinia at high nutrient supply can be attributed to the combination of (1) a high potential productivity, (2) a high percentage biomass allocation to the roots, (3) an extensive root system exploiting a large soil volume, and (4) plasticity in the spatial arrangement of leaf layers over its tall canopy. In the species under study the allocation patterns entailed no apparent trade-off between the abilities to compete for above- and belowground resources. This study suggests that this trade-off can be overcome by: (1) plasticity in the spatial arrangement of leaf layers and roots, and (2) compensatory phenotypic and species-specific differences in specific leaf area and specific root length.     

Differential belowground allelopathic effects of leaf and root of Mikania micrantha

This study evaluates the relative contributions of leaves and roots to the belowground allelopathic effects of Mikania micrantha. The hypothesis that leaves contribute more to the allelopathic effect than roots was experimentally tested. We assessed the allelopathic effects of aqueous extracts from Mikania leaves and roots on the seed germination and seedling growth of two co-occurring woody plants in southern China, Lagerstroemia indica L. and Robinia pseudoacacia L. The results showed that the aqueous extracts from Mikania leaves and roots had inhibitory effects on the woody species. Allelopathic activity depended on the concentration of the extracts, target species, and the extract sources (i.e., leaves vs. roots of Mikania). Leaf extract showed stronger allelopathic effects than root extract on germination percentage, initial germination time, speed of germination, and shoot height; while root extract had greater allelopathic effects on roots than leaf extract. The latter phenomenon might greatly promote the invasion success of Mikania due to more direct and effective allelopathy of root. Our results suggest that allelopathy of root extract on belowground biomass might be greater than that of leaf extract for some species in contrast allelopathy of leaf extract on belowground biomass might also be greater than that of root extract for other species, at least for their effects on root growth of the target species.     

Dominant Grasses Suppress Local Diversity in Restored Tallgrass Prairie

Warm‐season (C₄) grasses commonly dominate tallgrass prairie restorations, often at the expense of subordinate grasses and forbs that contribute most to diversity in this ecosystem. To assess whether the cover and abundance of dominant grass species constrain plant diversity, we removed 0, 50, or 100% of tillers of two dominant species (Andropogon gerardii or Panicum virgatum) in a 7‐year‐old prairie restoration. Removing 100% of the most abundant species, A. gerardii, significantly increased light availability, forb productivity, forb cover, species richness, species evenness, and species diversity. Removal of a less abundant but very common species, P. virgatum, did not significantly affect resource availability or the local plant community. We observed no effect of removal treatments on critical belowground resources, including inorganic soil N or soil moisture. Species richness was inversely correlated with total grass productivity and percent grass cover and positively correlated with light availability at the soil surface. These relationships suggest that differential species richness among removal treatments resulted from treatment induced differences in aboveground resources rather than the belowground resources. Selective removal of the dominant species A. gerardii provided an opportunity for seeded forb species to become established leading to an increase in species richness and diversity. Therefore, management practices that target reductions in cover or biomass of the dominant species may enhance diversity in established and grass‐dominated mesic grassland restorations.     

Consequences of variation in species diversity in a community of root-feeding herbivores for nematode dynamics and host plant biomass

To date, no study has explicitly addressed effects of variation in species diversity of root‐feeding herbivores on host plant biomass. Root‐feeding nematodes typically occur in multi‐species communities. In a three‐year field experiment, we investigated how variation in species diversity of root‐feeding nematodes affected nematode dynamics and response of the dune grass Ammophila arenaria to root‐feeder activity. This plant species needs regular burial by fresh beach sand to remain vigorous, suggesting that A. arenaria benefits from a temporary escape from root‐feeding soil organisms and that root‐feeders are involved in plant degeneration in stabilized dunes. We created series of ceased and continued sand burial and added the endoparasitic nematodes Meloidogyne maritima, Heterodera arenaria and Pratylenchus penetrans alone or in combination to A. arenaria. We included treatments with and without the whole soil community, measured plant biomass and quantified numbers of nematodes. Addition of H. arenaria and P. penetrans decreased numbers of M. maritima juveniles and delayed the first appearance in time of both juveniles and females, while numbers of males only decreased when plants had been buried. Burial with sand and addition of the other two endoparasites affected numbers of H. arenaria juveniles, while numbers of P. penetrans were low and not affected. Shoot biomass of A. arenaria was lower when M. maritima had been added alone than when the three species had been added together. Addition of root zone soil decreased biomass of all plant parts. Burial with sand decreased aboveground shoot biomass, whereas it increased belowground shoot and root biomass. Our results point at idiosyncratic effects of nematode diversity on A. arenaria biomass. Heterodera arenaria and P. penetrans protected their host by reducing numbers and delaying activity of M. maritima to a later stage in the growth season, when root‐feeding activity was less harmful for plant biomass development.     

Minimizing polymerase biases in metabarcoding

DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or “barcode,” from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product. The accuracy of both occurrence and relative abundance estimates can be affected by a variety of biological and technical biases. For example, taxa with larger biomass may be better represented in environmental samples than those with smaller biomass. Here, we explore how polymerase choice, a potential source of technical bias, might influence results in metabarcoding experiments. We compared potential biases of six commercially available polymerases using a combination of mixtures of amplifiable synthetic sequences and real sedimentary DNA extracts. We find that polymerase choice can affect both occurrence and relative abundance estimates and that the main source of this bias appears to be polymerase preference for sequences with specific GC contents. We further recommend an experimental approach for metabarcoding based on results of our synthetic experiments.