Authors are often faced with the decision of whether to maximize traditional impact metrics or minimize costs when choosing where to publish the results of their research. Many subscription-based journals now offer the option of paying an article processing charge (APC) to make their work open. Though such “hybrid” journals make research more accessible to readers, their APCs often come with high price tags and can exclude authors who lack the capacity to pay to make their research accessible. Here, we tested if paying to publish open access in a subscription-based journal benefited authors by conferring more citations relative to closed access articles. We identified 146,415 articles published in 152 hybrid journals in the field of biology from 2013–2018 to compare the number of citations between various types of open access and closed access articles. In a simple generalized linear model analysis of our full dataset, we found that publishing open access in hybrid journals that offer the option confers an average citation advantage to authors of 17.8 citations compared to closed access articles in similar journals. After taking into account the number of authors, Journal Citation Reports 2020 Quartile, year of publication, and Web of Science category, we still found that open access generated significantly more citations than closed access (p < 0.0001). However, results were complex, with exact differences in citation rates among access types impacted by these other variables. This citation advantage based on access type was even similar when comparing open and closed access articles published in the same issue of a journal (p < 0.0001). However, by examining articles where the authors paid an article processing charge, we found that cost itself was not predictive of citation rates (p = 0.14). Based on our findings of access type and other model parameters, we suggest that, in the case of the 152 journals we analyzed, paying for open access does confer a citation advantage. For authors with limited budgets, we recommend pursuing open access alternatives that do not require paying a fee as they still yielded more citations than closed access. For authors who are considering where to submit their next article, we offer additional suggestions on how to balance exposure via citations with publishing costs.

The SCARECROW (SCR) transcription factor plays a key role in plant growth and development. However, we know very little about the role of SCR regulated pathways in plant development. Here, we used the homozygous scr1 mutant Arabidopsis thaliana (Wassilewskija ecotype), which had a T-DNA insertion in the SCR coding region and lacks a detectable SCR transcript. This scr1 mutant has a determinate mode of root growth, shoot agravitropism and abnormal internal architecture in all organs examined. To screen for mutants that suppress the scr1 abnormal phenotypes, we exposed homozygous scr1 seeds to ethyl methane sulphonate (EMS) mutagen. Upon growth out of these mutagenized seeds, thirteen suppressor mutant-harboring strains were identified. All thirteen suppressor-harboring strains were homozygous for scr1 and lacked the SCR transcript. Ten scr hypocotyl gravitropic suppressor lines showed improved hypocotyl gravitropic response. These ten suppressors fall into six complementation groups suggesting six different gene loci. Similarly, three independent scr root length suppressor lines rescued only the root growth phenotype and fell into three complementation groups, suggesting the involvement of three different gene loci. These suppressors might identify novel functions of the SCR gene in plant development.

Cover crops are considered an integral component of agroecosystems because of their positive impacts on biotic and abiotic indicators of soil health. At present, we know little about the impact of cover crop types and diversity on the organic carbon (OC) contents of different soil aggregate-size classes. In this study, we investigated the effect of cover plant diversity on OC contents of different soil aggregates, such as macro- (<2000–500 μm), meso- (<500–250 μm), and micro-aggregates (<250 μm). Our experiment included a total of 12 experimental treatments in triplicate; six different monoculture treatments such as chickling vetch (Vicia villosa), crimson clover (Trifolium incarnatum), hairy vetch (Vicia villosa), field peas (Pisum sativum), oilseed radish (Raphanus sativus), and mighty mustard (Brassica juncea), and their three- and six-species mixture treatments, including one unplanted control treatment. We performed this experiment usingdeep pots that contained soil collected from a corn-soybean rotation field. At vegetative maturity of cover plants (about 70 days), we took soil samples, and the soil aggregate-size classes were separated by the dry sieving. We hypothesized that cover crop type and diversity will improve OC contents of different soil aggregate-size classes. We found that cover plant species richness weakly positively increased OC contents of soil macro-aggregates (p = 0.056), whereas other aggregate-size classes did not respond to cover crop diversity gradient. Similarly, the OC contents of macroaggregates varied significantly (p = 0.013) under cover crop treatments, though neither monoculture nor mixture treatments showed significantly higher OC contents than the control treatment in this short-term experiment. Interestingly, the inclusion of hairy vetch and oilseed radish increased and decreased the OC contents of macro- and micro-aggregates, respectively. Moreover, we found a positive correlation between shoot biomass and OC contents of macroaggregates. Overall, our results suggest that species-rich rather than -poor communities may improve OC contents of soil macroaggregates, which constitute a major portion of soil systems, and are also considered as important indicators of soil functions.

Purpose The effects of microbes and agrochemicals on crop plants are previously reported via seed treatments. We know little about the impacts of fungicides and microbial seed treatments on soybean shoot and root traits. Methods We investigated the effects of separate consortia of two plant growth-promoting rhizobacteria (PGPR) such as Bacillus simplex R180 and Burkholderia ambifaria C628, two Fusarium species ( Fusarium oxysporum and Fusarium graminearum ) ( Fusarium ), and Fungicides seed treatments on soybean traits. Results and Conclusions The PGPR and Fusarium increased and reduced the root and shoot dry mass of soybean plants, respectively. Fusarium infected plants had a relatively higher trichome leaf density followed by the PGPR , Control , Fungicide + PGPR , and Fungicides treatments. The PGPR increased P contents, while Fusarium reduced Mg and Mn contents of soybean shoot tissues. The nutrient contents of large and fine roots also varied across the seed treatments. Overall, fine roots showed higher mineral contents than large roots. Soybean roots showed relatively higher mineral contents such as Mg, Zn, Ca, Mn, Cu, B, Fe, and Mo in the fungicide + PGPR and fungicide treatments. Root K contents were substantially higher in the microbial than chemical treatments. The reduced and increased trichome density as well as tissue P contents in response to the Fungicides and microbial ( PGPR, Fusarium ) treatments, respectively, suggest the negative and positive effects of fungicides and microbes on soybean root and shoot traits. In conclusion, chemicals, pathogenic and beneficial microbes may influence plant shoot and root traits that are important for plant growth and development.

Although microbes influence plant growth, little is known about the impact of microbial diversity on plant fitness trade-offs, intraspecific-interactions, and soil nutrient dynamics in the context of biodiversity-ecosystem functioning (BEF) research. The BEF theory states that higher species richness can enhance ecosystem functioning. Thus, we hypothesize that rhizobacterial species richness will alter sorghum ( Sorghum bicolor L.) growth, soil nutrient dynamics and interactions (antagonism or synergism) in a nutrient-poor greenhouse soil. Using six rhizobacterial species in a BEF experiment, we tested the impact of a species richness gradient (0, 1, 3, 5 or 6 species per community) on plant growth, nutrient assimilation, and soil nutrient dynamics via seed-inoculation. Our experiment included, one un-inoculated control, six rhizobacterial monoculture (Pseudomonas poae, Pseudomonas sp., Bacillus pumilus., Pantoea agglomerance., Microbacterium sp., and Serratia marcescens ) , and their nine mixture treatments in triplicate (48). Rhizobacterial species richness enhanced per pot above- or below-ground dry mass. However, the per plant growth and plant nutrient assimilation declined, most likely, due to microbial-driven competitive interactions among sorghum plants. But nevertheless, some rhizobacterial monoculture and mixture treatments improved per plant (shoot and root) growth and nutrient assimilation as well. Soil nutrient contents were mostly lower at higher plant-associated rhizobacterial diversity; among these, the soil Zn contents decreased significantly across the rhizobacterial diversity gradient. Rhizobacterial diversity promoted synergistic interactions among soil nutrients and improved root–soil interactions. Overall, our results suggest that a higher rhizobacterial diversity may enhance soil–plant interactions and total productivity under resource limited conditions.

The continuous cropping (CC) of major agricultural, horticultural, and industrial crops is an established practice worldwide, though it has significant soil health-related concerns. However, a combined review of the effects of CC on soil health indicators, in particular omics ones, remains missing. The CC may negatively impact multiple biotic and abiotic indicators of soil health, fertility, and crop yield. It could potentially alter the soil biotic indicators, which include but are not limited to the composition, abundance, diversity, and functioning of soil micro- and macro-organisms, microbial networks, enzyme activities, and soil food web interactions. Moreover, it could also alter various soil abiotic (physicochemical) properties. For instance, it could increase the accumulation of toxic metabolites, salts, and acids, reduce soil aggregation and alter the composition of soil aggregate-size classes, decrease mineralization, soil organic matter, active carbon, and nutrient contents. All these alterations could accelerate soil degradation. Meanwhile, there is still a great need to develop quantitative ranges in soil health indicators to mechanistically predict the impact of CC on soil health and crop yield gaps. Following ecological principles, we strongly highlight the significance of inter-, mixture-, and rotation-cropping with cover crops to sustain soil health and agricultural production.

Cover crops may influence soil health and functioning. However, little is known about the role of belowground root architectural traits in linking cover crop diversity with rhizosphere soil ecosystem properties. We hypothesize that cover crop diversity may improve root traits, which in return, could influence its effects on essential indicators of soil physicochemical heterogeneity, such as the composition of soil aggregate-size classes and nutrients, and the soil organic matter (SOM) and soil organic carbon (SOC) contents. We studied the impact of plant diversity on root traits and soil properties. The four soil aggregate-size classes, such as large macro ( 2000 mu m), small macro(<2000-500 mu m), meso(<500-250 mu m), and micro-aggregates (<250 mu m) were separated by the dry sieving. Root traits such as surface area (cm(2)) and length (cm) were quantified by image analysis using Winrhizo. The soil nutrient, SOM, and SOC contents were determined by standard methods. We used Fox's (2005) method for partitioning the selection and complementarity effects on plant productivity. Plant diversity improved productivity, root architectural traits, root coverage, the composition of soil aggregate-size classes and nutrients, SOM and SOC contents across the soil depth. It increased and decreased the relative abundance of mesoand micro-aggregates, respectively. Both root architectural traits and SOC contents positively correlated with several soil edaphic properties essential for physicochemical heterogeneity, health, and functioning. Our results suggest that competition among plant roots in species-rich than poor communities may improve rhizosphere soil carbon storage, the composition of soil aggregate-size classes, and nutrients.

The plant root system influences plant growth and development due to its phenotypic, physiological, metabolomic, and microbiomic traits. Broadly speaking, it is characterized by primary (stem-attached large), secondary (primary-attached medium), and fine (secondary-attached hair-like) roots. The role of root branching order and categories (fine, medium, and large) in influencing microbial communities in the rhizosphere and root environments is not clear. We studied whether and how different root categories influence the composition of root and rhizosphere microbial communities in young peach trees. Using next-generation 16S rRNA amplicon sequencing (V3–V4 region), we profiled the microbial communities of roots and rhizosphere environments from phylum to species-level taxonomies. We demonstrated that different root categories showed a unique microbial community composition. Interestingly, fine or small roots recruited more diverse and species-rich microbial communities, very likely due to their better mineral contents (e.g., Mo, Fe, Mn, S, Zn, Cu, K, and P) and exposure with soil, though more research is needed to establish these relationships. Small roots and their rhizosphere environments showed a higher abundance of important bacterial taxa (e.g., Bradyrhizobium, Pseudomonas, Streptomyces, Burkholderia, Sphingomonas) that are previously known to play important roles in soil disease suppressiveness, plant growth, nutrient fixation, solubilization, and cycling. We suggest that linking microbial communities and their functions to root branching order and categories may enhance our understanding of rhizospheric interactions, soil disease suppressiveness, and their role in tree fruit performance.

The root system influences plant fitness, health, and productivity via its phenotypic traits (phenes) such as root length, biomass, density, volume, and surface area. Although these traits differentially impact the release of 20 to 80% of total photosynthates as root exudates, their role in influencing microbial communities in the rhizosphere and root environments is not clear. The root phenes or architecture significantly alter soil biophysical and edaphic properties such as aggregation, structure, pH, moisture, temperature, and nutrient stoichiometry (C:N, C:P, and N:P ratios, etc.). Meantime, the exteriors and interiors of various root types demonstrate a tremendous phenotypic plasticity in their cellular structure, anatomy, cell types, shapes, metabolisms and biochemical profiles. These heterogeneities in the rhizosphere and endosphere create micro-environments and ecological niches for diverse microbial species to foster beneficial rhizospheric interactions. Results from the root systems of some agricultural, forest and model plants suggest that root phenes selectively filter and recruit different microbial communities. However, microbial colonization of root and rhizosphere environments may also occur through vertical transmission. We suggest that plant breeders should nevertheless consider root phenome and biota while developing new cultivars. Linking root phenome to microbiome (or its functional traits) and crop management practices may enhance our understanding of rhizospheric interactions, and their role in developing climate-resilient rhizosphere ecosystems.

The phyllosphere supports a tremendous diversity of microbes and other organisms. However, little is known about the colonization and survival of pathogenic and beneficial bacteria alone or together in the phyllosphere across the whole plant life-cycle under herbivory, which hinders our ability to understand the role of phyllosphere bacteria on plant performance. We addressed these questions in experiments using four genetically and biogeographically diverse accessions of Arabidopsis thaliana, three ecologically important bacterial strains (Pseudomonas syringae DC3000, Xanthomonas campestris, both pathogens, and Bacillus cereus, plant beneficial) under common garden conditions that included fungus gnats (Bradysia spp.). Plants supported greater abundance of B. cereus over either pathogenic strain in the phyllosphere under such greenhouse conditions. However, the Arabidopsis accessions performed much better (i.e., early flowering, biomass, siliques, and seeds per plant) in the presence of pathogenic bacteria rather than in the presence of the plant beneficial B. cereus. As a group, the plants inoculated with any of the three bacteria (Pst DC3000, Xanthomonas, or Bacillus) all had a higher fitness than uninoculated controls under these conditions. These results suggest that the plants grown under the pressure of different natural enemies, such as pathogens and an herbivore together perform relatively better, probably because natural enemies induce host defense against each other. However, in general, a positive impact of Bacillus on plant performance under herbivory may be due to its plant-beneficial properties. In contrast, bacterial species in the mixture (all three together) performed poorer than as monocultures in their total abundance and host plant growth promotion, possibly due to negative interspecific interactions among the bacteria. However, bacterial species richness linearly promoted seed production in the host plants under these conditions, suggesting that natural enemies diversity may be beneficial from the host perspective. Collectively, these results highlight the importance of bacterial community composition on plant performance and bacterial abundance in the phyllosphere.

Understanding the mechanisms of microbiome species coexistence is one of the major challenges confronted by microbiome ecologists today. Recent research largely advocates that the niche, biogeographic, and neutral/stochastic processes interactively determine the microbiome community composition across spatio-temporal scales in the ecosystem. However, current research is mainly exploratory and descriptive, and it is still difficult to link the observed microbiome species or functional trait diversity patterns to the ecosystem functioning on local, regional, and global scales. Similarly, whether and how climate and land-use changes impact the patterns of microbiome functional ecology remains to be studied. Moreover, little is known about how climate and land-use changes are linked to evolution or loss of microbial functional traits. Future research should nevertheless investigate the patterns of microbiome functional diversity across the velocity of climate and land-use changes, and attempt to integrate the patterns with functions in broader contexts of functional traits and community ecology.

UNLABELLED:Acute myocardial infarction (AMI) triggers mobilization of bone marrow (BM)-derived stem/progenitor cells (BMSPCs) through poorly understood processes. Recently, we postulated a major role for bioactive lipids such as sphingosine-1 phosphate (S1P) in mobilization of BMSPCs into the peripheral blood (PB). We hypothesized that elevating S1P levels after AMI could augment BMSPC mobilization and enhance cardiac recovery after AMI. After AMI, elevating bioactive lipid levels was achieved by treating mice with the S1P lyase inhibitor tetrahydroxybutylimidazole (THI) for 3 days (starting at day 4 after AMI) to differentiate between stem cell mobilization and the known effects of S1P on myocardial ischemic pre- and postconditioning. Cardiac function was assessed using echocardiography, and myocardial scar size evolution was examined using cardiac magnetic resonance imaging. PB S1P and BMSPCs peaked at 5 days after AMI and returned to baseline levels within 10 days (p < .05 for 5 days vs. baseline). Elevated S1P paralleled a significant increase in circulating BMSPCs (p < .05 vs. controls). We observed a greater than twofold increase in plasma S1P and circulating BMSPCs after THI treatment. Mechanistically, enhanced BMSPC mobilization was associated with significant increases in angiogenesis, BM cell homing, cardiomyocytes, and c-Kit cell proliferation in THI-treated mice. Mice treated with THI demonstrated better recovery of cardiac functional parameters and a reduction in scar size. Pharmacological elevation of plasma bioactive lipids after AMI could contribute to BMSPC mobilization and could represent an attractive strategy for enhancing myocardial recovery and improving BMSC targeting. SIGNIFICANCE:Acute myocardial infarction (AMI) initiates innate immune and reparatory mechanisms through which bone marrow-derived stem/progenitor cells (BMSPCs) are mobilized toward the ischemic myocardium and contribute to myocardial regeneration. Although it is clear that the magnitude of BMSPC mobilization after AMI correlates with cardiac recovery, the molecular events driving BMSPC mobilization and homing are poorly understood. The present study confirms the role of bioactive lipids in BMSPC mobilization after AMI and proposes a new strategy that improves cardiac recovery. Inhibiting sphingosine-1 phosphate (S1P) lyase (SPL) allows for the augmentation of the plasma levels of S1P and stem cell mobilization. These findings demonstrate that early transient SPL inhibition after MI correlates with increased stem cell mobilization and their homing to the infarct border zones. Augmenting BMSPC mobilization correlated with the formation of new blood vessels and cardiomyocytes and c-Kit cell proliferation. These novel findings on the cellular level were associated with functional cardiac recovery, reduced adverse remodeling, and a decrease in scar size. Taken together, these data indicate that pharmacological elevation of bioactive lipid levels can be beneficial in the early phase after cardiac ischemic injury. These findings provide the first evidence that a carefully timed transient pharmacological upregulation of bioactive lipids after AMI could be therapeutic, because it results in significant cardiac structural and functional improvements.

Sixty-eight commercial and primitive cultivars belonging to aromatic (basmati), non-aromatic (coarse) and japonica type were used during present investigation. A considerable level of polymorphism was observed among aromatic, nonaromatic and japonica cultivars for the majority of the morphological characters measured. Cluster and principal component analyses were used to classify rice cultivars on the basis of phenotypic traits. Dendrogram was generated for the Euclidean distance and phenotypically all the cultivars were classified into three major groups corresponding to the forms of indica rice cultivated in Pakistan, i.e., aromatic (Basmati) and non-aromatic (Non-basmati) with few exceptions. Clustering of the cultivars did not show any pattern of association between the morphological characters and the origin of the cultivars. Instead cultivar groups were associated with their morphological similarities and type of indica rice cultivated in various regions of Pakistan. Regardless of the limitation in estimating total genetic variation, the current study indicated that agromorphological traits were helpful for preliminary characterization and can be used as a broad-spectrum approach to assess genetic diversity among morphologically distinguishable rice cultivars.

Grain proteins from 173 rice landraces (Oryza sativa L.) were electrophoretically separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Densitometric scanning of the electrophoretic profiles permitted the estimation of the relative concentration of 25 polypeptide fractions, which were used as variables for the calculation of similarity coefficients between these accessions. A considerable variation was observed in glutelin subunits and Wx gene product. Very low variation was observed in prolamin subunits. Lower genetic distance based on total seed protein profile may be attributed to narrow genetic base. This electrophoretically detectable protein polymorphism in rice grain can be used in further breeding proposes and variety development. Our results suggest that screening of landraces on the basis of variation in seed storage protein profile using SDS-PAGE could be highly effective tool to identify valuable rice genetic resources.

Cereal crops that have rigid non-cellulose components in the cell wall tissues of leaves and high starch and protein content in grains face limitations in DNA extraction. Advanced molecular genetic techniques such as mapping and marker-assisted selection programs require pure and quick DNA extraction. In this study, we developed methods for isolating high-quality genomic DNA from leaves and seeds of major cereal crops with minor modifications. DNA yields ranged from 300 to 1800 ng for 0.01 g seed or leaf tissue.

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice (Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection.

Information on genetic diversity and relationships among rice genotypes from Pakistan is currently very limited. Molecular marker analysis can truly be beneficial in analyzing the diversity of rice germplasm providing useful information to broaden the genetic base of modern rice cultivars. The objective of this study was to evaluate the genetic polymorphism of 75 rice accessions and improved cultivars using random amplified polymorphic DNA (RAPD) technique. Twenty-eight decamer-primers generated a total of 145 RAPD fragments, of which 116 (80%) were polymorphic. The number of amplification products produced by each primer varied from 3 to 9 with an average of 5.2 alleles primer(-1). The size of amplified fragments ranged from 250 to 4000bp. A dendrogram was generated from minimal variance algorithm using Ward method. All the 75 genotypes were grouped into two main groups corresponding to aromatic and non-aromatic types of indica rice. Clustering of accessions did not show any significant pattern of association between the RAPD fingerprints and collection sites. This type of analysis grouping different rice accessions in relation to fragrance, a major rice quality determinant, and varietal group is extremely useful to develop a core collection and gene bank management. Further more, the information revealed by the RAPDs regarding genetic variation is helpful to the plant breeder in selecting diverse parents and for future orientation of rice breeding program.

Genetic diversity was studied in 234 accessions of locally collected Brassica species for total seed protein content through sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). These accessions were collected from different locations of Pakistan. After the study of these accessions on SDS-PAGE, 28 reproducible bands were used for cluster analysis and with the help of these bands, genetic diversity were estimated. Out of 28, four major bands were observed. Dendogram was constructed and the accessions were divided into two main groups comprising 11 clusters. The results obtained from these clusters showed minimum genetic diversity in these accessions on SDS-PAGE level. Due to low genetic diversity on SDS-PAGE level, it is suggested that two dimensional (2D)-electrophoresis can be used for protein study.

The microsatellite or simple sequence repeat (SSR) marker analysis was done to determine the allelic diversity and relationship among thirty-five Asian cultivars of rice including 19 aromatic, 13 non-aromatic and 3 japonica type cultivars. A total of 144 alleles were detected at the 32 SSR loci, of which 141 (98%) were polymorphic. The number of alleles generated by each marker ranged from 2 to 13 with an average of 4.5 alleles per marker. The size of smallest and largest allele ranged from 8 (RM122) to as high as 71 (RM302). Polymorphism information content (PIC) values ranged between 0.157 (RM19, RM55) and 0.897 (RM70), with an average of 0.603 per marker. Basmati rice varieties amplified different alleles at 15 of the SSR loci than those in the japonica and/ or indica rice varieties. A number of SSRs were identified that could be utilized to differentiate between basmati and other non-basmati rice varieties. The RM252 and RM310 showed a clear differentiation of japonica cultivars from other ones. Pair-wise Nei and Li's similarity coefficients ranged from 0.19 to 0.90. The dendrogram based on the cluster analysis by microsatellite polymorphism, grouped 35 rice cultivars into two major groups effectively differentiating the tall, late maturing and slender aromatic cultivars from the short statured, early, short bold and long bold non-aromatic cultivars. These results could be useful for monitoring purity, genotype identification and for plant variety protection.