Relationship between leaf vein traits of three dominant Quercus species and ecological factors in the Qinling Mountains, China.

We investigated the inter- and intra-species differences of leaf vein traits of three dominant Quercus species, Q. wutaishanica, Q. aliena var. acutiserrata, and Q. variabilis of Niubeiling (subtropical humid climate) and Taohuagou (warm temperate semi-humid climate), located in the eastern and western Qinling Mountains. The nine examined leaf vein traits included primary leaf vein width, secondary leaf vein width, mean fine vein width, primary vein density, fine vein density, vein areole diameter, areole density, 3D fine vein surface area, and fine vein volume. We further elucidated the influencing mechanisms and regulatory pathways of biotic and abiotic factors on leaf vein traits. The results showed that species identity had significant effects on eight out of nine leaf vein traits except 3D fine vein surface area, while habitat had significant effects on primary leaf vein width, secondary leaf vein width, vein areole diameter, fine vein density, and areole density. Altitude had significant effects on primary vein density, mean fine vein width, vein areole diameter, fine vein density and areole density. Habitat, tree species identity, and altitude had significantly interactive effects on primary leaf vein density, 3D fine vein surface area, and fine vein volume. There were significant differences in primary leaf vein width, mean fine vein width, areole density, 3D fine vein surface area, fine vein volume, primary vein density of Q. wutaishanica between the two studied habitats, but the differences were only found in secondary leaf vein width and areole density of Q. aliena var. acutiserrata and Q. variabilis. The examined leaf vein traits were influenced both by biotic and abiotic factors, with varying effect sizes. Among the biotic factors, petiole length, leaf length and width ratio had strong effect on leaf vein traits. Among the abiotic factors, climatic and soil factors had high effect size on vein traits, with the former being higher than the latter. Leaf vein traits were affected directly by biotic factors, but indirectly by abiotic factors (soil and climatic factors) via regulating biotic factors (leaf stoichiometry and leaf phenotypic traits).

Antibiotics and antibiotic resistance gene dynamics in the composting of antibiotic fermentation waste - A review.

Fate of antibiotics and antibiotic resistance genes (ARGs) during composting of antibiotic fermentation waste (AFW) is a major concern. This review article focuses on recent literature published on this subject. The key findings are that antibiotics can be removed effectively during AFW composting, with higher temperatures, appropriate bulking agents, and suitable pretreatments improving their degradation. ARGs dynamics during composting are related to bacteria and mobile genetic elements (MGEs). Higher temperatures, suitable bulking agents and an appropriate C/N ratio (30:1) lead to more efficient removal of ARGs/MGEs by shaping the bacterial composition. Keeping materials dry (moisture less than 30%) and maintaining pH stable around 7.5 after composting could inhibit the rebound of ARGs. Overall, safer utilization of AFW can be realized by optimizing composting conditions. However, further removal of antibiotics and ARGs at low levels, degradation mechanism of antibiotics, and spread mechanism of ARGs during AFW composting require further investigation.

Quantifying health risks of plastisphere antibiotic resistome and deciphering driving mechanisms in an urbanizing watershed.

Microplastics (MPs) ubiquitous in environments promote the dissemination of antibiotic resistance genes (ARGs), threatening ecosystem safety and human health. However, quantitative assessments of the health risks of ARGs (HRA) in plastisphere and an in-depth exploration of their driving mechanisms are still lacking. Here, the microbiomes, ARGs, and community assembly processes of five types of MPs in an urbanizing watershed were systematically investigated. By fully considering the abundance, clinical availability, human pathogenicity, human accessibility, and mobility of 660 ARGs in plastisphere, the HRA on MPs were quantified and compared. Polyethylene had the highest HRA among the five MP types, and urbanization further increased its risk index. In addition to abiotic factors, more complex biotic factors have been shown to drive HRA in plastisphere. Specifically, dispersal limitation accounted for the increasing diversity and interaction of bacteria that determined HRA in plastisphere. Further analysis of metabolic functions indicated that a higher HRA was accompanied by decreased normal metabolic functions of plastisphere microbiota due to the higher fitness costs of ARGs. This study advances the quantitative surveillance of HRA in plastisphere and understanding of its driving mechanisms. This will be helpful for the management of both MPs and ARGs treatments for human health.

Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns.

Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.

Knockdown of GmD53a confers strigolactones mediated rhizobia interaction and promotes nodulation in soybean.

BACKGROUND: Strigolactones (SLs) play a key role in modulating plant root growth, shoot branching, and plant-symbiont interaction. However, despite their significance, the components of SL biosynthesis and signaling in soybean and their role in soybean-rhizobia interaction is unknown. METHODS: In this study, we identified and functionally characterized the GmD53a from soybean. The GmD53a ORFs were amplified from root cDNA using primers for GmD53a RNA interference. To induce transgenic hairy roots of soybean, electric shock was used to transform pB7WG1WG2 vectors containing GmD53a knockdown and GUS into K599 strains of Agrobacterium rhizogenes. The hairy roots and nodules were collected and examined for root nodules ratio and RNA was extracted after 4 weeks of rhizobia inoculation. RESULTS: A tissue-specific expression assay showed that GmD53a was differentially expressed in plant parts, predominantly in the stem and nodule. Furthermore, its expression was significantly up-regulated during rhizobia infection and varied with nodule formation. The GmD53a-knockdown chimerical plants were produced to further check its role in soybean nodulation in comparison with control GUS. In knockdown lines, the GmD53a (suppressor of strigolactone MAX2) has a higher number of nodules compared to control lines. Furthermore, the expression levels of several nodulation genes essential for initiation and formation of nodules were altered in GmD53a-knockdown lines. CONCLUSION: The results revealed that SL biosynthesis and signaling are not conserved but also have close interaction between SL and legume rhizobia.

[Non-structural carbohydrate content of trees and its influencing factors at multiple spatial-temporal scales: A review]. / æ ‘æœ¨éžç»“æž„æ€§ç¢³æ°´åŒ–åˆç‰©å«é‡å¤šæ—¶ç©ºå°ºåº¦å˜åŒ–ç‰¹å¾åŠå ¶å½±å“å› ç´ ç ”ç©¶è¿›å±•.

Non-structural carbohydrates (NSC) are essential substances for the tree growth and metabolism, and play an important role in environmental adaptation of trees. At temporal scale, NSC contents in trees have limited inter-annual variation, which could be attributed to the strategy of tree growth and carbon storage. Different factors influence NSC contents of trees in various climatic regions, which change substantially at the seasonal scale. At spatial scale, the variations of NSC content in trees show an insignificantly decreasing trend with the decreases of latitude at global and continental scales, which are mainly related to the hydrothermal gradients. The trend at regional scale is opposite because of the decrease of hydrothermal gradients and lower sample frequency. More sophisticated relations exist between the variations of NSC content in trees and altitudes, which are caused by species-specific characteristics and the variations of micro-habitat conditions. The variations of NSC content in trees at multiple spatial-temporal scales are generally determined by both biotic and abiotic factors, which are mainly dependent on the tradeoff among photosynthate production, respiratory depletion, and tree growth. Furthermore, the methods used for the determination of NSC content are different, which results in great uncertainties in comparing conclusions from different studies. The methods used for sample collection and measurement of NSC should be improved and unified to enhance the comparison among different studies. The NSC contents of trees in different age classes should be measured with all organs collected at multiple spatial-temporal scales. The underlying mechanisms, significance of NSC storage, transformation and allocation on tree growth and survival should be further discussed.

Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique.

The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling in forest soils. However, our knowledge of WIF richness and distribution patterns in different forest biomes is limited. Here, we used pyrotag sequencing of the fungal internal transcribed spacer (ITS2) region to characterize the deadwood mycobiome of two tree species with greatly different wood characteristics (Schima superba and Pinus massoniana) in a Chinese subtropical forest ecosystem. Specifically, we tested (i) the effects of tree species and wood quality properties on WIF OTU richness and community composition; (ii) the role of biotic and abiotic factors in shaping the WIF communities; and (iii) the relationship between WIF OTU richness, community composition and decomposition rates. Due to different wood chemical properties, we hypothesized that the WIF communities derived from the two tree species would be correlated differently with biotic and abiotic factors. Our results show that deadwood in subtropical forests harbors diverse fungal communities comprising six ecological functional groups. We found interesting colonization patterns for this subtropical biome, where Resinicium spp. were highly detected in both broadleaved and coniferous deadwood. In addition, the members of Xylariales were frequently found in Schima. The two deadwood species differed significantly in WIF OTU richness (Pinus > Schima) and community composition (P < 0.001). Variations in WIF community composition of both tree species were significantly explained by wood pH and ecological factors (biotic: deadwood species, basal area and abiotic: soil pH), but the WIF communities derived from each tree species correlated differently with abiotic factors. Interestingly, we found that deadwood decomposition rate significantly correlated with WIF communities and negatively correlated with WIF OTU richness. We conclude that the pattern of WIF OTU richness and community composition are controlled by multiple interacting biotic and abiotic factors. Overall, our study provides an in-depth picture of the deadwood mycobiome in this subtropical forest. Furthermore, by comparing our results to results from temperate and boreal forests we contribute to a better understanding of patterns of WIF communities across different biomes and geographic locations.

Identification and characterization of phages parasitic on bradyrhizobia nodulating groundnut (Arachis hypogaea L.) in South Africa.

In this study, three lytic phages (namely, PRSA-1, PRSA-2 and PRSA-26) were isolated and characterized for their morphology, host range, profile and restriction endonuclease banding pattern of genome size. The susceptible rhizobial isolates were identified by nifH and glnII sequence analysis. The results showed that all phages had polyhedral head with non-contractile tail which confirmed their relationship with the Siphoviridae family. All the three phages produced highly distinct plaques on their host bradyrhizobial lawn, and were highly sensitive to chloroform. The phage genome sizes ranged from 34.7 to 53.1 kbp. The phages were tested against groundnut-nodulating bradyrhizobial strains TUTAHSA75, TUTAHSA155 and TUTAHSA126 isolated from South African soils. The results revealed different bacterial susceptibilities to phages. Bradyrhizobial isolate TUTAHSA126 was susceptible to all three phages (i.e. PRSA-1, PRSA-2 and PRSA-26), TUTAHSA155 to two phages (i.e. PRSA-1, PRSA-2), and TUTAHSA75 to only one phage (i.e. PRSA-1). Phylogenetic analysis of nifH and glnII gene sequences of the phage-susceptible bradyrhizobial isolates revealed their close relatedness to a diverse group of Bradyrhizobium species. Phage PRSA-1 could parasitize on all three bradyrhizobial strains, which indicates its potential role in horizontal gene transfer through lysogenic conversion, and/or genetic transduction in soil microbial environments.

Regeneration complexities of Pinus gerardiana in dry temperate forests of Indian Himalaya.

Pinus gerardiana is considered an important species in dry temperate forests of North-Western Indian Himalaya because of its influence on ecological processes and economic dependence of local people in the region. But, large numbers of biotic and abiotic factors have affected P. gerardiana in these forests; hence, there is a crucial need to understand the regeneration dynamics of this tree species. The present investigation was conducted in P. gerardiana forests to understand vegetation pattern and regeneration processes on different sites in the region. Statistical analysis was performed to know variability in growing stock and regeneration on sample plots, while correlation coefficients and regression models were developed to find the relationship between regeneration and site factors. The vegetation study showed dominance of P. gerardiana, which is followed by Cedrus deodara, Pinus wallichiana and Quercus ilex in the region. The growing stock of P. gerardiana showed steep increasing and then steadily declining trend from lower to higher diameter class. The distribution of seedling, sapling, pole and trees was not uniform at different sites and less number of plots in each site were observed to have effective conditions for continuous regeneration, but mostly showed extremely limited regeneration. Regeneration success ranging from 8.44 to 15.93 % was recorded in different sites of the region, which suggests that in different sites regeneration success is influenced by collection of cone for extracting seed, grazing/browsing and physico-chemical properties of soil. Regeneration success showed significant correlation and relationship with most of abiotic and biotic factors. The regeneration success is lower than the requirement of sustainable forest, but varies widely among sites in dry temperate forests of Himalaya. More forest surveys are required to understand the conditions necessary for greater success of P. gerardiana in the region.

Exploring valid reference genes for quantitative real-time PCR analysis in Plutella xylostella (Lepidoptera: Plutellidae).

Quantitative real-time PCR (qRT-PCR), a primary tool in gene expression analysis, requires an appropriate normalization strategy to control for variation among samples. The best option is to compare the mRNA level of a target gene with that of reference gene(s) whose expression level is stable across various experimental conditions. In this study, expression profiles of eight candidate reference genes from the diamondback moth, Plutella xylostella, were evaluated under diverse experimental conditions. RefFinder, a web-based analysis tool, integrates four major computational programs including geNorm, Normfinder, BestKeeper, and the comparative ΔCt method to comprehensively rank the tested candidate genes. Elongation factor 1 (EF1) was the most suited reference gene for the biotic factors (development stage, tissue, and strain). In contrast, although appropriate reference gene(s) do exist for several abiotic factors (temperature, photoperiod, insecticide, and mechanical injury), we were not able to identify a single universal reference gene. Nevertheless, a suite of candidate reference genes were specifically recommended for selected experimental conditions. Our finding is the first step toward establishing a standardized qRT-PCR analysis of this agriculturally important insect pest.

Métodos y usos agrícolas de la ingeniería genética aplicada al cultivo del arroz / Methods and agricultural uses of genetic engineering applied to rice crop

En biotecnología de arroz se han logrado avances en transformación genética, con importantes resultados en el mejoramiento genético de variedades elite de las subespecies japónica e índica. Con el propósito de revisar los métodos y los usos agrícolas de la ingeniería genética aplicada al cultivo del arroz, se usaron varias palabras claves en idioma inglés en algunas de las bases de datos de revistas científicas indexadas, disponibles en el Sistema Nacional de Bibliotecas de la Universidad Nacional de Colombia (SINAB), seleccionando documentos publicados entre 2000 y 2011. La base de esta revisión inicial, se complementó con artículos publicados en fechas anteriores, que se consideraron relevantes, debido a que implicaban cambios metodológicos importantes. Desde que se logró producir la primera planta transgénica de arroz a finales de los 80´s, varios protocolos para la transferencia de genes se han empleado con éxito logrando la modificación genética de más de 60 cultivares de arroz. Para ello se han empleado sistemas de transformación tanto directos como indirectos. Se han realizado modificaciones de rasgos importantes en el cultivo, tales como la resistencia a factores bióticos (insectos, hongos, bacterias, virus, nematodos), tolerancia a factores abióticos (salinidad, sequía, altas y bajas temperaturas, inmersión), y mejoramiento de características agronómicas (calidad nutricional, rendimiento, uso de nutrientes, tolerancia a herbicidas).

In rice biotechnology advances have been made in genetic transformation, with significant results in breeding elite varieties of japonica and indica subspecies. In order to review the methods and agricultural uses of genetic engineering applied to rice, calves were used several words in English in some of the databases of scientific journals available in the National Libraries National University of Colombia (SINAB), selecting papers published between 2000 and 2011. Based on this initial review, it addition to some articles published at earlier dates, which were considered relevant because they involved significant methodological changes. Since it was able to produce the first transgenic rice plant in the late 80's, several protocols for gene transfer have been used successfully achieving the genetic modification of more than 60 rice cultivars. For this transformation systems have been used both direct and indirect. There have been significant changes in the crop traits such as resistance to biotic (insects, fungi, bacteria, viruses, nematodes), tolerance to abiotic (salinity, drought, high and low temperatures, immersion), improved features agronomic (nutritional quality, yield, nutrient use, herbicide tolerance).