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Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.

Soil fungi, protists, and animals (i.e., the eukaryome) play a critical role in key ecosystem functions in terrestrial ecosystems. Yet, we lack a holistic understanding of the processes shaping the global distribution of the eukaryome. We conducted a molecular analysis of 193 composite soil samples spanning the world's major biomes. Our analysis showed that the importance of selection processes was higher in the community assemblage of smaller-bodied and wider niche breadth organisms. Soil pH and mean annual precipitation were the primary determinants of the community structure of eukaryotic microbes and animals, respectively. We further found contrasting latitudinal diversity patterns and strengths for soil eukaryotic microbes and animals. Our results point to a potential link between body size and niche breadth of soil eukaryotes and the relative effect of ecological processes and environmental factors in driving their biogeographic patterns.

There were errors in the name of author László G. Nagy and in affiliation no. 31 in the original publication. The original article has been corrected.

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.

Occurrence of chalkiness in rice is attributed to genetic and environmental factors, especially high temperature (HT). Te HT induces heat stress, which in turn compromises many grain qualities, especially transparency. Chalkiness in rice is commonly studied together with other quality traits such as amylose content, gel consistency, and protein storage. In addition to the fundamental QTLs, some other QTLs have been identifed which accelerate chalkiness occurrence under HT condition. In this review, some of the relatively stable chalkiness, amylose content, and gel consistency related QTLs have been presented well. Genetically, HT efect on chalkiness is explained by the location of certain chalkiness gene in the vicinity of high-temperature responsive genes. With regard to stable QTL distribution and availability of potential material resources, there is still feasibility to find out novel stable QTLs related to chalkiness under HT condition. A better understanding of those achievements is essential to develop new rice varieties with a reduced chalky grain percentage. Therefore, we propose the pyramiding of relatively stable and nonallelic QTLs controlling low chalkiness endosperm into adaptable rice varieties as pragmatic approach to mitigate HT effect

The effects of deficit irrigation technique on growth and fruit quality of roselle (Hibiscus sabdariffa L.) was observed. The result shows that minimum weight of the yield was obtained from treatment grown with well watered (WW) condition. Plant height was affected by reduction of water application. Regulated deficit irrigation (RDI) tended to decrease all means of growth parameter except stem fresh and dry weight. RDI shows significant effect on yields, where the reduction of 50% water produce more fruits compared to control plants. The impact of RDI was not significant effect on physiological change of roselle. Thus, RDI could be a feasible technique for Roselle production as it saves large amounts of water with reduction on plant growth but increase the yield as compared to well watered (WW) of roselle.

The experiment consisted of five treatments of fermented plant juice (FPJ) and fermented fruit juice (FFJ). The treated plants with FPJ and FFJ produced early flowers and fruits compared to untreated plants due to the enhanced production of auxin and essential nutrients. Total soluble solids were also observed to increase after 10 weeks of FPJ and FFJ application. Photosynthesis rate increased in all treatments except T3; while transpiration rate increased only at T4 compared to control. The findings we clearly suggested to use both combinations as FPJ water spinach for enhancing the vegetative growth of tomato plants than FPJ bamboo shoots (T3 and T5), while FFJ pineapple for better reproductive development of tomato plants rather than FFJ banana (T5) for ensuring future sustainable eco-friendly agriculture practices.

Study was conducted to evaluate the effects of two types of fertilizers (SRI and Kamila) on growth and physiological changes of MD2 pineapple. Results showed significant changes to the growth of the MD2 pineapple due to either use of soil with NPK or in combination. Application of NPK and SRI fertilizers showed the best performance on plant height and width from beginning until 10 weeks after treatment (WAT) while for leaf length fertilizer-Kamila combination showed the best performance until 10 WAT. Equally for the chlorophyll content, the treatment Kamila also showed the best performance at 6 MAT. Analysis of leaf of the pineapple plant showed that there was a decrease in nutrient content of most the elements in 3 MAT. But for nutrient analysis of soil, the outcomes showed that at 3 MAT the nutrients content increased especially in treatment of Kamila fertilizer combination. The nutrient contents of most of the elements were also very low from what has been expected, but the result of nutrient content in soil treated with Kamila - a controlled-release fertilizer showed a good result. Addition of controlled release fertilizer (Kamila) with SRI formulation showed positive improvement in the plant growth of pineapple variety MD2 compared to the plants without SRI formulation.

The application of indigenous microorganism (IMO) and system of rice intensification (SRI) Anak formulation on growth and nutrient uptake of rice variety MR219 at nursery level was carried out. Results showed the highest plant height, leaf area, fresh and dry weight of rice variety MR219 when treated with IMO and SRI Anak formulation. Accumulation of N, P and K content in leaf and root tissue is much affected by spraying with SRI formulation. IMO had less influence in increasing the nutrient content in leaf and root tissue at nursery level. IMO and SRI formulation is potentially to be used as bio-fertilizer and bio-regulator to reduce environmental problems.

The physico-chemical properties of abscisic acid (ABA) and IAA treated roselle calyces stored in different storage temperature was determined in this study. Mature roselle was dipped in distilled water (control),10-4 mol/l of ABA and 10-4mol/l of IAA for 5 minutes. All treated calyces were kept at ambient temperature (23°C) for 4 days, or stored at cold storage (10°C) for 8 days. Low temperature (10°C) can prolong the shelf life of roselle about 4 days longer than ambient storage (23°C). However, plant growth regulator (ABA or IAA) only showed minimal effect on quality and shelf life of roselle. Therefore,the application of higher concentration of ABA or IAA as well as dipping for more than 5 minutes can influence the postharvest quality and shelf life of roselle calyces, respectively.

Today, there is a collection of a tremendous amount of bio-data because of the computerized applications worldwide. Therefore, scholars have been encouraged to develop effective methods to extract the hidden knowledge in these data. Consequently, a challenging and valuable area for research in artificial intelligence has been created. Bioinformatics creates heuristic approaches and complex algorithms using artificial intelligence and information technology in order to solve biological problems. Intelligent implication of the data can accelerate biological knowledge discovery. Data mining, as biology intelligence, attempts to find reliable, new, useful and meaningful patterns in huge amounts of data. Hence, there is a high potential to raise the interaction between artificial intelligence and bio-data mining. The present paper argues how artificial intelligence can assist bio-data analysis and gives an up-to-date review of different applications of bio-data mining. It also highlights some future perspectives of data mining in bioinformatics that can inspire further developments of data mining instruments. Important and new techniques are critically discussed for intelligent knowledge discovery of different types of row datasets with applicable examples in human, plant and animal sciences. Finally, a broad perception of this hot topic in data science is given.

This study was undertaken to determine the effects of varied salinity regimes on the morphological traits (plant height, number of leaves, number of flowers, fresh and dry weight) and major mineral composition of 13 selected purslane accessions. Most of the morphological traits measured were reduced at varied salinity levels (0.0, 8, 16, 24 and 32 dS m-1), but plant height was found to increase in Ac1 at 16 dS m-1 salinity, and Ac13 was the most affected accession. The highest reductions in the number of leaves and number of flowers were recorded in Ac13 at 32 dS m-1 salinity compared to the control. The highest fresh and dry weight reductions were noted in Ac8 and Ac6, respectively, at 32 dS m-1 salinity, whereas the highest increase in both fresh and dry weight was recorded in Ac9 at 24 dS m-1 salinity compared to the control. In contrast, at lower salinity levels, all of the measured mineral levels were found to increase and later decrease with increasing salinity, but the performance of different accessions was different depending on the salinity level. A dendrogram was also constructed by UPGMA based on the morphological traits and mineral compositions, in which the 13 accessions were grouped into 5 clusters, indicating greater diversity among them. A three-dimensional principal component analysis also confirmed the output of grouping from cluster analysis.

Segregation distortion analysis in plant breeding is highly important because deviation factors are occasionally serious barriers for introgression of genes of interest into cultivated species. Also, the identification of major QTLs by high linkage disequilibrium is highly useful for breeders in order for crop improvement programs and the further fine mapping of particular genes. Consequently, simultaneous consideration of segregation distortion and linkage disequilibrium leads to developing fertile hybrids and normal inheritance of agronomically favorable genes. Hence, the goal of this study was to investigate genomic regions known to contain fragrance quantitative trait loci (QTLs) in terms of segregation distortion and linkage disequilibrium pattern, and to seek for a possible relationship between them using codominant markers on chromosomes 3, 4, and 8 in a set containing 189 F2 progenies. For the first time, we discovered the presence and extent of segregation distortion and linkage disequilibrium across the fragrance chromosomal areas of rice. The high frequency of skewed allelic segregations in the chromosomes 3 and 4 supports reports of possible gametic selection (ga) and hybrid sterility (S) genes. Finally, the highest linkage disequilibrium values, the lowest recombination frequency, and the shortest distances were observed in the chromosomal regions without segregation distortion. High linkage disequilibrium correlations between markers at short distances may show that such markers can maintain high linkage disequilibrium with linked QTLs and are influential for both MAS and QTL mapping analysis. Moreover, an indirect relationship between segregation distortion and linkage disequilibrium was detected, and thus linkage disequilibrium maps were introduced as useful diagnostic tools for segregation distortion.

Tinospora tuberculata Beumee is an aromatic shrub with pharmacological properties and belongs to the Menispermaceae family. We assessed T. tuberculata for its ability to suppress growth of weeds in rice fields. In seedling bioassays, the rate of seed germination and the radicle and hypocotyl lengths of barnyardgrass, rice and weedy rice seedlings were reduced as the concentration of aqueous water extracts and volatile organic compounds increased compared to the control. In a glasshouse experiment, T. tuberculata leaf powder also exhibited effective reduction in the emergence and growth of weeds in rice fields. Applications at rates of 4 t ha− 1 completely suppressed emergence of barnyardgrass, sprangletop and smallflower umbrella. The chemical compositions of extracts and volatiles were analyzed by GC–MS and HS-SPME-GC–MS. The results showed that 7 of 43 components in the leaf aqueous extract, as compared to 5 of 15 compounds in the stem aqueous extract, are known to be toxic compounds. Moreover, eight main volatile organic compounds were identified, which accounted for 97 and 95% of the whole fresh and dry leaf volatiles, respectively. We observed qualitative and quantitative differences in the compounds present in the dry and fresh leaf. Confocal laser scanning microscope images showed that the volatile emissions and aqueous extracts also inhibited the main root diameter, and the number and elongation of root hairs of tested weeds in rice fields. These results suggest that T. tuberculata contains a significant source of plant growth inhibitors. Hence, it can be used as a mulch to suppress weeds in rice fields and for developing new herbicide based on phytotoxic compounds release by this plant.

MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with ‘MR84’, a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223–SCU015RM (1.63 cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars.

Segregation distortion analysis in plant breeding is highly important because deviation factors are occasionally serious barriers for introgression of genes of interest into cultivated species. Also, the identification of major QTLs by high linkage disequilibrium is highly useful for breeders in order for crop improvement programs and the further fine mapping of particular genes. Consequently, simultaneous consideration of segregation distortion and linkage disequilibrium leads to developing fertile hybrids and normal inheritance of agronomically favorable genes. Hence, the goal of this study was to investigate genomic regions known to contain fragrance quantitative trait loci (QTLs) in terms of segregation distortion and linkage disequilibrium pattern, and to seek for a possible relationship between them using codominant markers on chromosomes 3, 4, and 8 in a set containing 189 F2 progenies. For the first time, we discovered the presence and extent of segregation distortion and linkage disequilibrium across the fragrance chromosomal areas of rice. The high frequency of skewed allelic segregations in the chromosomes 3 and 4 supports reports of possible gametic selection (ga) and hybrid sterility (S) genes. Finally, the highest linkage disequilibrium values, the lowest recombination frequency, and the shortest distances were observed in the chromosomal regions without segregation distortion. High linkage disequilibrium correlations between markers at short distances may show that such markers can maintain high linkage disequilibrium with linked QTLs and are influential for both MAS and QTL mapping analysis. Moreover, an indirect relationship between segregation distortion and linkage disequilibrium was detected, and thus linkage disequilibrium maps were introduced as useful diagnostic tools for segregation distortion.

Herbicides produce a wide range of toxic side-effects that pose a potential hazard to the environment. The development of natural herbicide is one method of addressing these issues. Tinospora tuberculata is an aromatic shrub with pharmacological properties and belongs to the Menispermaceae family. Herbicidal potential of aerial parts of T.tuberculata on germination and seedling growth of rice (Oryza sativa L.) and two rice weeds, barnyardgrass (Echinochloa crus-galli L.) and weedy rice (Oryza sativa L.complex) were evaluated. Six concentrations of methanol and water extract (3.12, 6.25, 12.5, 25, 50, and 100 g L−1) were compared with the control (distilled water). The magnitude of the phytotoxicity effects at the same concentration levels in the test plants was dependent on the source of the extract (either leaf or stem) and types of solvent (water or methanol). Leaf extract was found to have greater suppressive property than the stem extract and the methanol extracts of leaf and stem were present in higher phytotoxic compared with respective water extracts. The gas chromatography–mass spectrometry (GC-MS) and ultra-fast liquid chromatography (UFLC) analysis confirmed methanol extracts and leaf extracts contained higher number and amount of chemical compounds than did those of the water extracts and stem extracts, respectively. Benzoic acid (highest allelopathic activity) was found in the highest concentration in the methanol leaf extract,while this compound was not identified in the water leaf extract. On the other hand, the predominant compound was orientin (lowest allelopathic activity) from stem extracts. Therefore, the herbicidal activity of each extract (leaf methanol extract, leaf water extract, stem methanol extract, and stem water extract) was dependent on their number, concentration, combination and inhibitory activity of the compounds. In the glasshouse experiments, allelopathic potential of powder and methanol extract of T. tuberculata leaf as pre emerge

A glasshouse experiment was conducted in Universiti Putra Malaysia (UPM) to evaluate the regeneration and yield potential in purslane using both seeds and stem cuttings of 20 collected accessions from different locations in Western Peninsular Malaysia. Analysis results revealed significant variations (P< 0.05) for morphological traits viz., plant height, number of main branches, number of nodes, internodal distance, stem diameter, number of leaves, leaf area, number of flowers, root length, fresh and dry weight but no significant difference were observed for physiological traits viz., total chlorophyll, net photosynthesis, stomatal conductance, transpiration, water vapor deficit and for either major micro or macro minerals. Hope our research findings will eliminate the doubt of using cutting methods for purslane propagation and cultivation among producers and consumers and will promote their determination to follow purslane production in this summer at any season and anywhere. To the best of our knowledge, this is the first attempt to evaluate and to detect any significant variations arising in morphological, physiological, and especially mineral nutrition in purslane propagated through cuttings vs. through seeds.