Bacterial 16S rDNA sequence data, incorporating sequences > 1 kb, were retrieved from published rumen library studies and public databases, then were combined and analysed to assess the diversity of the rumen microbial ecosystem as indicated by the pooled data. Low G+C Gram positive bacteria (54%) and the Cytophaga-Flexibacter-Bacteroides (40%) phyla were most abundantly represented. The diversity inferred by combining the datasets was much wider than inferred by individual studies, most likely due to different diets enriching for bacteria with different fermentative activities. A total of 341 operational taxonomic units (OTU) was predicted by the Chao1 non-parametric estimator approach. Phylogenetic and database analysis demonstrated that 89% of the diversity had greatest similarity to organisms which had not been cultivated, and that several sequences are likely to represent novel taxonomic groupings. Furthermore, of the 11% of the diversity represented by cultured isolates (> 95% 16S rDNA identity), not all of the bacteria were of ruminal origin. This study therefore reinforces the need to reconcile classical culture-based rumen microbiology with molecular ecological studies to determine the metabolic role of uncultivated species.

16 17 As the world's population increases, demands on staple crops like rice (Oryza sativa L.) will also 18 increase, requiring additional fresh water supplies for irrigation of rice fields. Safe alternate wetting 19 and drying (AWD) is a water management technique that is being adopted across a number of 20 countries to reduce the water input for rice cultivation. The impact of AWD on plant growth, yield 21 and grain quality is not well understood. A field trial of AWD was conducted at Mymensingh, 22 Bangladesh over two boro (dry) seasons using eight field plots, four under AWD and four 23 continuously flooded (CF). This manuscript describes the results of check cultivar BRRI dhan28 which 24 was replicated in 35-40 rows per plot giving a total of 140-160 replicates per treatment. A study on 25 the soil solution concentration of many elements indicated that manganese, iron, zinc, and arsenic 26 were different under AWD conditions compared to CF on a number of sampling time points, but did 27 not show a pattern related to the AWD treatment. A survey of soil strength using a penetrometer 28 detected a small, but significant, hardening of the surface soil of the AWD plots. At harvest the shoot 29 and grain mass was significantly greater for the plants grown under AWD (9.0-9.4% and 12.0-15.4%, 30 respectively) with the plants grown under AWD having a greater number of productive tillers. 31Physiological examination in the first year showed that although AWD decreased (~21%) leaf 32 elongation rate (LER) of recently transplanted seedlings during the first drying cycle, subsequent 33 drying cycles did not affect LER, while tillering was slightly increased by AWD and there was evidence 34 of higher leaf abscisic acid (ABA) in AWD plants. In the second year analysis of six phytohormones 35 revealed that AWD increased plant foliar iso-pentenyladenine (iP) concentrations by 37% while leaf 36 trans-zeatin concentrations decreased (36%) compared to CF plants. The elemental composition of 37 the shoots and grains was also examined. In both years AWD decreased grain concentration of 38 sulphur (by 4% and 15%), calcium (by 6% and 9%), iron (by 11% and 16%), and arsenic (by 14% and 39 26%), while it increased the grain concentration of manganese (by 19% and 28%), copper (by 81% 40 and 37%), and cadmium (by 28% and 67%). These results indicate that plants grown under safe AWD 41 conditions at this site have an increased grain mass compared to plants grown under CF, and this 42 may be partly due to a high number of productive tillers. AWD decreases the concentration of 43 arsenic in the grains in this site, but it elevates the concentration of cadmium. 44 45 Key words: Rice, alternate wetting and drying, arsenic, cadmium, pore water 46 48 between 35-60% of their dietary calorie intake (Fageria, 2007). Irrigated lowland rice systems 49 produce ~75% of global rice (Fageria, 2007). Producing high yield under irrigated systems requires 50 large quantities of water (Bouman, 2009). It is estimated that to produce 1 kg of rice gra...

Associations between proteins and RNA–RNA duplexes are important in post-transcriptional regulation of gene expression. The CLASH (Cross-linking, Ligation and Sequencing of Hybrids) technique captures RNA–RNA interactions by physically joining two RNA molecules associated with a protein complex into a single chimeric RNA molecule. These events are relatively rare and considerable effort is needed to detect a small number of chimeric sequences amongst millions of non-chimeric cDNA reads resulting from a CLASH experiment. We present the “hyb” bioinformatics pipeline, which we developed to analyse high-throughput cDNA sequencing data from CLASH experiments. Although primarily designed for use with AGO CLASH data, hyb can also be used for the detection and annotation of chimeric reads in other high-throughput sequencing datasets. We examined the sensitivity and specificity of chimera detection in a test dataset using the BLAST, BLAST+, BLAT, pBLAT and Bowtie2 read alignment programs. We obtained the most reliable results in the shortest time using a combination of preprocessing with Flexbar and subsequent read-mapping using Bowtie2. The “hyb” software is distributed under the GNU GPL (General Public License) and can be downloaded from https://github.com/gkudla/hyb.