Bela Tiwari

Open software for biologists: from famine to feast.

Developing and deploying specialized computing systems for specific research communities is achievable, cost effective and has wide-ranging benefits.

Pyrosequencing of Mytilus galloprovincialis cDNAs: tissue-specific expression patterns.

Background Mytilus species are important in marine ecology and in environmental quality assessment, yet their molecular biology is poorly understood. Molecular aspects of their reproduction, hybridisation between species, mitochondrial inheritance, skewed sex ratios of offspring and adaptation to climatic and pollution factors are priority areas. Methodology/Principal Findings To start to address this situation, expressed genetic transcripts from M. galloprovincialis were pyrosequenced. Transcripts were isolated from the digestive gland, foot, gill and mantle of both male and female mussels. In total, 175,547 sequences were obtained and for foot and mantle, 90% of the sequences could be assembled into contiguous fragments but this reduced to 75% for the digestive gland and gill. Transcripts relating to protein metabolism and respiration dominated including ribosomal proteins, cytochrome oxidases and NADH dehydrogenase subunits. Tissue specific variation was identified in transcripts associated with mitochondrial energy metabolism, with the digestive gland and gill having the greatest transcript abundance. Using fragment recruitment it was also possible to identify sites of potential small RNAs involved in mitochondrial transcriptional regulation. Sex ratios based on Vitelline Envelop Receptor for Lysin and Vitelline Coat Lysin transcript abundances, indicated that an equal sex distribution was maintained. Taxonomic profiling of the M. galloprovincialis tissues highlighted an abundant microbial flora associated with the digestive gland. Profiling of the tissues for genes involved in intermediary metabolism demonstrated that the gill and digestive gland were more similar to each other than to the other two tissues, and specifically the foot transcriptome was most dissimilar. Conclusions Pyrosequencing has provided extensive genomic information for M. galloprovincialis and generated novel observations on expression of different tissues, mitochondria and associated microorganisms. It will also facilitate the much needed production of an oligonucleotide microarray for the organism.

Spatial scaling of arbuscular mycorrhizal fungal diversity is affected by farming practice

Evidence suggests that microbial communities show patterns of spatial scaling which can be driven by geographical distance and environmental heterogeneity. Here we demonstrate that human management can have a major impact on microbial distribution patterns at both the local and landscape scale. Mycorrhizal fungi are vital components of terrestrial ecosystems, forming a mutualistic symbiosis with plant roots which has a major impact on above ground ecology and productivity. We used contrasting agricultural systems to investigate the spatial scaling of the most widespread mycorrhizal fungus group, the arbuscular mycorrhizal fungi (AMF). Using multiple sampling sites with a maximum separation of 250 km we describe for the first time the roles which land management, environmental heterogeneity and geographical distance play in determining spatial patterns of microbial distribution. Analysis of AMF taxa-area relationships at each sampling site revealed that AMF diversity and spatial turnover was greater under organic relative to conventional farm management. At the regional scale (250 km) distance-decay analyses showed that there was significant change in AMF community composition with distance, and that this was greater under organic relative to conventional management. Environmental heterogeneity was found to be the major factor determining turnover of AMF taxa at the landscape scale. Overall we demonstrate that human management can play a key role in determining the turnover of microbial communities at both the local and regional scales.

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11–15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 fosmid was identified in a pooled shotgun sequence data set of 100 fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic fosmid libraries.

eGenomics: Genomes and the environment

As concerns over climate change, pollution andother anthropogenic changes to the environmentincrease, interest in finding new solutions forunderstanding and mitigating these conditions isgrowing. The emerging discipline of environmentalgenomics investigates how living organisms adaptto and are impacted by their environments, usinggenomic technologies. The UK Natural Environ-ment Research Council (NERC) funds environ-mental genomic research and has recently investedover £26 million in two science programmes inthis area: ‘Environmental Genomics’ and ‘Post-Genomics and Proteomics’. To support researchersworking in this area, NERC has created the NERCEnvironmental Bioinformatics Centre (