Day-length is central to maintaining consistent seasonal diversity in marine bacterioplankton

Marine bacterial diversity is vast, but seasonal variation in diversity is poorly understood. Here we present the longest bacterial diversity time series consisting of monthly (72) samples from the western English Channel over a 6 year period (2003-2008) using 747,494 16SrDNA-V6 amplicon-pyrosequences. Although there were characteristic cycles for each phylum, the overall community cycle was remarkably stable year after year. The majority of taxa were not abundant, although on occasion these rare bacteria could dominate the assemblage. Bacterial diversity peaked at the winter solstice and showed remarkable synchronicity with day-length, which had the best explanatory power compared to a combination of other variables (including temperature and nutrient concentrations). Day-length has not previously been recognised as a major force in structuring microbial communities

Bias in culture-independent assessments of microbial biodiversity in the global ocean

On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has 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 SAR 11 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 sequenced data set of 100 fosmid clones. This under-representation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation; functional metabolic profiling and fragment recruitment. Analysis revealed a similar under-representation of low-GC Flavobacteriaceae. We speculate that the fosmid bias may be due to DNA fragmentation during preparation due to the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that while fosmid libraries can be extremely useful, caution must be used when directly inferring community composition from metagenomic fosmid libraries

Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes

Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques

Marine phytoplankton in a high CO2 world

Marine phytoplankton is responsible for ~50% of global primary productivity, it supports the oceanic food web and affects biogeochemical cycles. I participated in a large mesocosm experiment that observed altered community structure and carbon drawdown in response to increased CO2. There was a 27% reduction in community primary production at the peak of an Emiliania huxleyi-dominated bloom in mesocosms initially at 760 ppm CO2 compared to present day pCO2. There were changes in community structure but not dominance; Synechococcus and large pico-eukaryote abundances were reduced by ~60%, E. huxleyi was reduced by ~50%. A number of E. huxleyi strains persisted throughout the experiment in both treatments and no malformation or significant change in lith size occurred at increased CO2. In a second field experiment in the oligotrophic ocean off the Canary Islands, 760 ppm pCO2 did not change community structure or cell division rates of Synechococcus, Prochlorococcus or pico-eukaryotes.In laboratory experiments, I maintained the diatom, Thalassiosira pseudonana CCMP1335 at 760 ppm and present day pCO2 for ~100 generations in gas equilibrated continuous cultures – one of the longest experiments that has been attempted to investigate the effect of increased CO2 on marine phytoplankton. No clear evidence of adaptation or acclimation to increased CO2 was found, neither were there consistent changes in transcription of RuBisCO or carbonic anhydrase genes. Non-calcified E. huxleyi CCMP1516 and calcified CCMP371 grown in gas equilibrated semi-continuous cultures for several weeks showed no change in cell division rate at 760 ppm CO2. An understanding of the underlying changes in communities is required for modelling responses to increasing CO2, molecular tools may prove useful for this task. The strong community response in the mesocosms shows that rising atmospheric CO2 can greatly affect phytoplankton productivity and biogeochemical cycling.EThOS - Electronic Theses Online ServiceNatural Environment Research CouncilGBUnited Kingdo

The Response of Thalassiosira pseudonana to Long-Term Exposure to Increased CO2 and Decreased pH

The effect of ocean acidification conditions has been investigated in cultures of the diatom Thalassiosira pseudonana CCMP1335. Expected end-of-the-century pCO2 (aq) concentrations of 760 µatm (equivalent to pH 7.8) were compared with present-day condition (380 µatm CO2, pH 8.1). Batch culture pH changed rapidly because of CO2 (aq) assimilation and pH targets of 7.8 and 8.1 could not be sustained. Long-term (∼100 generation) pH-auxostat, continuous cultures could be maintained at target pH when cell density was kept low (<2×105 cells mL−1). After 3 months continuous culture, the C:N ratio was slightly decreased under high CO2 conditions and red fluorescence per cell was slightly increased. However, no change was detected in photosynthetic efficiency (Fv/Fm) or functional cross section of PS II (σPSII). Elevated pCO2 has been predicted to be beneficial to diatoms due to reduced cost of carbon concentration mechanisms. There was reduced transcription of one putative δ-carbonic anhydrase (CA-4) after 3 months growth at increased CO2 but 3 other δ-CAs and the small subunit of RUBISCO showed no change. There was no evidence of adaptation or clade selection of T. pseudonana after ∼100 generations at elevated CO2. On the basis of this long-term culture, pH change of this magnitude in the future ocean may have little effect on T. pseudonana in the absence of genetic adaption

Change in Emiliania huxleyi virus assemblage diversity but not in host genetic composition during an ocean acidification mesocosm experiment

Effects of elevated pCO2 on Emiliania huxleyi genetic diversity and the viruses that infect E. huxleyi (EhVs) have been investigated in large volume enclosures in a Norwegian fjord. Triplicate enclosures were bubbled with air enriched with CO2 to 760 ppmv whilst the other three enclosures were bubbled with air at ambient pCO2; phytoplankton growth was initiated by the addition of nitrate and phosphate. E. huxleyi was the dominant coccolithophore in all enclosures, but no difference in genetic diversity, based on DGGE analysis using primers specific to the calcium binding protein gene (gpa) were detected in any of the treatments. Chlorophyll concentrations and primary production were lower in the three elevated pCO2 treatments than in the ambient treatments. However, although coccolithophores numbers were reduced in two of the high-pCO2 treatments; in the third, there was no suppression of coccolithophores numbers, which were very similar to the three ambient treatments. In contrast, there was considerable variation in genetic diversity in the EhVs, as determined by analysis of the major capsid protein (mcp) gene. EhV diversity was much lower in the high-pCO2 treatment enclosure that did not show inhibition of E. huxleyi growth. Since virus infection is generally implicated as a major factor in terminating phytoplankton blooms, it is suggested that no study of the effect of ocean acidification in phytoplankton can be complete if it does not include an assessment of viruses

Comparative mapping and targeted-capture sequencing of the gametocidal loci in Aegilops sharonensis

Gametocidal (Gc) chromosomes or elements in species such as Aegilops sharonensis are preferentially transmitted to the next generation through both the male and female gametes when introduced into wheat. Furthermore, any genes, e.g. genes that control agronomically important traits, showing complete linkage with gametocidal elements, are also transmitted preferentially to the next generation without the need for selection. The mechanism for the preferential transmission of the gametocidal elements appears to occur by the induction of extensive chromosome damage in any gametes that lack the gametocidal chromosome in question. Previous studies on the mechanism of the gametocidal action in Ae. sharonensis indicates that at least two-linked elements are involved. The first, the ‘breaker’ element, induces chromosome breakage in gametes, which have lost the gametocidal elements while the second, the ‘inhibitor’ element, prevents the chromosome breakage action of the ‘breaker’ element in gametes, which carry the Gc elements. In this study, we have used comparative genomic studies to map 54 single nucleotide polymorphism (SNP) markers in an Ae. sharonensis 4SshL introgression segment in wheat and have also identified 18 candidate genes in Ae. sharonensis for the ‘breaker’ element through targeted sequencing of this 4SshL introgression segment. This valuable genomic resource will aide in further mapping the Gc locus that could be exploited in wheat breeding to produce new, superior varieties of wheat

Reporting to Improve Reproducibility and Facilitate Validity Assessment for Healthcare Database Studies V1.0.

PURPOSE: Defining a study population and creating an analytic dataset from longitudinal healthcare databases involves many decisions. Our objective was to catalogue scientific decisions underpinning study execution that should be reported to facilitate replication and enable assessment of validity of studies conducted in large healthcare databases. METHODS: We reviewed key investigator decisions required to operate a sample of macros and software tools designed to create and analyze analytic cohorts from longitudinal streams of healthcare data. A panel of academic, regulatory, and industry experts in healthcare database analytics discussed and added to this list. CONCLUSION: Evidence generated from large healthcare encounter and reimbursement databases is increasingly being sought by decision-makers. Varied terminology is used around the world for the same concepts. Agreeing on terminology and which parameters from a large catalogue are the most essential to report for replicable research would improve transparency and facilitate assessment of validity. At a minimum, reporting for a database study should provide clarity regarding operational definitions for key temporal anchors and their relation to each other when creating the analytic dataset, accompanied by an attrition table and a design diagram. A substantial improvement in reproducibility, rigor and confidence in real world evidence generated from healthcare databases could be achieved with greater transparency about operational study parameters used to create analytic datasets from longitudinal healthcare databases

Validation of the care transition measure in multi-ethnic South-East Asia in Singapore

10.1186/1472-6963-12-256BMC Health Services Research121

Defining seasonal marine microbial community dynamics

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables