Flux variability of phyto- and zooplankton communities in the Mauritanian coastal upwelling between 2003 and 2008

Continuous multiyear records of sediment-trap-gained microorganism fluxes are scarce. Such studies are important to identify and to understand the main forcings behind seasonal and multiannual evolution of microorganism flux dynamics. Here, we assess the long-term flux variations and population dynamics of diatoms, coccolithophores, calcareous and organic dinoflagellate cysts, foraminifera and pteropods in the eastern boundary upwelling ecosystem of the Canary Current. A multiannual, continuous sediment trap experiment was conducted at the mooring site CBeu (Cap Blanc eutrophic; ∼20∘ N, 18∘ W; trap depth is ca. 1300 m) off Mauritania (northwest Africa), between June 2003 and March 2008. Throughout the study, the reasonably consistent good match of fluxes of microorganisms and bulk mass reflects the seasonal occurrence of the main upwelling season and relaxation and the contribution of microorganisms to mass flux off Mauritania. A clear successional pattern of microorganisms, i.e., primary producers followed by secondary producers, is not observed. High fluxes of diatoms, coccolithophores, organic dinoflagellate cysts, and planktonic foraminifera occur simultaneously. Peaks of calcareous dinoflagellate cysts and pteropods mostly occurred during intervals of upwelling relaxation. A striking feature of the temporal variability of population occurrences is the persistent pattern of seasonal groups contributions. Species of planktonic foraminifera, diatoms, and organic dinoflagellate cysts typical of coastal upwelling, as well as cooler-water planktonic foraminifera and the coccolithophore Gephyrocapsa oceanica, are abundant at times of intense upwelling (late winter through early summer). Planktonic foraminifera and calcareous dinoflagellate cysts are dominant in warm pelagic surface waters, and all pteropod taxa are more abundant in fall and winter when the water column stratifies. Similarly, coccolithophores of the upper and lower photic zones, together with Emiliania huxleyi, and organic dinoflagellate cysts dominate the assemblage during phases of upwelling relaxation and deeper layer mixing. A significant shift in the “regular” seasonal pattern of taxa relative contribution is observed between 2004 and 2006. Benthic diatoms strongly increased after fall 2005 and dominated the diatom assemblage during the main upwelling season. Additional evidence for a change in population dynamics is the short dominance of the coccolithophore Umbilicosphaera annulus, the occurrence of the pteropod Limacina bulimoides and the strong increase in the flux of calcareous dinoflagellate cysts, abundant in warm tropical oligotrophic waters south of the study area after fall 2005. Altogether, this suggests that pulses of southern waters were transported to the sampling site via the northward Mauritania Current. Our multiannual trap experiment provides a unique opportunity to characterize temporal patterns of variability that can be extrapolated to other eastern boundary upwelling ecosystems (EBUEs), which are experiencing or might experience similar future changes in their plankton community

Validated age and growth estimates for Carcharhinus obscurus in the northwestern Atlantic Ocean, with pre- and post management growth comparisons

This paper is not subject to U.S. copyright. The definitive version was published in Environmental Biology of Fishes 97 (2014): 881-896, doi:10.1007/s10641-013-0189-4.Age and growth estimates for the dusky shark, Carcharhinus obscurus, were derived from vertebral centra collected in the northwestern Atlantic Ocean. Sample collection spanned the years prior to and following the implementation of management measures (1963–2010). Growth was compared pre- and post- population depletion and pre- and post- management to investigate the possibility of density-mediated shifts in age and growth parameters over time. There was no evidence of difference between periods for either sex. Additionally, bomb radiocarbon dating was used to determine the periodicity of band pair formation. Results support the traditional interpretation of annual band pairs up to approximately 11 years of age. After this time, vertebral counts considerably underestimate true age. Maximum validated ages were estimated to be between 38 and 42 years of age (an increase of 15 to 19 years over the band count estimates), confirming longevity to at least 42 years of age. Growth curves estimated using only validated data were compared to those generated using band pair counts. Logistic growth parameters derived from validated vertebral length-at-age data were L ∞  = 261.5 cm FL, L o  = 85.5 cm, t o  = 4.89 year and g = 0.15 year−1 for the sexes combined. Revised estimates of age at maturity were 17.4 years for males and 17.6 years for females

IsoRankN: spectral methods for global alignment of multiple protein networks

Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best mapping between all nodes of the two networks. In this article, our aim is to improve upon existing global alignment results. Better network alignment will enable, among other things, more accurate identification of functional orthologs across species. Results: We introduce IsoRankN (IsoRank-Nibble) a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error tolerant and computationally efficient.National Science Council of Taiwan (NSC-096-2917-I- 002-114)National Science Council of Taiwan (NSC-095-2221-E-001-016-MY3)Fannie and John Hertz Foundatio

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads. Combinatorial sequence tagging can be used to examine hundreds of samples with far fewer primers than is required when sequence tags are incorporated at only a single end. The number of reads generated permitted saturating or near-saturating analysis of samples of the vaginal microbiome. The large number of reads al- lowed an in-depth analysis of errors, and we found that PCR-induced errors composed the vast majority of non-organism derived species variants, an ob- servation that has significant implications for sequence clustering of similar high-throughput data. We show that the short reads are sufficient to assign organisms to the genus or species level in most cases. We suggest that this method will be useful for the deep sequencing of any short nucleotide region that is taxonomically informative; these include the V3, V5 regions of the bac- terial 16S rRNA genes and the eukaryotic V9 region that is gaining popularity for sampling protist diversity.Comment: 28 pages, 13 figure

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

The Current Use of Drug-Eluting Balloons and Stents in Peripheral Arterial Disease: An Online Survey by the Cardiovascular and Interventional Radiological Society of Europe (CIRSE).

PURPOSE: To assess the current use of drug-eluting devices for peripheral arterial disease (PAD) among interventional radiologists following the controversy caused by the 2018 meta-analysis suggesting an increased mortality risk for paclitaxel-eluting devices. METHODS: An anonymous survey was sent to 7035 CIRSE members via email; only complete responses were included and statistically analysed. RESULTS: Three hundred and seven members (4.4%) completed the survey. Among these, 95.8% indicated that they personally perform peripheral vascular procedures. Thirty-eight percentage of respondents did not see any change of practice since 2018, while 47% reported that the use of drug-eluting devices decreased; for 13%, the use stopped altogether, while it increased in 3% of responses. 45.6% of respondents also felt the impact of the controversy in terms of pricing, availability or directives from hospital administration. A large majority of respondents (83.7%) who perform peripheral vascular procedures consider the use of these devices as safe, 12.9% were undecided and 3.4% did not consider them as safe. Among the respondents who do not perform endovascular procedures, 77% considered these devices as safe and 23% were undecided. CONCLUSION: Although the 2018 meta-analysis had a disruptive impact on the use of drug-eluting devices in PAD, with the increasing body of evidence available, a majority of respondents continue to believe in the safety of these devices for use in femoropopliteal disease

Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

Phylogenetic profiling has been widely used for comparing bacterial communities, but has so far been impossible to apply to viruses because of the lack of a single marker gene analogous to 16S rRNA. Here we developed a reference tree approach for matching viral sequences and applied it to the largest viral datasets available. The resulting technique, Shotgun UniFrac, was used to compare host-associated and non-host-associated phage communities (130 total metagenomes), and revealed a profound split similar to that found with bacterial communities. This new informatics approach complements analysis of bacterial communities and promises to provide new insights into viral community dynamics, such as top-down versus bottom-up control of bacterial communities by viruses in a range of systems

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected