Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability

Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using ¹³C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant ¹³C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant ¹³C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.

Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface

Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi.OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi.OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76-5.05 Mbps, and contained "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi.OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology.

Giovannoni et al. reply

Replying to S. Våge, J. E. Storesund & T. F. Thingstad Nature 499, http://dx.doi.org/10.1038/nature12387 (2013). In the debate about top-down versus bottom-up control, most would argue that both are important. The most probable scenario is that in the absence of high rates of transport, the equilibrium between these competing processes determines bacterial abundance. In their Brief Communication Arising, Våge and co-workers respond to our Letter, arguing the case for defense specialism. ‘Defence specialism’ is not synonymous with ‘defence’. Because of the prevalence of viruses, it is probable that most bacteria have acquired defences against predation. ‘Defence specialism’ refers to success by defence, in the sense that a cell might allocate a large proportion of its resources to defence and thereby become successful.

Weekly combination of non-pegylated liposomal doxorubicin and taxane in first-line breast cancer: wALT trial (phase I-II)

BACKGROUND

Through different pharmacodynamic-kinetic interactions, weekly administration of proved efficacy agents can overcome resistance with lower toxicity and greater benefit. Based on this assumption, we designed a phase I-II trial with weekly non-pegylated liposomal anthracycline and taxane in first-line breast cancer patients.

PATIENTS AND METHODS

We enrolled 56 previously untreated metastatic breast cancer patients; they were randomly assigned to receive paclitaxel (Taxol) (50 mg/mq) or docetaxel (Taxotere) (30 mg/mq) combined with non-pegylated liposomal anthracycline (25 mg/mq) on days 1, 8 and 15 every 4 weeks. The primary end points were the clinical benefit and treatment-related toxic effects assessment. Secondary end points were time-to-disease progression (TTP) and overall survival (OS).

RESULTS

The overall clinical benefit was 87.04%. World Health Organization G3-4 toxic effects included neutropenia (45%), anemia (44%), complete alopecia (83%), severe onycholysis and neuropathy. The 24% of patients developed left ventricular ejection fraction reduction but none >10% with recover after treatment completion. The median absolute decrease from baseline was 1%. Median TTP was 11 months and median OS was 23 months.

CONCLUSIONS

Combined weekly administration of taxane and non-pegylated liposomal anthracycline is well tolerated and clinical benefit data encourage phase III study design.

The importance of culturing bacterioplankton in the 'omics' age

Progress in the culturing of microorganisms that are important to ocean ecology has recently accelerated, and technology has been a factor in these advances. However, rather than a single technological breakthrough, a combination of methods now enable microbiologists to screen large numbers of cultures and manipulate cells that are growing at the low biomass densities that are characteristic of those found in seawater. The value of ribosomal RNA databases has been reaffirmed, as they provide nucleic-acid probes for screening to identify important new species in culture. The new cultivation approaches have focused on specific targets that ecological studies suggest are significant for geochemical transformations, such as SAR11. Here, we review how to cultivate marine oligotrophs and why it is worth the effort.

Experience in Italy in the development and application of clinical guidelines for low back pain

Clinical Guidelines (CG) reflect the up to date scientific knowledge in the treatment of Low Back Pain (LBP). The diffusion of CG and their everyday application by health care professionals is a significant problem. As most CG are developed in English, the concerns are obviously greater in non English-speaking countries. The first CG on LBP by the Quebec Task Force (1987) was introduced in 1990 by the Gruppo di Studio della Scoliosi (GSS). Some studies where planned to verify their everyday application. The first one was carried on in Mantua, and evaluated the assessment of patients by General Practitioners (GPs): there is a clear tendency to over-prescribe examinations in acute cases, while in chronic cases under-prescription is sometimes seen. An educational approach was then proposed through a number of meetings, with fable

RESULTS

A third experience verified the help GPs could receive through two different educative interventions such as a booklet and a direct access to a classical Back School. In acute patients a Booklet is useful, while Back School is not; at long term follow-up, chronic cases were significantly reduced only by the Back School approach. Finally, the Abruzzo Study's results on GPs management through computer-assisted evaluation is reported. The second part of the paper deals on the new experiences that are underway on the application of Diagnostic-Therapeutic Pathways (DTP) to Low Back Disorders.

Sevoflurane analgesia in obstetrics: a pilot study

Continuous and intermittent administration of inhalational anesthetics has been successfully employed for treating pain during labor. We conjectured that intermittent sevoflurane administration would be effective for pain relief during labor without side effects to the mother or fetus. Fifty parturients breathed a mixture of 2-3% sevoflurane, oxygen and air before each uterine contraction began. The patients assessed the quality of analgesia by using a visual analogue scale (0-10) before the administration of sevoflurane and after each uterine contraction. All parturients but one were satisfied, demonstrating a mean visual analogue score before and after sevoflurane administration of 8.7 +/- 1.1 and 3.3 +/- 1.5, respectively. Apgar scores at 1 and 5 min were 9 (range 5-9) and 10 (range 8-10), respectively. Our findings suggest that sevoflurane could be effective for the treatment of labor pain.

Origin and Phylogeny of Microbes Living in Permanent Antarctic Lake Ice

A BSTRACTThe phylogenetic diversity of bacteria and cyanobacteria colonizing sediment particles in the permanent ice cover of an Antarctic lake was characterized by analyses of 16S rRNA genes amplified from environmental DNA. Samples of mineral particles were collected from a depth of 2.5 m in the 4-m-thick ice cover of Lake Bonney, McMurdo Dry Valleys, Antarctica. A rRNA gene clone library of 198 clones was made and characterized by sequencing and oligonucleotide probe hybridization. The library was dominated by representatives of the cyanobacteria, proteobacteria, and Planctomycetales, but also contained diverse clones representing many other microbial groups, including the Acidobacterium/Holophaga division, the Green Non-Sulfur division, and the Actinobacteria. Six oligonucleotide probes were made for the most abundant clades recovered in the library. To determine whether the ice microbial community might originate from wind dispersal of the algal mats found elsewhere in Taylor Valley, the probes were hybridized to 16S rDNAs amplified from three samples of terrestrial cyanobacterial mats collected at nearby sites, as well as to bacterial 16S rDNAs from the lake ice community. The results demonstrate the presence of a diverse microbial community dominated by cyanobacteria in the lake ice, and also show that the dominant members of the lake ice microbial community are found in terrestrial mats elsewhere in the area. The lake ice microbial community appears to be dominated by organisms that are not uniquely adapted to the lake ice ecosystem, but instead are species that originate elsewhere in the surrounding region and opportunistically colonize the unusual habitat provided by the sediments suspended in lake ice.

Development and application of oligonucleotide probes for identification of Lactococcus lactis subsp. cremoris

Lactococcus lactis subsp. cremoris is of considerable interest to the dairy industry, which relies upon the few available strains for the manufacture of cheddar cheese free of fermented and fruity flavors. The subspecies cremoris differs from related subspecies by the lack of a few phenotypic traits. Our purpose was to identify unique rRNA sequences that could be used to discriminate L. lactis subsp. cremoris from related subspecies. The 16S rRNAs from 13 Lactococcus strains were partially sequenced by using reverse transcriptase to identify domains unique to L. lactis subsp. cremoris. All five strains of the subspecies cremoris had a unique base sequence in a hypervariable region located 70 to 100 bases from the 5' terminus. In this region, all L. lactis subsp. lactis biovar diacetylactis strains examined had a sequence identical to that of L. lactis subsp. lactis 7962, which was different from other strains of the subspecies lactis by only one nucleotide at position 90 (Escherichia coli 16S rRNA structural model) (J. Brosius, J. L. Palmer, J. P. Kennedy, and H. F. Noller, Proc. Natl. Acad. Sci. USA 75:4801-4805, 1978). Oligonucleotide probes specific for the genus Lactococcus (212RLa) and for the subspecies cremoris (68RCa) were synthesized and evaluated by hybridization to known rRNAs as well as fixed whole cells. Efficient and specific hybridization to the genus-specific probe was observed for the 13 Lactococcus strains tested. No hybridization was seen with the control species. All five strains of the subspecies cremoris hybridized to the subspecies-specific probe.

A unique type of eubacterial 5S rRNA in members of the order Planctomycetales

Analysis of the 5S ribosomal RNA from members of the eubacterial order Planctomycetales, i.e., Planctomyces, Pirella, Gemmata, and Isosphaera, reveals several unexpected features. Firstly, the primary structures are significantly shorter than those of the majority of eubacteria and vary in length between 109 and 111 nucleotides. Secondly, the lack of an insertion at position 66 is a feature not encountered before in prokaryotic 5S rRNAs. Thirdly, as compared to the proposed eubacterial "minimal" 5S rRNA structure (Erdmann and Wolters 1986) the secondary structure contains numerous base-pair transversions. The isolated position of the planctomycetes as an individual eubacterial division and the phylogenetic position of its genera are in accord with the results obtained from 16S rRNA cataloguing.

[Reactivation of the allogenous component of experimental skin inflammation after exposure to ultraviolet rays]

The effects of U.V. radiation induced cutaneous erythema on an experimental inflammation focus in another part of the body have been studied. The skin inflammation caused by carbon dioxide snow was used as a model. The onset of erythema is followed by reactivation of the diminishing inflammation process. It is therefore deduced that such effects are transmitted humorally and that reactivation is caused by histamine circulation. Histamine is released locally from the U.V. induced erythema and, entering into the circulation, increased the permeability of the microvessels in the inflamed area. This sends inactive chemical mediators to the interstitial sector where the appropriate conditions for their activation exist.