Classification of a moderately oxygen-tolerant isolate from baby faeces as Bifidobacterium thermophilum

<p>Abstract</p> <p>Background</p> <p>Bifidobacteria are found at varying prevalence in human microbiota and seem to play an important role in the human gastrointestinal tract (GIT). Bifidobacteria are highly adapted to the human GIT which is reflected in the genome sequence of a <it>Bifidobacterim longum </it>isolate. The competitiveness against other bacteria is not fully understood yet but may be related to the production of antimicrobial compounds such as bacteriocins. In a previous study, 34 <it>Bifidobacterium </it>isolates have been isolated from baby faeces among which six showed proteinaceous antilisterial activity against <it>Listeria monocytogenes</it>. In this study, one of these isolates, RBL67, was further identified and characterized.</p> <p>Results</p> <p><it>Bifidobacterium </it>isolate RBL67 was classified and characterized using a polyphasic approach. RBL67 was classified as <it>Bifidobacterium thermophilum </it>based on phenotypic and DNA-DNA hybridization characteristics, although 16S rDNA analyses and partial <it>gro</it>EL sequences showed higher homology with <it>B. thermacidophilum </it>subsp. <it>porcinum </it>and <it>B. thermacidophilum </it>subsp. <it>thermacidophilum</it>, respectively. RBL67 was moderately oxygen-tolerant and was able to grow at pH 4 and at a temperature of 47°C.</p> <p>Conclusion</p> <p>In order to assign RBL67 to a species, a polyphasic approach was used. This resulted in the classification of RBL67 as a <it>Bifidobacterium thermophilum </it>strain. To our knowledge, this is the first report about <it>B. thermophilum </it>isolated from baby faeces since the <it>B. thermophilum </it>strains were related to ruminants and swine faeces before. <it>B. thermophilum </it>was previously only isolated from animal sources and was therefore suggested to be used as differential species between animal and human contamination. Our findings may disapprove this suggestion and further studies are now conducted to determine whether <it>B. thermophilum </it>is distributed broader in human faeces. Furthermore, the postulated differentiation between human and animal strains by growth above 45°C is no longer valid since <it>B. thermophilum </it>is able to grow at 47°C. In our study, 16S rDNA and partial <it>gro</it>EL sequence analysis were not able to clearly assign RBL67 to a species and were contradictory. Our study suggests that partial <it>gro</it>EL sequences may not be reliable as a single tool for species differentiation.</p

Intermittent bioirrigation and oxygen dynamics in permeable sediments: An experimental and modeling study of three tellinid bivalves

To explore the dynamic nature of geochemical conditions in bioirrigated marine permeable sediments, we studied the hydraulic activity of three tellinacean bivalve molluscs (the Pacific species Macoma nasuta and Macomona liliana, and the northern Atlantic and Pacific species Macoma balthica). We combined porewater pressure sensing, time-lapse photography and oxygen imaging to quantify the durations and frequencies of tellinid irrigation activity and the associated oxygen dynamics in the sediment. Porewater pressure records of all tellinids were dominated by intermittent porewater pressurization, induced by periodic water injection into the sediment through their excurrent siphons, which resulted in intermittent oxygen supply to subsurface sediments. The irrigation (two–12 minutes long) and intervals between subsequent irrigation bouts (1.5–13 minutes) varied among tellinid species and individual sizes. For large M. liliana and M. nasuta, the average intervals between irrigation bouts were sufficiently long (10 minutes and four minutes, respectively) to allow complete oxygen consumption in between irrigation bouts in all tested sediment types. Irrigation patterns of smaller conspecifics and the smaller species M. balthica were characterized by significantly shorter separation of irrigation bouts, which resulted in more continuous oxygenation of the sediment. Transport-reaction modeling confirmed these species- and size-specific geochemical signatures and indicated that the geochemical character of the sediment is largely conditioned by the interplay between temporal irrigation patterns and sedimentary oxygen consumption rates. For large tellinids, model simulations indicated that oscillatory rather than stationary geochemical conditions are prevalent in a wide range of sediment types, with oxic pockets collapsing completely between periods of active irrigation. Based on the model results we developed analytical approximations that allow estimation of spatio-temporal characteristics of sediment oxygenation for a wide range of sediment types and infaunal activity patterns. Our results emphasize the need to consider the intermittent nature of bioirrigation when studying the geochemical impact of infauna in permeable sediments

A review of assessment methods for river hydromorphology

The work leading to this paper has received funding for the EU’s FP7 under Grant Agreement No. 282656 (REFORM

Quantifying bioirrigation using ecological parameters: a stochastic approach†

Irrigation by benthic macrofauna has a major influence on the biogeochemistry and microbial community structure of sediments. Existing quantitative models of bioirrigation rely primarily on chemical, rather than ecological, information and the depth-dependence of bioirrigation intensity is either imposed or constrained through a data fitting procedure. In this study, stochastic simulations of 3D burrow networks are used to calculate mean densities, volumes and wall surface areas of burrows, as well as their variabilities, as a function of sediment depth. Burrow networks of the following model organisms are considered: the polychaete worms Nereis diversicolor and Schizocardium sp., the shrimp Callianassa subterranea, the echiuran worm Maxmuelleria lankesteri, the fiddler crabs Uca minax, U. pugnax and U. pugilator, and the mud crabs Sesarma reticulatum and Eurytium limosum. Consortia of these model organisms are then used to predict burrow networks in a shallow water carbonate sediment at Dry Tortugas, FL, and in two intertidal saltmarsh sites at Sapelo Island, GA. Solute-specific nonlocal bioirrigation coefficients are calculated from the depth-dependent burrow surface areas and the radial diffusive length scale around the burrows. Bioirrigation coefficients for sulfate obtained from network simulations, with the diffusive length scales constrained by sulfate reduction rate profiles, agree with independent estimates of bioirrigation coefficients based on pore water chemistry. Bioirrigation coefficients for O(2 )derived from the stochastic model, with the diffusion length scales constrained by O(2 )microprofiles measured at the sediment/water interface, are larger than irrigation coefficients based on vertical pore water chemical profiles. This reflects, in part, the rapid attenuation with depth of the O(2 )concentration within the burrows, which reduces the driving force for chemical transfer across the burrow walls. Correction for the depletion of O(2 )in the burrows results in closer agreement between stochastically-derived and chemically-derived irrigation coefficient profiles

Upscaling Flow and Transport Processes

Peer reviewe

The rise and fall of methanotrophy following a deepwater oil-well blowout

The blowout of the Macondo oil well in the Gulf of Mexico in April 2010 injected up to 500,000 tonnes of natural gas, mainly methane, into the deep sea1. Most of the methane released was thought to have been consumed by marine microbes between July and August 20102, 3. Here, we report spatially extensive measurements of methane concentrations and oxidation rates in the nine months following the spill. We show that although gas-rich deepwater plumes were a short-lived feature, water column concentrations of methane remained above background levels throughout the rest of the year. Rates of microbial methane oxidation peaked in the deepwater plumes in May and early June, coincident with a rapid rise in the abundance of known and new methane-oxidizing microbes. At this time, rates of methane oxidation reached up to 5,900 nmol l−1 d−1—the highest rates documented in the global pelagic ocean before the blowout4. Rates of methane oxidation fell to less than 50 nmol l−1 d−1 in late June, and continued to decline throughout the remainder of the year. We suggest the precipitous drop in methane consumption in late June, despite the persistence of methane in the water column, underscores the important role that physiological and environmental factors play in constraining the activity of methane-oxidizing bacteria in the Gulf of Mexico