TY  - JOUR
A1  - Beisner, Beatrix E.
A1  - Grossart, Hans-Peter
A1  - Gasol, Josep M.
T1  - A guide to methods for estimating phago-mixotrophy in nanophytoplankton
JF  - Journal of plankton research
N2  - Growing attention to phytoplankton mixotrophy as a trophic strategy has led to significant revisions of traditional pelagic food web models and ecosystem functioning. Although some empirical estimates of mixotrophy do exist, a much broader set of in situ measurements are required to (i) identify which organisms are acting as mixotrophs in real time and to (ii) assess the contribution of their heterotrophy to biogeochemical cycling. Estimates are needed through time and across space to evaluate which environmental conditions or habitats favour mixotrophy: conditions still largely unknown. We review methodologies currently available to plankton ecologists to undertake estimates of plankton mixotrophy, in particular nanophytoplankton phago-mixotrophy. Methods are based largely on fluorescent or isotopic tracers, but also take advantage of genomics to identify phylotypes and function. We also suggest novel methods on the cusp of use for phago-mixotrophy assessment, including single-cell measurements improving our capacity to estimate mixotrophic activity and rates in wild plankton communities down to the single-cell level. Future methods will benefit from advances in nanotechnology, micromanipulation and microscopy combined with stable isotope and genomic methodologies. Improved estimates of mixotrophy will enable more reliable models to predict changes in food web structure and biogeochemical flows in a rapidly changing world.
KW  - flow cytometry
KW  - phagotrophy
KW  - phytoplankton
KW  - methods
KW  - fluorescence
KW  - microscopy
KW  - FISH
KW  - isotopic methods
KW  - phylotypes
KW  - carbon flows
KW  - gene sequencing
Y1  - 2019
U6  - https://doi.org/10.1093/plankt/fbz008
SN  - 0142-7873
SN  - 1464-3774
VL  - 41
IS  - 2
SP  - 77
EP  - 89
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Swidsinski, Alexander
A1  - Loening-Baucke, Vera
A1  - Schulz, Stefan
A1  - Manowsky, Julia
A1  - Verstraelen, Hans
A1  - Swidsinski, Sonja
T1  - Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders
JF  - Systematic and Applied Microbiology
N2  - Sections of fecal cylinders were analyzed using fluorescence in situ hybridization targeting 180 bacterial groups. Samples were collected from three groups of women (N = 20 each) treated for bacterial vaginosis with ciprofloxacin + metronidazole. Group A only received the combined antibiotic regimen, whereas the A/Sb group received concomitant Saccharomyces boulardii CNCM I-745 treatment, and the A.Sb group received S. boulardii prophylaxis following the 14-day antibiotic course. The number of stool cylinders analyzed was 188 out of 228 in group A, 170 out of 228 in group A/Sb, and 172 out of 216 in group Ash. The colonic biomass was organized into a separate mucus layer with no bacteria, a 10-30 mu m broad unstirred transitional layer enriched with bacteria, and a patchy fermentative area that mixed digestive leftovers with bacteria. The antibiotics suppressed bacteria mainly in the fermentative area, whereas abundant bacterial clades retreated to the transitional mucus and survived. As a result, the total concentration of bacteria decreased only by one order. These effects were lasting, since the overall recovery of the microbial mass, bacterial diversity and concentrations were still below pre-antibiotic values 4 months after the end of antibiotic treatment. Sb-prophylaxis markedly reduced antibiotic effects and improved the recovery rates. Since the colon is a sophisticated bioreactor, the study indicated that the spatial anatomy of its biomass was crucial for its function. (C) 2015 The Authors. Published by Elsevier GmbH. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
KW  - FISH
KW  - Colonic microbiota
KW  - Antibiotics
KW  - Bioreactor
KW  - Saccharomyces boulardii
KW  - Clostridium difficile
Y1  - 2016
U6  - https://doi.org/10.1016/j.syapm.2015.11.002
SN  - 0723-2020
VL  - 39
SP  - 67
EP  - 75
PB  - Nature Publ. Group
CY  - Jena
ER  -