A novel algorithm for the determination of bacterial cell volumes that is unbiased by cell morphology

In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls

Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and Aurantivirga of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls. IMPORTANCE The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for deriving ecological processes like bottom-up and top-down control. In this study, we determined growth by numerical abundance and calibrated microscopy-based methods to determine the frequency of dividing cells and subsequently calculate taxon-specific cell division rates in situ. The cell division and mortality rates of two oligotrophic (SAR11 and SAR86) and two copiotrophic (Bacteroidetes and Aurantivirga) taxa during two spring phytoplankton blooms showed a tight coupling for all four taxa throughout the blooms without any temporal offset. Unexpectedly, SAR11 showed high cell division rates days before the bloom while cell abundances remained constant, which is indicative of strong top-down control. Microscopy remains the method of choice to understand ecological processes like top-down and bottom-up control on a cellular level.

A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea)

A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm³), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm³). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.

Dense macrophyte cover has significant structural and functional influence on planktonic microbial communities leading to bacterial success

We intend to assess how macrophyte cover affects planktonic microbial communities by changing the physical and chemical environment, and how macrophyte-derived DOC affects the balance between autotrophy and heterotrophy/chemoorganotrophy in a shallow lake. The structure and production of phytoplankton and bacterioplankton in the open water of a large shallow lake and in the littoral zone were compared at two sampling stations with different macrophyte cover. According to the obtained results, uncoupling between bacterioplankton and phytoplankton was observed due to the high content of organic carbon of emergent macrophyte origin. While phytoplankton were regulated by TSS, bacterioplankton (in both heterotrophic and photoheterotrophic forms) were determined by dissolved organic carbon. As a result of these processes, the littoral and pelagic zones in the lake are completely separated from each other. In open water the autotrophic processes dominated, but at the sampling stations inside the reed belt, the metabolic processes shifted in the direction of chemoorganotrophy. Our results suggest that increase of macrophyte cover in shallow water bodies will increase the significance of microbe-based carbon pathways and weakens the efficiency of carbon transport from primary producers to higher trophic levels through the planktonic food chain.

Repeated exposure of nosocomial pathogens to silver does not select for silver resistance but does impact ciprofloxacin susceptibility

The rise of antimicrobial resistant bacteria coupled with a void in antibiotic development marks Antimicrobial Resistance as one of the biggest current threats to modern medicine. Antimicrobial metals are being developed and used as alternative anti-infectives, however, the existence of known resistance mechanisms and limited data regarding bacterial responses to long-term metal exposure are barriers to widespread implementation. In this study, a panel of reference and clinical strains of major nosocomial pathogens were subjected to serial dosage cycles of silver and ciprofloxacin. Populations exposed to silver initially showed no change in sensitivity, however, increasingly susceptibility was observed after the 25th cycle. A control experiment with ciprofloxacin revealed a selection for resistance over time, with silver treated bacteria showing faster adaptation. Morphological analysis revealed filamentation in Gram negative species suggesting membrane perturbation, while sequencing of isolated strains identified mutations in numerous genes. These included those encoding for efflux systems, chemosensory systems, stress responses, biofilm formation and respiratory chain processes, although no consistent locus was identified that correlated with silver sensitivity. These results suggest that de novo silver resistance is hard to select in a range of nosocomial pathogens, although silver exposure may detrimentally impact sensitivity to antibiotics in the long term. STATEMENT OF SIGNIFICANCE: The adaptability of microbial life continuously calls for the development of novel antibiotic molecules, however, the cost and risk associated with their discovery have led to a drying up in the pipeline, causing antimicrobial resistance (AMR) to be a major threat to healthcare. From all available strategies, antimicrobial metals and, more specifically, silver showcase large bactericidal spectrum and limited toxic effect which coupled with a large range of processes available for their delivery made these materials as a clear candidate to tackle AMR. Previous reports have shown the ability of this metal to enact a synergistic effect with other antimicrobial therapies, nevertheless, the discovery of Ag resistance mechanisms since the early 70s and limited knowledge on the long term influence of silver on AMR poses a threat to their applicability. The present study provides quantitative data on the influence of silver based therapies on AMR development for a panel of reference and clinical strains of major nosocomial pathogens, revealing that prolonged silver exposure may detrimentally impact sensitivity to antibiotics.

When the heat is on: High temperature resistance of buds from European tree species

The heat resistance of meristematic tissues is crucial for the survival of plants exposed to high temperatures, as experienced during a forest fire. Although the risk and frequency of forest fires are increasing due to climate change, knowledge about the heat susceptibility of buds, which enclose apical meristems and thus enable resprouting and apical growth, is scarce. In this study, the heat resistance of buds in two different phenological stages was experimentally assessed for 10 European tree species. Cellular heat tolerance of buds was analyzed by determining the electrolyte leakage following heat exposure. Further, the heat insulation capability was tested by measuring the time required to reach lethal internal temperatures linked to bud traits. Our results highlighted differences in cellular heat tolerance and insulation capability among the study species. The phenological stage was found to affect both the thermal stability of cells and the buds' insulation. Further, a good relationship between size-related bud traits and insulation capability was established. Species-specific data on the heat resistance of buds give a more accurate picture of the fire susceptibility of European tree species and provide useful information for estimating tree post-fire responses more precisely.

Aerobic anoxygenic phototrophs are highly abundant in hypertrophic and polyhumic waters

Aerobic anoxygenic phototrophs (AAPs) are a group of photoheterotrophic bacteria common in natural waters. Here, AAP abundance and contribution to total bacterial abundance and biomass were investigated to test whether the trophic status of a lake or content of coloured dissolved organic matter (CDOM) play a role in determining AAP distribution and abundance in shallow inland lakes, with special focus on hypertrophic and polyhumic waters. Twenty-six different shallow lakes in Hungary were monitored. AAP abundance and biomass were determined by epifluorescence microscopy. The lakes exhibit a broad range of CDOM (2-7000 mg Pt L-1) and phytoplankton biomass (2-1200 μg L-1 chlorophyll a concentration). Very high AAP abundance (up to 3 × 107 cells mL-1) was observed in polyhumic and hypertrophic shallow lakes. AAP abundance was influenced by phytoplankton biomass and CDOM content, and these effects were interrelated. As determined, 40 μg L-1 chlorophyll a and 52 mg Pt L-1 CDOM are threshold levels above which these effects have a synergistic relationship. Hence, the observed high AAP abundance in some soda pans is a consequence of combined hypertrophy and high CDOM content. AAP contribution was influenced by total suspended solids (TSS) content: the success of AAP cells could be explained by high TSS levels, which might be explained by the decrease of their selective grazing control.

Abundance of Common Aerobic Anoxygenic Phototrophic Bacteria in a Coastal Aquaculture Area

Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10–53% of the total bacterial assemblage. By examining pufM gene sequence, a common phylogenetic AAnPB species was found in all sampling sites through the year. The common species and other season-specific species were phylogenetically close to unculturable clones recorded in the Sargasso Sea and Pacific Ocean. The present study suggests that the common species may be a cosmopolitan species with worldwide distribution that is abundant not only in the oligotrophic open ocean but also in eutrophic aquaculture areas.

Single-image based methods used for non-invasive volume estimation of cancer spheroids: a practical assessing approach based on entry-level equipment

BACKGROUND

Cancer multicellular spheroids are commonly used as 3D tumour models for testing drugs and radiotherapy treatments. The volume plays a key role in analysis of the results. Several methods have been proposed in the literature to compute the spheroid's volume from one 2D microscopy image (i.e. a single projection). However, the literature lacks reviews summarising the different methods available. Furthermore, there are no well-established approaches by which to compare the different methods and determine the best one.

OBJECTIVE

In this work we (a) revise the existing single-image based methods used to estimate the volume of multicellular spheroids, also providing different implementations for classical spherical and ellipsoidal pre-defined models; (b) present an upgrade of a volume estimation software recently proposed, Reconstruction and Visualization from a Single Projection (ReViSP), just validated by using four real spheroids imaged in 3D with a light-sheet microscope; (c) propose a quality assessing approach for single-image based methods, relying on 3D home-made macroscopic synthetic models mimicking the shapes of real multicellular spheroids.

RESULTS

Seven image-based methods used to estimate the volume of spheroids were compared using six 3D home-made synthetic models. First, the material used to make the synthetic models was characterised to estimate its density. Then, the ground-truth volume of the 3D models was measured by simply weighing them. The volume instances estimated by the different methods were compared with ground truth. ReViSP attained the best result three times out of six and on average.

CONCLUSIONS

The results obtained proved that (a) different implementations for the classical spherical and ellipsoidal pre-defined models may lead to very different results; (b) ReViSP is the best single-image based method available today to estimate the volume of multicellular spheroids.

A Simple yet Accurate Method for the Estimation of the Biovolume of Planktonic Microorganisms

Determining the biomass of microbial plankton is central to the study of fluxes of energy and materials in aquatic ecosystems. This is typically accomplished by applying proper volume-to-carbon conversion factors to group-specific abundances and biovolumes. A critical step in this approach is the accurate estimation of biovolume from two-dimensional (2D) data such as those available through conventional microscopy techniques or flow-through imaging systems. This paper describes a simple yet accurate method for the assessment of the biovolume of planktonic microorganisms, which works with any image analysis system allowing for the measurement of linear distances and the estimation of the cross sectional area of an object from a 2D digital image. The proposed method is based on Archimedes' principle about the relationship between the volume of a sphere and that of a cylinder in which the sphere is inscribed, plus a coefficient of 'unellipticity' introduced here. Validation and careful evaluation of the method are provided using a variety of approaches. The new method proved to be highly precise with all convex shapes characterised by approximate rotational symmetry, and combining it with an existing method specific for highly concave or branched shapes allows covering the great majority of cases with good reliability. Thanks to its accuracy, consistency, and low resources demand, the new method can conveniently be used in substitution of any extant method designed for convex shapes, and can readily be coupled with automated cell imaging technologies, including state-of-the-art flow-through imaging devices.

Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow

Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

Cancer multicellular spheroids: volume assessment from a single 2D projection

Volume is one of the most important features for the characterization of a tumour on a macroscopic scale. It is often used to assess the effectiveness of care treatments, thus making its correct evaluation a crucial issue for patient care. Similarly, volume is a key feature on a microscopic scale. Multicellular cancer spheroids are 3D tumour models widely employed in pre-clinical studies to test the effects of drugs and radiotherapy treatments. Very few methods have been proposed to estimate the tumour volume arising from a 2D projection of multicellular spheroids, and even fewer have been designed to provide a 3D reconstruction of the tumour shape. In this work, we propose Reconstruction and Visualization from a Single Projection (ReViSP), an automatic method conceived to reconstruct the 3D surface and estimate the volume of single cancer multicellular spheroids, or even of spheroid cultures. As the input parameter ReViSP requires only one 2D projection, which could be a widefield microscope image. We assessed the effectiveness of our method by comparing it with other approaches. To this purpose, we used a new strategy that allowed us to achieve accurate volume measurements based on the analysis of home-made 3D objects, built by mimicking the spheroid morphology. The results confirmed the effectiveness of our method for both 3D reconstruction and volume assessment. ReViSP software is distributed as an open source tool.