The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population

Background: The bacterial taxon Polynucleobacter necessarius subspecies asymbioticus represents a group of planktonic freshwater bacteria with cosmopolitan and ubiquitous distribution in standing freshwater habitats. These bacteria comprise,1 % to 70 % (on average about 20%) of total bacterioplankton cells in various freshwater habitats. The ubiquity of this taxon was recently explained by intra-taxon ecological diversification, i.e. specialization of lineages to specific environmental conditions; however, details on specific adaptations are not known. Here we investigated by means of genomic and experimental analyses the ecological adaptation of a persistent population dwelling in a small acidic pond. Findings: The investigated population (F10 lineage) contributed on average 11 % to total bacterioplankton in the pond during the vegetation periods (ice-free period, usually May to November). Only a low degree of genetic diversification of the population could be revealed. These bacteria are characterized by a small genome size (2.1 Mb), a relatively small number of genes involved in transduction of environmental signals, and the lack of motility and quorum sensing. Experiments indicated that these bacteria live as chemoorganotrophs by mainly utilizing low-molecular-weight substrates derived from photooxidation of humic substances. Conclusions: Evolutionary genome streamlining resulted in a highly passive lifestyle so far only known among free-living bacteria from pelagic marine taxa dwelling in environmentally stable nutrient-poor off-shore systems. Surprisingly, such a lifestyle is also successful in a highly dynamic and nutrient-richer environment such as the water column of the investigate

Effects of an anionic surfactant (FFD-6) on the energy and information flow between a primary producer (Scenedesmus obliquus) and a consumer (Daphnia magna)

The effects of a commercially available anionic surfactant solution (FFD-6) on growth and morphology of a common green alga (Scenedesmus obliquus) and on survival and clearance rates of the water flea Daphnia magna were studied. The surfactant-solution elicited a morphological response (formation of colonies) in Scenedesmus at concentrations of 10–100 μl l−1 that were far below the No Observed Effect Concentration (NOEC) value of 1,000 μl l−1 for growth inhibition. The NOEC-value of FFD-6 for colony-induction was 3 μl l−1. Daphnia survival was strongly affected by FFD-6, yielding LC50–24h and LC50–48h of 148 and 26 μl l−1, respectively. In addition, clearance rates of Daphnia feeding on unicellular Scenedesmus were inhibited by FFD-6, yielding a 50% inhibition (EC50–1.5h) at 5.2 μl l−1 with a NOEC of 0.5 μl l−1. When Daphnia were offered FFD-6-induced food in which eight-celled colonies (43 × 29 μm) were most abundant, clearance rates (~0.14 ml ind.−1 h−1) were only 25% the rates of animals that were offered non-induced unicellular (15 × 5 μm) Scenedesmus (~0.56 ml ind.−1 h−1). As FFD-6 concentrations in the treated food used in the experiments were far below the NOEC for clearance rate inhibition, it is concluded that the feeding rate depression was caused by the altered morphology of the Scenedesmus moving them out of the feeding window of the daphnids. The surfactant evoked a response in Scenedesmus that is similar to the natural chemically induced defensive reaction against grazers and could disrupt the natural information conveyance between these plankton organisms

Shape and size in phytoplankton ecology: do they matter?

This paper summarises the outcomes of the 14th Workshop of the International Association of Phytoplankton Taxonomy and Ecology (IAP). The authors mostly addressed their contributions on the following topics: morphological and morpho-functional descriptors of phytoplankton, size and shape structure of phytoplankton related to different kinds of environmental variables and the role of morphological and physiological plasticity of phytoplankton in maintaining the (apparently) same populations under different environmental conditions. Case studies from different kinds of aquatic environments (deep and shallow lakes, reservoirs with different age, purpose and trophic state, floodplain wetlands mostly in the temperate region but also from subtropical and tropical ones) have shown that similar environmental forcing calls for similar morpho-functional properties even though the corresponding associations can be markedly different on species level

Microcolony Formation by Single-Cell Synechococcus Strains as a Fast Response to UV Radiation▿

UV radiation (UVR) has different effects on prokaryotic cells, such as, for instance, filamentation and aggregation in bacteria. Here we studied the effect of UVR on microcolony formation in two freshwater Synechococcus strains of different ribotypes (group B and group I) and phycobiliprotein compositions (phycoerythrin [PE] and phycocyanin [PC]). Each strain was photoacclimated at two light intensities, low light (LL) (10 μmol m−2 s−1) and moderate light (ML) (100 μmol m−2 s−1). The cultures were exposed for 6 days to treatments with UVR or without UVR. PE-rich Synechococcus acclimated to LL had a low carotenoid/chlorophyll a (car/chl) ratio but responded faster to UVR treatment, producing the highest percentages of microcolonies and of cells in microcolonies. Conversely, the same strain acclimated to ML, with a higher car/chl ratio, did not aggregate significantly. These results suggest that microcolony formation by PE-rich Synechococcus is induced by UVR if carotenoid levels are low. PC-rich Synechococcus formed a very low percentage of microcolonies in both acclimations even with low car/chl ratio. The different responses of the two Synechococcus strains to UVR depend on their pigment compositions. On the other hand, this study does not exclude that UVR-induced microcolony formation could also be related to specific ribotypes

Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS).

The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria