We studied the diversity of Limnohabitans using reverse line blot hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov reservoir (Czech Republic). To examine the succession of distinct lineages, we performed (i) a study of an intensive spring sampling program at the lacustrine part of the Římov reservoir (from ice melt through a phytoplankton peak to the clear-water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the compositions of distinct Limnohabitans lineages allowed for the identification of "generalists" that were always present throughout the whole season as well as "specialists" that appeared in the reservoir only for limited periods of time or irregularly. Our results indicate that some phytoplankton groups, such as cryptophytes or cyanobacteria, and zooplankton composition were the major factors modulating the distribution and dynamics of distinct Limnohabitans lineages. The highest Limnohabitans diversity was observed during the spring algal bloom, whereas the lowest was during the summer cyanobacterial bloom. The microdiversity also markedly increased upstream in the reservoir, being highest at the inflow, and thus likely reflecting strong influences of the watershed.IMPORTANCE The genus Limnohabitans is a typical freshwater bacterioplankton and is believed to play a significant role in inland freshwater habitats. This work is unique in detecting and tracing different closely related lineages of this bacterial genus in its natural conditions using the semiquantitative reverse line blot hybridization method and in discovering the factors influencing the microdiversity, subtype alternations, and seasonality.
- MeSH
- Comamonadaceae klasifikace genetika izolace a purifikace MeSH
- Cryptophyta růst a vývoj MeSH
- ekosystém MeSH
- eutrofizace MeSH
- fytoplankton růst a vývoj MeSH
- roční období MeSH
- sinice růst a vývoj MeSH
- sladká voda mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
The ecological relevance and factors shaping dynamics of Limnohabitans sp. have been largely studied by fluorescence in situ hybridization with a 16S rRNA probe targeting the R-BT group (lineages LimBCDE), but not lineage LimA. Consequently, ecology and distribution of LimA remained unknown. We developed a double hybridization strategy using a novel 23S rRNA probe specifically targeting LimA and LimE that in combination with the existing R-BT probe can discriminate LimA populations. This technique was applied for more than 1000 samples from 46 freshwater sites including long-term data sets from oligo-mesotrophic Lake Zurich, CH and meso-eutrophic Římov reservoir, CZ. LimA was ubiquitously distributed and highly abundant. Observed ecological preferences of LimA in Lake Zurich were in general similar to already reported for Limnohabitans with highest numbers in surface waters during growing seasons. Three times higher densities of LimA were detected in Římov reservoir, where they were significantly more abundant at the riverine zone especially after flood events that introduced fresh terrestrial DOM (dissolved organic matter). Moreover, statistical analyses of biological and physicochemical parameters obtained from small dynamic water bodies confirmed a correspondence between LimA and allochthonous DOM, in opposite to R-BT that was more related to algal primary production.
The competitive strength of four cosmopolitan freshwater betaproteobacterial isolates was investigated in the presence or absence of bacterivorous flagellates during continuous cultivation in artificial minimal medium at two dilution rates. Bacteria reached similar abundance and growth rate in monocultures, but in co-cultures, two strains (Acidovorax sp. and Massilia sp.) displayed significantly higher numbers and growth rates. These potential cross-feeding benefits were also supported by a high nutritional versatility of the two strains. In contrast, Hydrogenophaga sp. was seemingly less competitive or even inhibited by co-cultivation, and Limnohabitans planktonicus displayed striking abundance fluctuations. The latter two strains were least versatile in the uptake of different carbon sources and thus suffered more from interspecific competition. Moreover, remarkable strain-specific responses appeared when bacteria experienced increasing loss rates due to grazing and/or raised dilution rates. Limnohabitans planktonicus developed no successful defence strategy and was close to extinction. Massilia sp. formed grazing-resistant filaments exclusively at low dilution, but was highly reduced at increased flow-through. Acidovorax sp. was selectively ingested, but compensated grazing losses with accelerated growth rates and formed (co-)aggregates together with Hydrogenophaga sp. to escape predation at high flow-through. These species-specific interactions, growth responses and defence strategies strongly modulate mixed microbial assemblages and the microbial food web.
Two bacterial strains, II-B4(T) and II-D5(T), isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C(16 : 1)ω7c/C(16 : 1)ω6c, C(16 : 0), C(18 : 1)ω7c/C(18 : 1)ω6c and C(12 : 0). Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA-DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5(T) (=DSM 21594(T) =CIP 109844(T)), and Limnohabitans parvus sp. nov., with the type strain II-B4(T) (=DSM 21592(T) =CIP 109845(T)). The description of the genus Limnohabitans is emended accordingly.
- MeSH
- Comamonadaceae klasifikace genetika izolace a purifikace MeSH
- DNA bakterií genetika MeSH
- fenotyp MeSH
- fosfolipidy krev MeSH
- fylogeneze * MeSH
- mastné kyseliny chemie MeSH
- molekulární sekvence - údaje MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- sladká voda mikrobiologie MeSH
- techniky typizace bakterií MeSH
- ubichinon chemie MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
