The gyrB gene is a useful phylogenetic marker for exploring the diversity of flavobacterium strains isolated from terrestrial and aquatic habitats in Antarctica

Within the phylum Bacteroidetes, the gyrB gene, encoding for the B subunit of the DNA gyrase, has been used as phylogenetic marker for several genera closely related to Flavobacterium. The phylogenies of the complete 16S rRNA gene and the gyrB gene were compared for thirty-three Antarctic Flavobacterium isolates and twenty-three type strains from closely related Flavobacterium species. GyrB gene sequences provided a higher discriminatory power to distinguish between different Flavobacterium groups than 16S rRNA gene sequences. The gyrB gene is therefore a promising molecular marker for elucidating the phylogenetic relationships among Flavobacterium species and should be evaluated for all the other type strains of described Flavobacterium species. Combining the phylogeny of both genes, the new Antarctic Flavobacterium strains constitute fifteen Flavobacterium groups, including at least thirteen potentially new species together with one group of isolates probably belonging to the species F. micromati and one group close to F. gelidilacus

Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

Background: Copper dependent nitrite reductase, NirK, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct structural NirK classes and phylogenetic clades of NirK-type denitrifiers have previously been observed based on a limited set of NirK sequences, however, their environmental distribution or ecological strategies are currently unknown. In addition, environmental nirK-type denitrifiers are currently underestimated in PCR-dependent surveys due to primer coverage limitations that can be attributed to their broad taxonomic diversity and enormous nirK sequence divergence. Therefore, we revisited reported analyses on partial NirK sequences using a taxonomically diverse, full-length NirK sequence dataset. Results: Division of NirK sequences into two phylogenetically distinct clades was confirmed, with Clade I mainly comprising Alphaproteobacteria (plus some Gamma- and Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae, Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta and Gamma). Failure of currently available primer sets to target diverse NirK-type denitrifiers in environmental surveys could be attributed to mismatches over the whole length of the primer binding regions including the 3' site, with Clade II sequences containing higher sequence divergence than Clade I sequences. Simultaneous presence of both the denitrification and DNRA pathway could be observed in 67 % of all NirK-type denitrifiers. Conclusion: The previously reported division of NirK into two distinct phylogenetic clades was confirmed using a taxonomically diverse set of full-length NirK sequences. Enormous sequence divergence of nirK gene sequences, probably due to variable nirK evolutionary trajectories, will remain an issue for covering diverse NirK-type denitrifiers in amplicon-based environmental surveys. The potential of a single organism to partition nitrate to either denitrification or dissimilatory nitrate reduction to ammonium appeared to be more widespread than originally anticipated as more than half of all NirK-type denitrifiers were shown to contain both pathways in their genome

Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers

The estuarine nitrogen cycle can be substantially altered due to anthropogenic activities resulting in increased amounts of inorganic nitrogen (mainly nitrate). In the past, denitrification was considered to be the main ecosystem process removing reactive nitrogen from the estuarine ecosystem. However, recent reports on the contribution of dissimilatory nitrate reduction to ammonium (DNRA) to nitrogen removal in these systems indicated a similar or higher importance, although the ratio between both processes remains ambiguous. Compared to denitrification, DNRA has been underexplored for the last decades and the key organisms carrying out the process in marine environments are largely unknown. Hence, as a first step to better understand the interplay between denitrification, DNRA and reduction of nitrate to nitrite in estuarine sediments, nitrogen reduction potentials were determined in sediments of the Paulina polder mudflat (Westerschelde estuary). We observed high variability in dominant nitrogen removing processes over a short distance (1.6m) with nitrous oxide, ammonium and nitrite production rates differing significantly between all sampling sites. Denitrification occurred at all sites, DNRA was either the dominant process (two out of five sites) or absent, while nitrate reduction to nitrite was observed in most sites but never dominant. In addition, novel nitrate-to-ammonium reducers assigned to Thalassospira, Celenbacter, and Halomonas, for which DNRA was thus far unreported, were isolated, with DNRA phenotype reconfirmed through nrfA gene amplification. This study demonstrates high small scale heterogeneity among dissimilatory nitrate reduction processes in estuarine sediments and provides novel marine DNRA organisms that represent valuable alternatives to the current model organisms

Copepods controlling bacterial communities on fecal pellets

The traditional view of the marine food web depicts bacteria and copepods (mainly planktonic species) as separate units, indirectly connected via nutrient cycling and trophic cascade processes. In contrast, several recent studies have demonstrated that zooplankton and bacteria directly interact, physically, e.g. bacteria attached to zooplankton bodies and biologically, e.g. zooplankton feeding supports bacterial growth through their excretions. Copepods produce large numbers of fecal pellets in the marine environment. Almost immediately after egestion, pellets host extensive bacterial communities. Low amounts of fecal material in sediment traps indicate most part of fecal pellet production is retained in the water column as a result of high microbial degradation rates and planktonic copepods reworking the fecal pellets. First observations on the re-use of feces by benthic copepods points out that these crustaceans profit in a yet unknown way from fecal pellet bacteria. Recently it was illustrated that the benthic species Paramphiascella fulvofasciata increases its fecal pellet production according to its food source. Presumably the bacteria associated with fecal pellets create a trophic upgrading of the fecal material. A detailed characterization of these bacteria is crucial to understand the trophic pathways in the lower marine food web. Culture-independent molecular techniques (e.g. DGGE) showed the specificity of these communities. Shifts in the bacterial communities are caused by age, original food source (e.g. diatoms) and producer of the fecal pellet. Moreover, an additional grazing experiment illustrated the importance of the freshness of the initial food source for grazing preferences but also for the bacterial communities on the fecal pellets. Food of low quality was compensated by more diverse bacterial communities that were available for additional grazing. These results illustrated the importance of fecal bacteria in the transformation of organic matter and energy transfer in marine sediments

How endo- is endo-?: surface sterilization of delicate samples: a Bryopsis (Bryopsidales, Chlorophyta) case study

In the search for endosymbiotic bacteria, elimination of ectosymbionts is a key point of attention. Commonly, the surface of the host itself or the symbiotic structures are sterilized with aggressive substances such as chlorine or mercury derivatives. Although these disinfectants are adequate to treat many species, they are not suitable for surface sterilization of delicate samples. In order to study the bacterial endosymbionts in the marine green alga Bryopsis, the host plant's cell wall was mechanically, chemically and enzymatically cleaned. Merely a chemical and enzymatical approach proved to be highly effective. Bryopsis thalli treated with cetyltrimethylammonium bromide (CTAB) lysis buffer, proteinase K and bactericidal cleanser Umonium Master showed no bacterial growth on agar plates or bacterial fluorescence when stained with a DNA fluorochrome. Moreover, the algal cells were intact after sterilization, suggesting endophytic DNA is still present within these algae. This new surface sterilization procedure opens the way to explore endosymbiotic microbial communities of other, even difficult to handle, samples