Phosphorus chemistry and bacterial community composition interact in brackish sediments receiving agricultural discharges

Background

External nutrient discharges have caused eutrophication in many estuaries and coastal seas such as the Baltic Sea. The sedimented nutrients can affect bacterial communities which, in turn, are widely believed to contribute to release of nutrients such as phosphorus from the sediment.

Methods

We investigated relationships between bacterial communities and chemical forms of phosphorus as well as elements involved in its cycling in brackish sediments using up-to-date multivariate statistical methods. Bacterial community composition was determined by terminal restriction fragment length polymorphism and cloning of the 16S rRNA gene.

Results and Conclusions

The bacterial community composition differed along gradients of nutrients, especially of different phosphorus forms, from the estuary receiving agricultural phosphorus loading to the open sea. This suggests that the chemical composition of sediment phosphorus, which has been affected by riverine phosphorus loading, influenced on bacterial communities. Chemical and spatial parameters explained 25% and 11% of the variation in bacterial communities. Deltaproteobacteria, presumptively sulphate and sulphur/iron reducing, were strongly associated to chemical parameters, also when spatial autocorrelation was taken into account. Sulphate reducers correlated positively with labile organic phosphorus and total nitrogen in the open sea sediments. Sulphur/iron reducers and sulphate reducers linked to iron reduction correlated positively with aluminium- and iron-bound phosphorus, and total iron in the estuary. The sulphate and sulphur/iron reducing bacteria can thus have an important role both in the mineralization and mobilization of nutrients from sediment.

Significance

Novelty in our study is that relationships between bacterial community composition and different phosphorus forms, instead of total phosphorus, were investigated. Total phosphorus does not necessarily bring out interactions between bacteria and phosphorus chemistry since proportions of easily usable mobile (reactive) phosphorus and immobile phosphorus forms in different sediments can vary. Our study suggested possible feedbacks between different forms of phosphorus and bacterial community composition.     

Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria

Cyanobacteria are a rich source of natural products with interesting biological activities. Many of these are peptides and the end products of a non-ribosomal pathway. However, several cyanobacterial peptide classes were recently shown to be produced through the proteolytic cleavage and post-translational modification of short precursor peptides. A new class of bacteriocins produced through the proteolytic cleavage and heterocyclization of precursor proteins was recently identified from marine cyanobacteria. Here we show the widespread occurrence of bacteriocin gene clusters in cyanobacteria through comparative analysis of 58 cyanobacterial genomes. A total of 145 bacteriocin gene clusters were discovered through genome mining. These clusters encoded 290 putative bacteriocin precursors. They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide. The gene clusters could be classified into seven groups according to their gene organization and domain composition. This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups. Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.     

Does oxygen availability regulate sexual reproduction in local populations of the littoral cladoceran Alonella nana?

We investigated sexual reproduction patterns of a ubiquitous littoral cladoceran Alonella nana (Anomopoda, Chydoridae), using ecological and paleoecological approaches to clarify the forcing mechanisms behind its sexual reproduction. Contemporary sampling of A. nana populations in two environmentally different lakes showed abundant sexual reproduction in the lake with eutrophic, oxygen-deficient conditions and scarce gamogenesis in the oligotrophic, well-oxygenated lake. Sediment core studies from the same lakes indicated that comparable sexual reproduction patterns had prevailed for many centuries. However, in eutrophic Lake Hamptr?sk, A. nana increased its sexual reproduction from 1700 ad onward, consistently with decreasing trend in chironomid-inferred oxygen. The core samples, together with a surface sediment dataset of 25 lakes from southern and central Finland, showed a negative correlation between ephippia of A. nana and winter oxygen, although the surface sediment data per se did not show any significant correlation. When the dataset was scaled locally to include lakes in close proximity in southern Finland, the correlation became clearer. The results imply that the spatial and temporal variations in sexual reproduction of A. nana populations may partly be explained by differences in oxygen levels.     

Subfossil chydorid (Cladocera, Chydoridae) ephippia as paleoenvironmental proxies: evidence from boreal and subarctic lakes in Finland

Chydorids (Cladocera, Chydoridae) have two reproductive strategies: asexual reproduction that prevails during favorable environmental conditions and sexual reproduction that is induced by environmental stimuli associated with seasonal or aperiodic environmental stresses. These modes of reproduction can be recognized in the subfossil sedimentary records as parthenogenetic shells of females (asexual reproduction) and by ephippia (sexual reproduction). We studied the interrelations between subfossil chydorid ephippia and environmental variables by analyzing surface sediment samples obtained from 76 Finnish lakes across a latitudinal gradient (60–70°N). The results showed that the total chydorid ephippia (TCE) increases along the climate gradient from ~2 to 3% in the south to ~25% in the north and suggested a significant dependence (r ~ −0.8, P < 0.001) with several climate factors, especially that of mean July air temperature. We used this relationship to create a model for reconstructing past mean July air temperatures. A linear regression of the log₁₀ transformed TCE as a single independent variable explained 76% (SE ± 0.76°C) of the variance of the observed mean July air temperatures. Accordingly, we propose that this novel tool may be highly suitable for reconstructing paleotemperatures in cold-temperate environments.     

Nostophycin biosynthesis is directed by a hybrid polyketide synthase-nonribosomal peptide synthetase in the toxic cyanobacterium Nostoc sp. strain 152

Cyanobacteria are a rich source of natural products with interesting pharmaceutical properties. Here, we report the identification, sequencing, annotation, and biochemical analysis of the nostophycin (npn) biosynthetic gene cluster. The npn gene cluster spans 45.1 kb and consists of three open reading frames encoding a polyketide synthase, a mixed polyketide nonribosomal peptide synthetase, and a nonribosomal peptide synthetase. The genetic architecture and catalytic domain organization of the proteins are colinear in arrangement, with the putative order of the biosynthetic assembly of the cyclic heptapeptide. NpnB contains an embedded monooxygenase domain linking nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) catalytic domains and predicted here to hydroxylate the nostophycin during assembly. Expression of the adenylation domains and subsequent substrate specificity assays support the involvement of this cluster in nostophycin biosynthesis. Biochemical analyses suggest that the loading substrate of NpnA is likely to be a phenylpropanoic acid necessitating deletion of a carbon atom to explain the biosynthesis of nostophycin. Biosyntheses of nostophycin and microcystin resemble each other, but the phylogenetic analyses suggest that they are distantly related to one another.     

Localization of cytokinins in somatic and zygotic embryos of Tilia cordata using immunocytochemistry

Immunofluorescent and immunogold labeling was used to study the localization of cytokinins in developing somatic and zygotic embryos of Tilia cordata Miller. Broad-specificity polyclonal antibodies active against dihydrozeatin riboside (DHZR)/zeatin riboside (ZR)-type and isopentenyladenosine (iPR)-type cytokinins were used for immunolabeling. Immunofluorescent microscopy showed that these cytokinins were concentrated in highly cytoplasmic cells showing meristematic character. Cotyledon initials and primary meristems of heart-stage somatic embryos, as well as heart-stage zygotic embryos, were labeled. During elongation of embryos, cytokinin immunoreactive material was concentrated to areas having meristematic character. Root apex, shoot meristem, and cotyledon cells of somatic and zygotic cotyledonary embryos, as well as epidermal and subepidermal cell layers of the hypocotyl, showed the strongest immunoreaction. The nucleoli, especially, had a very strong signal. Results at the ultrastructural level with gold-conjugated protein A supported these conclusions. Gold particles were distributed in the nuclei, especially in the nucleoli and throughout the ground cytoplasm. They were occasionally associated with plastids and mitochondria, but seldom with other organelles.     

Expression of the calcium-binding protein S100A4 is markedly up-regulated by osmotic stress and is involved in the renal osmoadaptive response

Proteomic analysis of Inner Medullary Collecting Duct (IMCD3) cells adapted to increasing levels of tonicity (300, 600, and 900 mosmol/kg H(2)O) by two-dimensional difference gel electrophoresis and mass spectrometry revealed several proteins as yet unknown to be up-regulated in response to hypertonic stress. Of these proteins, one of the most robustly up-regulated (22-fold) was S100A4. The identity of the protein was verified by high pressure liquid chromatography-mass spectrometry. Western blot analysis confirmed increased expression with increased tonicity, both acute and chronic. S100A4 protein expression was further confirmed by immunocytochemical analysis. Cells grown in isotonic conditions showed complete absence of immunostaining, whereas chronically adapted IMCD3 cells had uniform cytoplasmic localization. The protein is also regulated in vivo as in mouse kidney tissues S100A4 expression was many -fold greater in the papilla as compared with the cortex and increased further in the papilla upon 36 h of thirsting. Increased expression of S100A4 was also observed in the medulla and papilla, but not the cortex of a human kidney. Data from Affymetrix gene chip analysis and quantitative PCR also revealed increased S100A4 message in IMCD3 cells adapted to hypertonicity. The initial expression of message increased at 8-10 h following exposure to acute sublethal hypertonic stress (550 mosmol/kg H(2)O). Protein and message half-life in IMCD3 cells were 85.5 and 6.8 h, respectively. Increasing medium tonicity with NaCl, sucrose, mannitol, and choline chloride stimulated S100A4 expression, whereas urea did not. Silencing of S100A4 expression using a stable siRNA vector (pSM2; Open Biosystems) resulted in a 48-h delay in adaptation of IMCD3 cells under sublethal osmotic stress, suggesting S100A4 is involved in the osmoadaptive response. In summary, we describe the heretofore unrecognized up-regulation of a small calcium-binding protein, both in vitro and in vivo, whose absence profoundly delays osmoadaptation and slows cellular growth under hypertonic conditions.     

Interlaboratory comparison of Taq Nuclease Assays for the quantification of the toxic cyanobacteria Microcystis sp

The application of quantitative real-time PCR has been proposed for the quantification of toxic genotypes of cyanobacteria. We have compared the Taq Nuclease Assay (TNA) in quantifying the toxic cyanobacteria Microcystis sp. via the intergenic spacer region of the phycocyanin operon (PC) and mcyB indicative of the production of the toxic heptapeptide microcystin between three research groups employing three instruments (ABI7300, GeneAmp5700, ABI7500). The estimates of mcyB genotypes were compared using (i) DNA of a mcyB containing strain and a non-mcyB containing strain supplied in different mixtures across a low range of variation (0-10% of mcyB) and across a high range of variation (20-100%), and (ii) DNA from field samples containing Microcystis sp. For all three instruments highly significant linear regression curves between the proportion of the mcyB containing strain and the percentage of mcyB genotypes both within the low range and within the high range of mcyB variation were obtained. The regression curves derived from the three instruments differed in slope and within the high range of mcyB variation mcyB proportions were either underestimated (0-50%) or overestimated (0-72%). For field samples cell numbers estimated via both TNAs as well as mcyB proportions showed significant linear relationships between the instruments. For all instruments a linear relationship between the cell numbers estimated as PC genotypes and the cell numbers estimated as mcyB genotypes was observed. The proportions of mcyB varied from 2 to 28% and did not differ between the instruments. It is concluded that the TNA is able to provide quantitative estimates on mcyB genotype numbers that are reproducible between research groups and is useful to follow variation in mcyB genotype proportion occurring within weeks to months.     

Quantitative Real-Time PCR Detection of Toxic Nodularia Cyanobacteria in the Baltic Sea

A specific quantitative real-time PCR (qPCR) method was developed for the quantification of hepatotoxin nodularin-producing Nodularia, one of the main bloom-forming cyanobacteria in the Baltic Sea. Specific PCR primers were designed for subunit F of the nodularin synthetase gene (ndaF), which encodes the NdaF subunit of the nodularin synthetase gene complex needed for nodularin production. The qPCR method was applied to water samples (a total of 120 samples) collected from the Baltic Sea in July 2004. As few as 30 ndaF gene copies ml⁻¹ of seawater could be detected, and thus, the method was very sensitive. The ndaF gene copy numbers and nodularin concentrations were shown to correlate in the Baltic seawater, indicating the constant production of nodularin by Nodularia. This qPCR method for the ndaF gene can be used for detailed studies of Nodularia blooms and their formation. ndaF gene copies and nodularin were detected mostly in the surface water but also in deeper water layers (down to 30 m). Toxic Nodularia blooms are not only horizontally but also vertically widely distributed, and thus, the Baltic fauna is extensively exposed to nodularin.