Alternativní zemědělství - informační bulletin č.6

Témata bulletinu Alternativní zemědělství č.6 jsou: Návštěva na farmách Biolandu, Je hnojení pouze náhrada živin?, Budeme mít odrůdy pro alternativní zemědělství?, Chov skotu v alternativních podmínkách ve SRN, Půdní pokryvy, Přechod k organickému vinohradnictví, Vliv současného životního prostředí, energie a techniky na život a především na člověka, Jak se pozná biopotravina?, Výroba a použití bioplynu v zemědělství

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization

An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers

Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil.

Bacteria were identified associated with biodegradation of aromatic pollutants biphenyl, benzoate, and naphthalene in a long-term polychlorinated biphenyl- and polyaromatic hydrocarbon-contaminated soil. In order to avoid biases of culture-based approaches, stable isotope probing was applied in combination with sequence analysis of 16 S rRNA gene pyrotags amplified from (13)C-enriched DNA fractions. Special attention was paid to pyrosequencing data analysis in order to eliminate the errors caused by either generation of amplicons (random errors caused by DNA polymerase, formation of chimeric sequences) or sequencing itself. Therefore, sample DNA was amplified, sequenced, and analyzed along with the DNA of a mock community constructed out of 8 bacterial strains. This warranted that appropriate tools and parameters were chosen for sequence data processing. (13)C-labeled metagenomes isolated after the incubation of soil samples with all three studied aromatics were largely dominated by Proteobacteria, namely sequences clustering with the genera Rhodanobacter Burkholderia, Pandoraea, Dyella as well as some Rudaea- and Skermanella-related ones. Pseudomonads were mostly labeled by (13)C from naphthalene and benzoate. The results of this study show that many biphenyl/benzoate-assimilating bacteria derive carbon also from naphthalene, pointing out broader biodegradation abilities of some soil microbiota. The results also demonstrate that, in addition to traditionally isolated genera of degradative bacteria, yet-to-be cultured bacteria are important players in bioremediation. Overall, the study contributes to our understanding of biodegradation processes in contaminated soil. At the same time our results show the importance of sequencing and analyzing a mock community in order to more correctly process and analyze sequence data

The Role of Cryotherapy in Vitreous Concentrations of Topotecan Delivered by Episcleral Hydrogel Implant

Transscleral diffusion delivery of chemotherapy is a promising way to reach the vitreal seeds of retinoblastoma, the most common intraocular malignancy in childhood. In this in vivo study, the delivery of topotecan via lens-shaped, bi-layered hydrogel implants was combined with transconjunctival cryotherapy to assess whether cryotherapy leads to higher concentrations of topotecan in the vitreous. The study included 18 New Zealand albino rabbits; nine rabbits received a topotecan-loaded implant episclerally and another nine rabbits received transconjunctival cryotherapy superotemporally 2 weeks before implant administration. Median vitreous total topotecan exposures (area under the curve, AUC) were 455 ng·h/mL for the cryotherapy group and 281 ng·h/mL for the non-cryotherapy group, and were significantly higher in the cryotherapy group, similar to maximum levels. Median plasma AUC were 50 ng·h/mL and 34 ng·h/mL for the cryotherapy and non-cryotherapy groups, respectively, with no statistically significant differences between them. In both groups, AUC values in the vitreous were significantly higher than in plasma, with plasma exposure at only approximately 11–12% of the level of vitreous exposure. The results confirmed the important role of the choroidal vessels in the pharmacokinetics of topotecan during transscleral administration and showed a positive effect of cryotherapy on intravitreal penetration, resulting in a significantly higher total exposure in the vitreous

Analysis of inorganic nutrients and contaminants available in the soil.

<p>Results shown are averages from 5 independently measured samples (performed commercially).</p>a<p>Based on method CZ_SOP_D06_07_121.</p>b<p>Based on method US EPA 8082.</p>c<p>Based on methods EPA 8270, EPA 8131, EPA 8091.</p>d<p>Based on method US EPA 200.7.</p

Bacterial strains used for the preparation of the mock community.

<p>Bacterial strains used for the preparation of the mock community.</p

Number of sequences obtained after sequence processing, after subtracting sequences detected also in control DNA (valid sequences), and after normalizing.

<p>Number of sequences obtained after sequence processing, after subtracting sequences detected also in control DNA (valid sequences), and after normalizing.</p

Top OTUs detected in ¹³C-DNA after incubation of soil with ¹³C-biphenyl, ¹³C-benzoate, and ¹³C-naphthalene.

<p>Identification was performed by mothur-implemented RDP reference files <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040653#pone.0040653-Wang1" target="_blank">[78]</a> and the closest type strain was determined by RDP Seqmatch with the representative sequence of each OTU <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040653#pone.0040653-Cole1" target="_blank">[76]</a>. The entire dataset is in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040653#pone.0040653.s002" target="_blank">Table S1</a>.</p>a<p>Relative abundance of sequences.</p>b<p>Identification of OTU based on identification of the representative at the level of genus as determined by RDP classifier (using 50% threshold).</p>c<p>Determined by RDP Seqmatch.</p>d<p>Score represents S_ab score – the number of (unique) 7-base oligomers shared between the sequence data and a given RDP sequence divided by the lowest number of unique oligos in either of the two sequences.</p>e<p>Refers to samples where the same OTU was detected.</p