1. Microbial ecology According to Caumette et al. (2015) the term ecology is derived from the Greek words “oikos” (the house and its operation) and “logos” (the word, knowledge or discourse) and can, therefore, be defined as the scientific field engaged in the “knowledge of the laws governing the house”. This, in extension, results in the simple conclusion that microbial ecology represents the study of the relationship between microorganisms, their co-occurring biota and the prevailing environmental conditions (Caumette et al. 2015). The term microbial ecology has been in use since the early 1960s (Caumette et al. 2015) and microbial ecologists have made astonishing discoveries since. Microbial life at extremes such as in the hydrothermal vents (see Dubilier et al. 2008 and references therein) or the abundance of picophytoplankton (Waterbury et al. 1979; Chisholm et al. 1988) in the deep and surface waters of the oceans, respectively, are only a few of many highlights. Nevertheless, a microbial ecologist who, after leaving the field early in their career, now intends to return would hardly recognise again their former scientific field. The main reason for this hypothesis is to be found in the advances made to the methodologies employed in the field. Most of these were developed for biomedical research and were subsequently hijacked, sometimes followed by minor modifications, by microbial ecologists. The Author presents in this thesis scientific findings which, although spanning only a fraction of the era of research into microbial ecology, have been obtained using various modern tools of the trade. These studies were undertaken by the Author during his employment as postdoctoral scientist at Warwick University (UK), as member of staff at Plymouth Marine Laboratory (UK) and as scientist at the TU Bergakademie Freiberg. Although the scientific issues and the environmental habitats investigated by the Author changed due to funding constraints or due to change of work place (i.e. from the marine to the mining environment) the research shared, by and large, a common aim: to further the existing understanding of microbial communities. The methodological approach chosen to achieve this aim employed both isolation followed by the characterisation of microorganisms and culture independent techniques. Both of these strategies utilised again a variety of methods, but techniques in molecular biology represent a common theme. In particular, the polymerase chain reaction (PCR) formed the work horse for much of the research since it has been routinely used for the amplification of a marker gene for strain identification or analysis of the microbial diversity. To achieve this, the amplicons were either directly sequenced by the Sanger approach or analysed via the application of genetic fingerprint techniques or through Sanger sequencing of individual amplicons cloned into a heterologous host. However, the Author did not remain at idle while with these ‘classical’ approaches for the analysis of microbial communities, but utilised the advances made in the development of nucleotide sequence analysis. In particular, the highly parallelised sequencing techniques (e.g. 454 pyrosequencing, Illumina sequencing) offered the chance to obtain both high genetic resolution of the microbial diversity present in a sample and identification of many individuals through sequence comparison with appropriate sequence repositories. Moreover, these next generation sequencing (NGS) techniques also provided a cost-effective opportunity to extent the characterisation of microbial strains to non-clonal cultures and to even complex microbial assemblages (metagenomics). The work involving the high throughput sequencing techniques has been undertaken in collaboration with Dr Jack Gilbert (PML, lateron at Argonne National Laboratory, USA) and, since at Freiberg, with Dr Anja Poehlein (Goettingen University). These colleagues are thanked for their support with sequence data handling and analyses.

No description available.

1. Microbial ecology According to Caumette et al. (2015) the term ecology is derived from the Greek words “oikos” (the house and its operation) and “logos” (the word, knowledge or discourse) and can, therefore, be defined as the scientific field engaged in the “knowledge of the laws governing the house”. This, in extension, results in the simple conclusion that microbial ecology represents the study of the relationship between microorganisms, their co-occurring biota and the prevailing environmental conditions (Caumette et al. 2015). The term microbial ecology has been in use since the early 1960s (Caumette et al. 2015) and microbial ecologists have made astonishing discoveries since. Microbial life at extremes such as in the hydrothermal vents (see Dubilier et al. 2008 and references therein) or the abundance of picophytoplankton (Waterbury et al. 1979; Chisholm et al. 1988) in the deep and surface waters of the oceans, respectively, are only a few of many highlights. Nevertheless, a microbial ecologist who, after leaving the field early in their career, now intends to return would hardly recognise again their former scientific field. The main reason for this hypothesis is to be found in the advances made to the methodologies employed in the field. Most of these were developed for biomedical research and were subsequently hijacked, sometimes followed by minor modifications, by microbial ecologists. The Author presents in this thesis scientific findings which, although spanning only a fraction of the era of research into microbial ecology, have been obtained using various modern tools of the trade. These studies were undertaken by the Author during his employment as postdoctoral scientist at Warwick University (UK), as member of staff at Plymouth Marine Laboratory (UK) and as scientist at the TU Bergakademie Freiberg. Although the scientific issues and the environmental habitats investigated by the Author changed due to funding constraints or due to change of work place (i.e. from the marine to the mining environment) the research shared, by and large, a common aim: to further the existing understanding of microbial communities. The methodological approach chosen to achieve this aim employed both isolation followed by the characterisation of microorganisms and culture independent techniques. Both of these strategies utilised again a variety of methods, but techniques in molecular biology represent a common theme. In particular, the polymerase chain reaction (PCR) formed the work horse for much of the research since it has been routinely used for the amplification of a marker gene for strain identification or analysis of the microbial diversity. To achieve this, the amplicons were either directly sequenced by the Sanger approach or analysed via the application of genetic fingerprint techniques or through Sanger sequencing of individual amplicons cloned into a heterologous host. However, the Author did not remain at idle while with these ‘classical’ approaches for the analysis of microbial communities, but utilised the advances made in the development of nucleotide sequence analysis. In particular, the highly parallelised sequencing techniques (e.g. 454 pyrosequencing, Illumina sequencing) offered the chance to obtain both high genetic resolution of the microbial diversity present in a sample and identification of many individuals through sequence comparison with appropriate sequence repositories. Moreover, these next generation sequencing (NGS) techniques also provided a cost-effective opportunity to extent the characterisation of microbial strains to non-clonal cultures and to even complex microbial assemblages (metagenomics). The work involving the high throughput sequencing techniques has been undertaken in collaboration with Dr Jack Gilbert (PML, lateron at Argonne National Laboratory, USA) and, since at Freiberg, with Dr Anja Poehlein (Goettingen University). These colleagues are thanked for their support with sequence data handling and analyses.

Überstände von Cyanobakterien sind ein vielversprechendes Produkt zur Förderung des Pflanzenwachstums, da sie alle Vorteile der freigesetzten bioaktiven Verbindungen, wie z. B. Phytohormone, enthalten, ohne die Zwänge der mikrobiellen Inokulationen. Es ist jedoch nur wenig darüber bekannt, wie Cyanobakterien die Reaktion der Pflanzen auf molekularer Ebene modulieren könnten. In dieser Studie wurde das in Chile heimische Gras Polypogon australis als Modell verwendet, um die Wirkung von Überständen aus Kulturen von sieben autochthonen Bodencyanobakterien zu untersuchen. Von diesen zeigten die Überstände der Kulturen von Trichormus sp. die beste wachstumsfördernde Wirkung auf P. australis. Die ICP-MS-Analyse ergab, dass die Überstände von Trichormus sp. eine ähnliche Nährstoffzusammensetzung aufwiesen wie das für das Wachstum der Cyanobakterien verwendete Medium BG-11, mit Ausnahme der Elemente P und Mn, die in der späten exponentiellen Phase der Kulturen verarmt waren. Dann wurden Überstände von Trichormus sp.-Kulturen, die in der späten exponentiellen Phase gesammelt wurden und die eine Menge von 32,7 pmol trans-Zeatin pro mg Chl-a enthielten, zur Bewertung der Reaktion von P. australis auf transkriptioneller Ebene verwendet. Ein BG-11-Medium, das frei von P und Mn war, wurde als Kontrolle verwendet. Ganzes Pflanzengewebe wurde 3 Stunden nach der Behandlung entnommen und für eine RNA-seq-Analyse verwendet. Die Ergebnisse zeigten, dass die Überstände von Trichormus sp. die Pflanzenreaktion hauptsächlich über die N- und Phytohormonwege modulierten, die in engem Zusammenhang mit dem C- und Lipidstoffwechsel stehen. Die behandelten Pflanzen wiesen 4 und 8 Tage nach der Anwendung größere Triebe auf als die Kontrollpflanzen, aber es wurden keine Unterschiede bei der Wurzellänge festgestellt. Dieser Phänotyp lässt sich durch die Induktion von Genen für die Gibberellin-Biosynthese in P. australis erklären, die durch andere Hormone wie Auxine, Brassinosteroide und Ethylen unterstützt wird. Andererseits wurde in mit P. australis behandelten Pflanzen eine induzierte systemische Resistenzreaktion beobachtet, die hauptsächlich durch einen Ethylen-Jasmonat-Crosstalk vermittelt wurde. Diese Arbeit unterstützt die Verwendung von Überständen als eine gute Option zur Förderung des Pflanzenwachstums.:Table of content Preliminary Page Resumen i Abstract ii Übersetzung iii DECLARATION ix 1. Introduction 1 1.1. Plant-growth promoting microorganisms 1 1.2. Soil cyanobacteria 2 1.3. Physiology of soil cyanobacteria 2 1.4. Cyanobacterial plant growth-promoting molecules 4 1.5. Plant response to bioactive compounds 6 1.6. Cyanobacterial supernatants 9 1.7. Polypogon australis as a plant study model 11 2. Methodology 13 2.1. Obtention of the cyanobacterial cultures 13 2.2. Supernatant collection from the cyanobacterial cultures 14 2.3. Cyanobacterial biomass quantification 15 2.3.1. Chlorophyll-a content 15 2.3.2. Biomass dry weight 15 2.3.3. Determination of the growth phases 15 2.4. Chemical characterization of the supernatants 16 2.4.1. Nitrate content 16 2.4.2. Total element content 16 2.4.3. Zeatin content 16 2.5. Preparation of the modified BG-11 medium (BG-11M medium) 17 2.6. Bioassays with cyanobacterial supernatants 18 2.6.1. Effect of supernatants of the 25 mL cultures on P. australis germination 18 2.6.2. Effect of supernatants of the 25 mL cultures on P. australis plants 18 2.6.3. Effect of supernatants of the 2,400 mL cultures on P. australis plants 19 2.7. Statistical analysis 19 2.8. Determination of transcriptional changes in P. australis. 20 2.8.1. Plant treatments and tissue collection 20 2.8.2. Total RNA extraction from plant tissue 20 2.8.3. DNA removal 20 2.8.4. mRNA sequencing, de novo assembly, and differential expression analysis 21 2.8.5. Contig annotation and functional classification 22 3. Results 24 3.1. Trichormus sp. cultures produce the highest biomass content 24 3.2. Trichormus sp. cultures have a low P content 25 3.3. Trichormus sp. supernatants have the best growth-promoting effect on the growth of P. australis 25 3.4. Supernatant nutrient content of Trichormus sp. cultures change through the growth phases 27 3.5. Supernatants used in the transcriptomic assay and BG-11M medium have a lower nutrient content than BG-11 medium 30 3.6. Trichormus sp. supernatants promote the growth of P. australis to a greater extent than the BG-11M medium 32 3.7. Trichormus sp. supernatants contain zeatin 33 3.8. Trichormus sp. supernatants modulated more P. australis genes than the BG-11M medium 34 3.9. Trichormus sp. supernatants regulate the gene expression of growth and defense responses in P. australis 37 4. Discussion 57 4.1. The plant-growth promoting effect of Thrichormus sp. supernatants 57 4.2. The role of P and Mn in the growth-promoting effect of Trichormus sp. supernatants 58 4.3. Modulation of P. australis N-metabolism by Trichormus sp. supernatants 59 4.4. P. australis nitrogen and carbon metabolism in response to Trichormus supernatants 63 4.5. P. australis phytohormone-metabolism modulated by Trichormus supernatants 64 4.6. The role of lipid metabolism in the response to Trichormus supernatants 67 4.7. P. australis defense response triggered by Trichormus supernatants 68 4.8. Phytohormone crosstalk and defense response in P. australis treated with Trichormus sp. supernatants 71 4.9. Perspectives and challenges for the biotechnological use of Trichormus sp. supernatants 73 5. Conclusion 76 Bibliographic references 77 Annexes 116 / Cyanobacterial supernatants are a promising plant growth-promoting product since they contain all the advantages of the released bioactive compounds, such as phytohormones, without the constraints of microbial inoculations. However, little is known about how cyanobacteria could modulate the plant response at a molecular level. In this research, the Chilean native grass, Polypogon australis, was used as a model for assaying the effect of supernatants obtained from cultures of seven autochthonous soil cyanobacteria. Of them, supernatants of Trichormus sp. cultures showed the best growth-promoting effects on P. australis. Analysis by ICP-MS showed that Trichormus sp. supernatants had a similar nutrient composition to the medium used for the cyanobacteria growth, BG-11, except for the elements P and Mn, which were depleted when the late exponential phase of the cultures was reached. Then, supernatants of Trichormus sp. cultures collected in the late exponential phase, which contained an amount of 32.7 pmol of trans-zeatin per mg of Chl-a, were employed for evaluating the P. australis response at a transcriptional level. A BG-11 medium free of P and Mn was utilized as a control. Whole plant tissue was collected 3 h-post treatment and used for an RNA-seq analysis. Results showed that Trichormus sp. supernatants modulated the plant response mainly by the N and phytohormones pathways, in close relation with C and lipid metabolism. Treated plants showed larger shoots than control plants 4 and 8 days after application, but no differences were observed in root length. This phenotype can be explained by the induction in P. australis of gibberellin biosynthesis genes, supported by other hormones such as auxins, brassinosteroids, and ethylene. On the other hand, an induced systemic resistance response was observed in P. australis-treated plants, mostly mediated by an ethylene-jasmonate crosstalk. This work supports the use of supernatants as a good plant growth-promoting option.:Table of content Preliminary Page Resumen i Abstract ii Übersetzung iii DECLARATION ix 1. Introduction 1 1.1. Plant-growth promoting microorganisms 1 1.2. Soil cyanobacteria 2 1.3. Physiology of soil cyanobacteria 2 1.4. Cyanobacterial plant growth-promoting molecules 4 1.5. Plant response to bioactive compounds 6 1.6. Cyanobacterial supernatants 9 1.7. Polypogon australis as a plant study model 11 2. Methodology 13 2.1. Obtention of the cyanobacterial cultures 13 2.2. Supernatant collection from the cyanobacterial cultures 14 2.3. Cyanobacterial biomass quantification 15 2.3.1. Chlorophyll-a content 15 2.3.2. Biomass dry weight 15 2.3.3. Determination of the growth phases 15 2.4. Chemical characterization of the supernatants 16 2.4.1. Nitrate content 16 2.4.2. Total element content 16 2.4.3. Zeatin content 16 2.5. Preparation of the modified BG-11 medium (BG-11M medium) 17 2.6. Bioassays with cyanobacterial supernatants 18 2.6.1. Effect of supernatants of the 25 mL cultures on P. australis germination 18 2.6.2. Effect of supernatants of the 25 mL cultures on P. australis plants 18 2.6.3. Effect of supernatants of the 2,400 mL cultures on P. australis plants 19 2.7. Statistical analysis 19 2.8. Determination of transcriptional changes in P. australis. 20 2.8.1. Plant treatments and tissue collection 20 2.8.2. Total RNA extraction from plant tissue 20 2.8.3. DNA removal 20 2.8.4. mRNA sequencing, de novo assembly, and differential expression analysis 21 2.8.5. Contig annotation and functional classification 22 3. Results 24 3.1. Trichormus sp. cultures produce the highest biomass content 24 3.2. Trichormus sp. cultures have a low P content 25 3.3. Trichormus sp. supernatants have the best growth-promoting effect on the growth of P. australis 25 3.4. Supernatant nutrient content of Trichormus sp. cultures change through the growth phases 27 3.5. Supernatants used in the transcriptomic assay and BG-11M medium have a lower nutrient content than BG-11 medium 30 3.6. Trichormus sp. supernatants promote the growth of P. australis to a greater extent than the BG-11M medium 32 3.7. Trichormus sp. supernatants contain zeatin 33 3.8. Trichormus sp. supernatants modulated more P. australis genes than the BG-11M medium 34 3.9. Trichormus sp. supernatants regulate the gene expression of growth and defense responses in P. australis 37 4. Discussion 57 4.1. The plant-growth promoting effect of Thrichormus sp. supernatants 57 4.2. The role of P and Mn in the growth-promoting effect of Trichormus sp. supernatants 58 4.3. Modulation of P. australis N-metabolism by Trichormus sp. supernatants 59 4.4. P. australis nitrogen and carbon metabolism in response to Trichormus supernatants 63 4.5. P. australis phytohormone-metabolism modulated by Trichormus supernatants 64 4.6. The role of lipid metabolism in the response to Trichormus supernatants 67 4.7. P. australis defense response triggered by Trichormus supernatants 68 4.8. Phytohormone crosstalk and defense response in P. australis treated with Trichormus sp. supernatants 71 4.9. Perspectives and challenges for the biotechnological use of Trichormus sp. supernatants 73 5. Conclusion 76 Bibliographic references 77 Annexes 116 / Los sobrenadantes de cianobacterias son prometedores productos promotores del crecimiento vegetal, pues contienen todas las ventajas de los compuestos bioactivos liberados, como fitohormonas, sin las limitaciones de las inoculaciones microbianas. Lamentablemente, poco se sabe sobre cómo las cianobacterias modularían la respuesta de las plantas a nivel molecular. En esta investigación, se utilizó la gramínea nativa chilena Polypogon australis como modelo para evaluar el efecto de sobrenadantes de cultivos de siete cianobacterias autóctonas de suelo. Los sobrenadantes de Trichormus sp. mostraron mejores efectos promotores del crecimiento de P. australis. Análisis mediante ICP-MS evidenciaron que estos sobrenadantes tenían un contenido nutricional similar al medio de crecimiento de las cianobacterias, BG-11, excepto por los elementos P y Mn, que se agotaron al alcanzarse la fase exponencial tardía de los cultivos. Para evaluar la respuesta de P. australis a nivel transcripcional, se emplearon sobrenadantes colectados en fase exponencial tardía de cultivos de Trichormus sp., que contenían una cantidad de 32,7 pmol de trans-zeatina por mg de Chl-a. Un medio BG-11 libre de P y Mn se utilizó como control. Tres horas después del tratamiento se recogió tejido de plantas completas y se le hizo un análisis de RNA-seq. Como resultado, los sobrenadantes principalmente modularon las vías de N y fitohormonas de la planta, en estrecha relación con los metabolismos de C y lípidos. Las plantas tratadas mostraron brotes más grandes que las plantas control, 4 y 8 días después de la aplicación, pero no se observaron diferencias en la longitud radicular. Este fenotipo puede explicarse por la inducción de biosíntesis de giberelina, apoyada por otras hormonas como auxinas, brasinoesteroides y etileno. Además, se observó una inducción de resistencia sistémica en las plantas tratadas, mediada por una interacción etileno-jasmonatos. Este trabajo corrobora el uso de sobrenadantes como una buena opción para promover el crecimiento de las plantas.:Table of content Preliminary Page Resumen i Abstract ii Übersetzung iii DECLARATION ix 1. Introduction 1 1.1. Plant-growth promoting microorganisms 1 1.2. Soil cyanobacteria 2 1.3. Physiology of soil cyanobacteria 2 1.4. Cyanobacterial plant growth-promoting molecules 4 1.5. Plant response to bioactive compounds 6 1.6. Cyanobacterial supernatants 9 1.7. Polypogon australis as a plant study model 11 2. Methodology 13 2.1. Obtention of the cyanobacterial cultures 13 2.2. Supernatant collection from the cyanobacterial cultures 14 2.3. Cyanobacterial biomass quantification 15 2.3.1. Chlorophyll-a content 15 2.3.2. Biomass dry weight 15 2.3.3. Determination of the growth phases 15 2.4. Chemical characterization of the supernatants 16 2.4.1. Nitrate content 16 2.4.2. Total element content 16 2.4.3. Zeatin content 16 2.5. Preparation of the modified BG-11 medium (BG-11M medium) 17 2.6. Bioassays with cyanobacterial supernatants 18 2.6.1. Effect of supernatants of the 25 mL cultures on P. australis germination 18 2.6.2. Effect of supernatants of the 25 mL cultures on P. australis plants 18 2.6.3. Effect of supernatants of the 2,400 mL cultures on P. australis plants 19 2.7. Statistical analysis 19 2.8. Determination of transcriptional changes in P. australis. 20 2.8.1. Plant treatments and tissue collection 20 2.8.2. Total RNA extraction from plant tissue 20 2.8.3. DNA removal 20 2.8.4. mRNA sequencing, de novo assembly, and differential expression analysis 21 2.8.5. Contig annotation and functional classification 22 3. Results 24 3.1. Trichormus sp. cultures produce the highest biomass content 24 3.2. Trichormus sp. cultures have a low P content 25 3.3. Trichormus sp. supernatants have the best growth-promoting effect on the growth of P. australis 25 3.4. Supernatant nutrient content of Trichormus sp. cultures change through the growth phases 27 3.5. Supernatants used in the transcriptomic assay and BG-11M medium have a lower nutrient content than BG-11 medium 30 3.6. Trichormus sp. supernatants promote the growth of P. australis to a greater extent than the BG-11M medium 32 3.7. Trichormus sp. supernatants contain zeatin 33 3.8. Trichormus sp. supernatants modulated more P. australis genes than the BG-11M medium 34 3.9. Trichormus sp. supernatants regulate the gene expression of growth and defense responses in P. australis 37 4. Discussion 57 4.1. The plant-growth promoting effect of Thrichormus sp. supernatants 57 4.2. The role of P and Mn in the growth-promoting effect of Trichormus sp. supernatants 58 4.3. Modulation of P. australis N-metabolism by Trichormus sp. supernatants 59 4.4. P. australis nitrogen and carbon metabolism in response to Trichormus supernatants 63 4.5. P. australis phytohormone-metabolism modulated by Trichormus supernatants 64 4.6. The role of lipid metabolism in the response to Trichormus supernatants 67 4.7. P. australis defense response triggered by Trichormus supernatants 68 4.8. Phytohormone crosstalk and defense response in P. australis treated with Trichormus sp. supernatants 71 4.9. Perspectives and challenges for the biotechnological use of Trichormus sp. supernatants 73 5. Conclusion 76 Bibliographic references 77 Annexes 116

Naturstoffe sind eine der wichtigsten Quellen für die Entwicklung neuer Pharmazeutika. Eine Vielzahl von bioaktiven Substanzen mit potentieller Anti-Krebs, Anti-HIV oder antimikrobieller Wirkung wurde aus der Gruppe der Cyanobakterien isoliert. Die meisten dieser Metabolite sind Peptide oder besitzen peptid-ähnliche Strukturen und werden nicht-ribosomal von großen, modular aufgebauten Enzymkomplexen gebildet. Vor kurzem konnte anhand der Patellamide gezeigt werden, dass zyklische Peptide auch ribosomal hergestellt werden können. Microcystis aeruginosa NIES298 produziert eine Reihe von Sekundärmetaboliten, unter anderem die nicht-ribosomalen Peptide Microcystin und Aeruginosin. Zwei weiteren von diesem Stamm produzierten Peptiden, Microcyclamid und Microviridin B, konnten bislang noch keine Gene zugeordnet werden. In dieser Studie wurden ribosomale Biosynthesewege für beide Peptidfamilien identifiziert. Die zur Biosynthese des cytotoxischen Hexapeptids Microcyclamid notwendigen Enzyme zeigen eine hohe Ähnlichkeit zu den Patellamid-Enzymen und weisen auf ähnliche Biosynthesemechanismen hin. Ein völlig neuer Syntheseweg, in dem bis dahin unbekannte ATP-grasp-Ligasen eine Rolle spielen, konnte für den trizyklischen Proteaseinhibitor Microviridin gefunden werden. Die erfolgreiche heterologe Expression dieses Peptids in E. coli bietet die Möglichkeit Bibliotheken von Microviridin-Varianten mit neuen oder verbesserten Bioaktivitäten zu konstruieren. Die systematische Suche nach ähnlichen Biosynthesegenen in Microcystis Laborstämmen und Gewässerproben zeigte eine weite Verbreitung und eine große Diversität der untersuchten Peptidklassen in Cyanobakterien, und stellt die Frage nach der natürlichen Funktion dieser Metabolite. Um erste Hinweise zu erhalten, wurden Trankriptions- und Expressionsstudien der Biosynthesegene durchgeführt. Schließlich konnten, mit Hilfe des so genannten „genome-mining“, neue Varianten der untersuchten Peptidklassen gefunden und aufgeklärt werden. / Microbial natural products represent a major source for the development of new therapeutic agents. A diverse array of compounds is produced by cyanobacteria, a heterogenous group of aerobic photoautotrophs. A variety of bioactive metabolites with potential anti-cancer, anti-microbial and anti-HIV activities have been isolated. Most of the compounds are peptides or possess peptidic structures and are usually made by large nonribosomal assembly lines. However, a ribosomal origin has recently been demonstrated for the biosynthesis of patellamides, cytotoxic cyclic peptides produced by cyanobacterial symbionts of ascidians. Microcystis aeruginosa NIES298 produces various peptides including microcystin, aeruginosin, microviridin and microcyclamide. For the latter two classes of peptides ribosomal biosynthesis pathways could be identified in the course of this study. The cytotoxic hexapeptide microcyclamide is formed through the activity of a set of enzymes closely related to those involved in patellamide biosynthesis. The multicyclic microviridin family of protease inhibitors are synthesised from a precursor peptide by a unique pathway involving uncharted ATP-grasp type ligases as well as an N-acetyltransferase and a specialised transporter peptidase. The successful expression of microviridin B in E. coli provides a promising base for engineering novel variants. Screening of Microcystis laboratory strains and field samples revealed a wide-spread occurrence and a great natural variety for both peptide classes, raising the question of the ecological role of such small cyclic peptides. Attempting to obtain some first hints to answer that question, transcription and expression studies of biosynthetic genes were performed. Finally, this work showed that such scanning approaches could lead to the discovery of novel peptide variants and demonstrated new examples of succesful genome mining.

Algae provide an important role in aquatic food web and biochemical cycles in aquatic systems. They are affected by different environmental factors, such as pH, light, temperature and nutrients. This study aimed to describe the composition abundance and density of phytoplankton in the Hoa Binh reservoir during period from March to December 2011. Phytoplankton samples were collected monthly at four sampling stations. Result obtained showed that 6 phytoplankton classes were recorded: Cyanobacteria, Chlorophyceae, Bacillariophyceae, Euglenophyceae, Dinophyceae and Cryptophyceae. Bacillariophyceae and Cyanobacteria were the most abundant phytoplankton families constituting 61% and 32% respectively of total phytoplankton community. Colony-forming and solitary filamentous-forming of Cyanobacteria group (e.g. Microcystis aeruginosa, M. wesenbergi and Oscillatoria sp. respectively) were a common component of phytoplankton community in the early summer and autumn periods (April and September). The total cell densities of phytoplankton varied seasonally from 84210 to 100x106 cell/L. Phytoplankton density varied with season with high values in early summer and winter (April and December) and low values in summer – autumn periods (from June to October). / Tảo đóng vai trò quan trọng trong mạng lưới thức ăn và chu trình sinh địa hóa của thủy vực và chúng chịu sự chi phối của nhiều yếu tố môi trường như ánh sáng, pH, nhiệt độ và dinh dưỡng. Nghiên cứu này trình bày đa dạng thành phần loài và biến động sinh khối thực vật phù du tại hồ chứa Hòa Bình từ tháng 3 đến tháng 12 năm 2011. Các mẫu thực vật nổi được thu thập hàng tháng tại 4 điểm. Kết quả đã xác định được 6 lớp tảo chính bao gồm: Vi khuẩn lam, tảo lục, tảo silic, tảo mắt, tảo giáp và tảo lông roi hai rãnh. Nhóm tảo silic và Vi khuẩn lam chiếm ưu thế với độ phong phú tương đối là 61% và 32% tương ứng trong quần xã thực vật nổi. Vi khuẩn lam dạng tập đoàn và dạng sợi (Microcystis aeruginosa, M. wesenberg, Oscillatoria sp. tương ứng) chiếm ưu thế trong quần xã thực vật nổi vào các thời điểm đầu hè và mùa thu (tháng 4 và tháng 9). Tổng mật độ tế bào thực vật nổi dao động từ 84210 đến 100 x106 cell/L. Mật độ thực vật nổi biển động theo mùa với sinh khối tê bào cao vào đầu hè và mùa đông (tháng 4 và tháng 12) và sinh khối tế bào thấp vào các mùa hè và thu (tháng 6 đến tháng 10).

This study aims to investigate the potential effects of environmental variables and the toxicity of nanosilver colloids synthesized by chemical reduction method on growth and development of phytoplankton community (the Microcystis genus dominance) in the eutrophication Tien lake water, Hanoi city, Vietnam. The variables analyzed including: physical (pH and Turbidity), chemical (content of NH4 +, PO4 3- and silver metal), biological (content of Chlorophyll-a, cell density). The characteristic of nanomaterial was confirmed by using UV-visible spectrophotometer, TEM and HR-TEM methods. The obtained silver nanoparticles (AgNPs) showed that their spherical form and uniform size varied from 10 to 15 nm. The experimental results showed that the samples treated with AgNPs inhibition on growth against M. aeruginosa at concentration 1 mg/l after 8 days. The content of silver in aquarium water decreased from 1 mg/l (D0) to 0.8 mg/l (D8). The contents of chlorophyll-a of phytoplankton community, including Microcystis genus in samples exposed with AgNPs were declined from 11.27 ± 0.56μg/L (D0) to 1.98 ± 0.37 μg/L (D8) . The environmental variables such as: pH, temperature, dissolved oxygen, turbidity, ammonium, phosphate...in the experiment were below the limit of the Vietnam Standard 08:2015/MONRE for surface water quality. / Mục đích của nghiên cứu này là khảo sát ảnh hưởng của vật liệu nano bạc tổng hợp bằng phương pháp khử hóa học đến sinh trưởng và phát triển của quần xã thực vật nổi (chủ yếu là chi Microcystis) trong nước hồ Tiền phú dưỡng, tại Hà Nội, Việt Nam. Các thông số phân tích bao gồm: thủy lý (pH và độ đục), hóa học (hàm lượng amoni, photphat và hàm lượng bạc kim loại), sinh học (hàm lượng chất diệp lục, mật độ tế bào). Đặc trưng của vật liệu được xác định bằng các phương pháp quang phổ UV-VIS, TEM và HR-TEM. Vật liệu nano bạc có dạng hình cầu, kích thước đồng nhất trong khoảng 10-15nm. Kết quả thử nghiệm sau 8 ngày cho thấy các mẫu có bổ sung vật liệu nano bạc ức chế sinh trưởng đối với vi khuẩn lam M. aeruginosa ở nồng độ 1mg/l. Hàm lượng bạc kim loại giảm từ 1 mg/l (ngày đầu tiên) xuống còn 0.8 mg/l (vào ngày cuối cùng). Sinh khối thực vật nổi trong đó có chi Microcystis trong mẫu xử lý với AgNPs đã giảm tương ứng từ 11.27 ± 0.56 μg/L (ngày đầu tiên, D0) xuống 1.98 ± 0.37 μg/L (ngày cuối cùng, D8). Các thông số môi trường của nước hồ đều nằm dưới giới hạn cho phép của QCVN 08:2015/BTNMT đối với chất lượng nước mặt.

This study aims to investigate the toxicity of copper material synthesized by chemical reduction method and effects of environmental variables on growth of phytoplankton community (dominated by Microcystis genus) in the Tien eutrophic lake, Hanoi, Vietnam. The variables analyzed include: physical (pH and Turbidity), chemical (content of NH4+, PO43- and copper metal), biological (content of Chlorophyll-a, cell density). The characteristic of nanomaterial was confirmed by using UVvisible spectrophotometer, XRD, SEM and TEM methods. The CuNPs showed they spherical form and uniform size about 20-40 nm. The experimental results showed that the treated with CuNPs inhibition on growth against phytoplankton after 8 days. The cell density of phytoplankton community and Microcystis genus in samples exposure with CuNPs declined after 8 days from 647.037 and 467.037 down to 381.111 and 202.592, respectively. / Mục đích của nghiên cứu này là khảo sát độc tính của vật liệu nano đồng được tổng hợp bằng phương pháp khử hóa học và ảnh hưởng của các yếu tố môi trường đến sinh trưởng và phát triển của quần xã thực vật nổi (chủ yếu là chi Microcystis) trong nước hồ Tiền phú dưỡng, tại Hà Nội, Việt Nam. Các thông số phân tích bao gồm: thủy lý (pH và độ đục), hóa học (hàm lượng amoni, photphat và hàm lượng đồng kim loại), sinh học (hàm lượng chất diệp lục, mật độ tế bào). Đặc trưng của vật liệu được xác định bằng các phương pháp quang phổ UV-VIS, XRD, SEM và TEM. Vật liệu nano đồng có dạng hình cầu, kích thước đồng nhất từ 20 đến 40 nm. Kết quả thử nghiệm sau 8 ngày cho thấy các mẫu có bổ sung vật liệu nano đồng ức chế sinh trưởng quần xã thực vật nổi ở nồng độ 1mg/l. Mật độ quần xã thực vật nổi và chi Microcystis trong mẫu xử lý với CuNPs đã giảm tương ứng sau 8 ngày từ 647.037 và 467.037 xuống còn 381.111 và 202.592.

Algae provide an important role in aquatic food web and biochemical cycles in aquatic systems. They are affected by different environmental factors, such as pH, light, temperature and nutrients. This study aimed to describe the composition abundance and density of phytoplankton in the Hoa Binh reservoir during period from March to December 2011. Phytoplankton samples were collected monthly at four sampling stations. Result obtained showed that 6 phytoplankton classes were recorded: Cyanobacteria, Chlorophyceae, Bacillariophyceae, Euglenophyceae, Dinophyceae and Cryptophyceae. Bacillariophyceae and Cyanobacteria were the most abundant phytoplankton families constituting 61% and 32% respectively of total phytoplankton community. Colony-forming and solitary filamentous-forming of Cyanobacteria group (e.g. Microcystis aeruginosa, M. wesenbergi and Oscillatoria sp. respectively) were a common component of phytoplankton community in the early summer and autumn periods (April and September). The total cell densities of phytoplankton varied seasonally from 84210 to 100x106 cell/L. Phytoplankton density varied with season with high values in early summer and winter (April and December) and low values in summer – autumn periods (from June to October). / Tảo đóng vai trò quan trọng trong mạng lưới thức ăn và chu trình sinh địa hóa của thủy vực và chúng chịu sự chi phối của nhiều yếu tố môi trường như ánh sáng, pH, nhiệt độ và dinh dưỡng. Nghiên cứu này trình bày đa dạng thành phần loài và biến động sinh khối thực vật phù du tại hồ chứa Hòa Bình từ tháng 3 đến tháng 12 năm 2011. Các mẫu thực vật nổi được thu thập hàng tháng tại 4 điểm. Kết quả đã xác định được 6 lớp tảo chính bao gồm: Vi khuẩn lam, tảo lục, tảo silic, tảo mắt, tảo giáp và tảo lông roi hai rãnh. Nhóm tảo silic và Vi khuẩn lam chiếm ưu thế với độ phong phú tương đối là 61% và 32% tương ứng trong quần xã thực vật nổi. Vi khuẩn lam dạng tập đoàn và dạng sợi (Microcystis aeruginosa, M. wesenberg, Oscillatoria sp. tương ứng) chiếm ưu thế trong quần xã thực vật nổi vào các thời điểm đầu hè và mùa thu (tháng 4 và tháng 9). Tổng mật độ tế bào thực vật nổi dao động từ 84210 đến 100 x106 cell/L. Mật độ thực vật nổi biển động theo mùa với sinh khối tê bào cao vào đầu hè và mùa đông (tháng 4 và tháng 12) và sinh khối tế bào thấp vào các mùa hè và thu (tháng 6 đến tháng 10).

Optimising illumination is essential for optimising the growth of phototrophic cells and their production of desired metabolites and/or biomass. This requires appropriate modulation of light and other key inputs and continuous online monitoring of their metabolic activities. Powerful non-invasive systems for cultivating heterotrophic organisms include shake flasks in online monitoring units, but they are rarely used for phototrophs because they lack the appropriate illumination design and necessary illuminatory power. This study presents the design and characterisation of a photosynthetic shake flask unit, illuminated from below by warm white light-emitting diodes with variable light intensities up to 2300 μmol m-2 s-1. The photosynthetic unit was successfully used, in combination with online monitoring of oxygen production, to cultivate Arthrospira platensis. In phototrophic growth under continuous light and a 16 h light/8 h dark cycle (light intensity: 180 μmol m-2 s-1), the oxygen transfer rate and biomass-related oxygen production were - 1.5 mmol L-1 h-1 and 0.18 mmol O2 gx-1 h-1, respectively. The maximum specific growth rate was 0.058 h-1, during the exponential growth phase, after which the biomass concentration reached 0.75 g L-1.