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.

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.

In der vorliegenden Arbeit wurde die Funktion der beiden cyanobakteriellen Phytochrome Cph1 und Cph2 untersucht. Dafür wurde zunächst das Wachstum von Mutanten mit einem inaktivierten cph1- bzw. cph2-Gen unter verschiedenen Lichtbedingungen analysiert. Das Wachstum aller Phytochrommutanten war unter Starklicht beeinträchtigt. Dahingegen wuchs die cph1-Mutante im FRL schlechter als der Wildtyp, während das Wachstum der cph2-Mutante im RL vermindert war. Eine cph1/cph2-Doppelmutante zeigte unter allen Lichtbedingungen eine Wachstumsreduktion, die der jeweiligen Einzelmutante ähnlich war. Die genaue Ursache für die Beeinträchtigung des Wachstums der Phytochrommutanten konnte nicht ermittelt werden. Die verschiedenen Aspekte der Photosynthese, wie Pigmentzusammensetzung, maximale Netto-Sauerstofffreisetzungsrate und 77K-Fluoreszenzemission, waren in den Phytochrommutanten nicht signifikant verändert. Bei Synechocystis sp. PCC 6803 konnte eine lichtgerichtete Bewegung beobachtet werden, wobei man aufgrund von Aktionsspektren der Motilität eine Funktion der Phytochrome oder phytochromähnlichen Proteine bei der Steuerung der phototaktischen Bewegung vermutet. Dem Cph1-Protein konnte hierfür keine Rolle zugeordnet werden. Dahingegen scheint der Photorezeptor Cph2 die lichtgerichtete Bewegung der Zellen in Richtung einer Blaulichtquelle zu inhibieren. Eine Interaktion mit einem klassischen Blaulicht-Rezeptor konnte ausgeschlossen werden. / The function of the cyanobacterial phytochromes Cph1 and Cph2 was investigated. At first, the growth of mutants with an inactivated cph1 or cph2 gene was analysed under different light conditions. The growth of all phytochrome mutants was affected under high-light conditions. However, the cph1 mutant grew slower than the wild type in far-red light, whilst the cph2 mutant revealed a reduced growth under red light conditions. A decreased growth of the cph1/cph2 double mutant was observed under all light conditions with a growth rate similar to the corresponding single mutant. The exact reason for the growth impairment of the phytochrome mutants could not be ascertained. Different aspects of photosynthesis (pigment composition, maximal net-oxygen evolution and 77K fluorescence emission) were not changed significantly in the phytochrome mutants. Synechocystis sp. PCC 6803 shows a movement towards a light source. Based on action spectra of motility phytochromes and phytochrome-like proteins are supposed to have a function in regulating the phototactic movement. An influence of the Cph1 protein in the phototactic movement was not demonstrated. Whereas, the Cph2 protein seems to be involved in the inhibition of the cell movement towards blue light. An interaction with a typical blue-light receptor was excluded.