DNA builds and strengthens the extracellular matrix in Myxococcus xanthus biofilms by interacting with exopolysaccharides.

One intriguing discovery in modern microbiology is the extensive presence of extracellular DNA (eDNA) within biofilms of various bacterial species. Although several biological functions have been suggested for eDNA, including involvement in biofilm formation, the detailed mechanism of eDNA integration into biofilm architecture is still poorly understood. In the biofilms formed by Myxococcus xanthus, a Gram-negative soil bacterium with complex morphogenesis and social behaviors, DNA was found within both extracted and native extracellular matrices (ECM). Further examination revealed that these eDNA molecules formed well organized structures that were similar in appearance to the organization of exopolysaccharides (EPS) in ECM. Biochemical and image analyses confirmed that eDNA bound to and colocalized with EPS within the ECM of starvation biofilms and fruiting bodies. In addition, ECM containing eDNA exhibited greater physical strength and biological stress resistance compared to DNase I treated ECM. Taken together, these findings demonstrate that DNA interacts with EPS and strengthens biofilm structures in M. xanthus

Reasoning on Starvation in AODV using Abstract State Machines

Abstract State Machines (ASMs) are very helpful in analyzing critical and complex systems, but they lack of inherent, domain-independent characterizations of computationally interesting properties. Our long-term research aims at providing an ASM-based characterization of the starvation-freedom property. To this end, in the present paper the Ad-hoc On-demand Distance Vector (AODV) routing protocol for Mobile Ad-hoc NETworks (MANETs) is modeled through ASMs, and starvation is studied. This experience suggests us to focus on vulnerable rules as the key issue that drives the risk of starvation within the ASM framework

Environmental stress responses in Lactococcus lactis

Bacteria can encounter a variety of physical conditions during their life. Bacterial cells are able to survive these (often adverse) conditions by the induction of specific or general protection mechanisms. The lactic acid bacterium Lactococcus lactis is widely used for the production of cheese. Before and during this process as well as in its natural habitats, it is subjected to several stressful conditions. Such conditions include oxidation, heating and cooling, acid, high osmolarity/dehydration and starvation. In many environments combinations of these parameters occur. Understanding the stress response behaviour of L. lactis is important to optimize its application in industrial fermentations and is of fundamental interest as L. lactis is a non-differentiating Gram-positive bacterium. The stress response mechanisms of L. lactis have drawn increasing attention in recent years. The presence in L. lactis of a number of the conserved systems (e.g. the heat shock proteins) has been confirmed. Some of the regulatory mechanisms responding to an environmental stress condition are related to those found in other Gram-positive bacteria. Other stress response systems are conserved at the protein level but are under control of mechanisms unique for L. lactis. In a number of cases exposure to a single type of stress provides resistance to other adverse conditions. The unravelling of the underlying regulatory systems gives insight into the development of such cross resistance. Taken together, L. lactis has a unique set of stress response mechanisms, most of which have been identified on the basis of homology with proteins known from other bacteria. A number of the regulatory elements may provide attractive tools for the development of food grade inducible gene expression systems. Here an overview of the growth limits of L. lactis and the molecular characterization of its stress resistance mechanisms is presented.

Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research

Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation

<p>Abstract</p> <p>Background</p> <p><it>Myxococcus xanthus </it>is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part because sporulation is normally initiated at the culmination of a complex starvation-induced developmental program and only inside multicellular fruiting bodies. To obtain a broad overview of the sporulation process and to identify novel genes necessary for differentiation, we instead performed global transcriptome analysis of an artificial chemically-induced sporulation process in which addition of glycerol to vegetatively growing liquid cultures of <it>M. xanthus </it>leads to rapid and synchronized differentiation of nearly all cells into myxospore-like entities.</p> <p>Results</p> <p>Our analyses identified 1 486 genes whose expression was significantly regulated at least two-fold within four hours of chemical-induced differentiation. Most of the previously identified sporulation marker genes were significantly upregulated. In contrast, most genes that are required to build starvation-induced multicellular fruiting bodies, but which are not required for sporulation <it>per se</it>, were not significantly regulated in our analysis. Analysis of functional gene categories significantly over-represented in the regulated genes, suggested large rearrangements in core metabolic pathways, and in genes involved in protein synthesis and fate. We used the microarray data to identify a novel operon of eight genes that, when mutated, rendered cells unable to produce viable chemical- or starvation-induced spores. Importantly, these mutants displayed no defects in building fruiting bodies, suggesting these genes are necessary for the core sporulation process. Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate.</p> <p>Conclusions</p> <p>These results suggest that microarray analysis of chemical-induced spore formation is an excellent system to specifically identify genes necessary for the core sporulation process of a Gram negative model organism for differentiation.</p

Columnaris disease in fish: a review with emphasis on bacterium-host interactions

Flavobacterium columnare (F. columnare) is the causative agent of columnaris disease. This bacterium affects both cultured and wild freshwater fish including many susceptible commercially important fish species. F. columnare infections may result in skin lesions, fin erosion and gill necrosis, with a high degree of mortality, leading to severe economic losses. Especially in the last decade, various research groups have performed studies aimed at elucidating the pathogenesis of columnaris disease, leading to significant progress in defining the complex interactions between the organism and its host. Despite these efforts, the pathogenesis of columnaris disease hitherto largely remains unclear, compromising the further development of efficient curative and preventive measures to combat this disease. Besides elaborating on the agent and the disease it causes, this review aims to summarize these pathogenesis data emphasizing the areas meriting further investigation

Rotating biological contactors for wastewater treatment - A review

Rotating biological contactors (RBCs) for wastewater treatment began in the 1970s. Removal of organic matter has been targeted within organic loading rates of up to 120 g m−2 d−1 with an optimum at around 15 g m−2 d−1 for combined BOD and ammonia removal. Full nitrification is achievable under appropriate process conditions with oxidation rates of up to 6 g m−2 d−1 reported for municipal wastewater. The RBC process has been adapted for denitrification with reported removal rates of up to 14 g m−2 d−1 with nitrogen rich wastewaters. Different media types can be used to improve organic/nitrogen loading rates through selecting for different bacterial groups. The RBC has been applied with only limited success for enhanced biological phosphorus removal and attained up to 70% total phosphorus removal. Compared to other biofilm processes, RBCs had 35% lower energy costs than trickling filters but higher demand than wetland systems. However, the land footprint for the same treatment is lower than these alternatives. The RBC process has been used for removal of priority pollutants such as pharmaceuticals and personal care products. The RBC system has been shown to eliminate 99% of faecal coliforms and the majority of other wastewater pathogens. Novel RBC reactors include systems for energy generation such as algae, methane production and microbial fuel cells for direct current generation. Issues such as scale up remain challenging for the future application of RBC technology and topics such as phosphorus removal and denitrification still require further research. High volumetric removal rate, solids retention, low footprint, hydraulic residence times are characteristics of RBCs. The RBC is therefore an ideal candidate for hybrid processes for upgrading works maximising efficiency of existing infrastructure and minimising energy consumption for nutrient removal. This review will provide a link between disciplines and discuss recent developments in RBC research and comparison of recent process designs are provided (Section 2). The microbial features of the RBC biofilm are highlighted (Section 3) and topics such as biological nitrogen removal and priority pollutant remediation are discussed (Sections 4 and 5). Developments in kinetics and modelling are highlighted (Section 6) and future research themes are mentioned

Phenotypic heterogeneity - towards the sociobiology of insect pathogenic Photorhabdus luminescens and the decision of being different

Photorhabdus luminescens are Gram-negative bacteria that live in symbiosis with soil nematodes and are simultaneously highly pathogenic towards insects. The bacteria exist in two phenotypically different forms, designated as primary (1°) and secondary (2°) cells. After prolonged cultivation up to 50% of 1° convert into 2° cells. An important difference between the two phenotypic forms is that 2° cells are unable to live in symbiosis with nematodes, and therefore are believed to remain in the soil after a successful infection cycle. Furthermore, as a 100% switching frequency would be fatal for the bacteria’s life cycle the switching process has to be tightly controlled. Therefore, the fate of 2° cells in soil as well as the regulation mechanism of phenotypic heterogeneity were the main focuses of this work. The P. luminescens subsp. laumondii TT01 strain as well as its rifampicin resistant mutant (TT01Rif) are the most common P. luminescens strains used in scientific research. However, the genome of TT01Rif has never been sequenced and referring to it as only TT01 in literature causes difficulties in clear assignment. As a first step of this work, both strains were compared genetically as well as phenotypically. Thereby, the TT01Rif strain could be identified as an independent isolate rather than a TT01 mutant and was therefore renamed into P. luminescens subsp. laumondii DJC. The new DJC reference genome enabled comparative transcriptome analysis of P. luminescens DJC 1° and 2°. Thereby, mediation of 1°-specific features such as e.g. bioluminescence, antibiotic production or pigmentation at transcriptional level could be proven as the respective genes were found to be down-regulated in 2° cells. Furthermore, the compiled data provides evidence that 2° cells of P. luminescens are better adapted to a life outside the host(s), presumably feeding from plant root exudates. Lastly, two novel transcriptional regulators, XreR1 and XreR2, could be identified. These regulators were found to play a major role in the process of phenotypic switching and initial insights about their molecular mechanisms were gained.Photorhabdus luminescens sind Gram-negative Bakterien, die in Symbiose mit Bodennematoden leben und gleichzeitig hoch pathogen gegenüber Insekten sind. Die Bakterien existieren in zwei phänotypisch unterschiedlichen Formen, die als primäre und sekundäre Zellen bezeichnet werden. Nach längerer Kultivierung entstehen aus bis zu 50% der Primärzellen, Sekundärzellen. Ein wichtiger Unterschied zwischen den beiden phänotypischen Formen besteht darin, dass Sekundärzellen nicht in der Lage sind, in Symbiose mit Nematoden zu leben, und daher nach einem erfolgreichen Infektionszyklus vermutlich im Boden verbleiben. Da eine 100-prozentige Konvertierung in Sekundärzellen den Lebenszyklus der Bakterien zum Erliegen brächte, muss diese streng reguliert sein. Daher wurde in dieser Arbeit das Schicksal der Sekundärzellen sowie die regulatorischen Abläufe die zu phänotypischer Heterogenität führen näher untersucht. Der Stamm P. luminescens subsp. laumondii TT01 sowie seine Rifampicin-resistente Mutante (TT01Rif) sind die in der wissenschaftlichen Forschung am häufigsten verwendeten P. luminescens Stämme. Die Tatsache, dass das TT01Rif Genom bisher nicht sequenziert wurde, beide Stämme jedoch in der Literatur als TT01 bezeichnet werden führt häufig zu Schwierigkeiten eindeutiger Zuordnung. Daher wurden als erster Schritt dieser Arbeit beide Stämme sowohl genetisch als auch phänotypisch verglichen. Dadurch konnte der TT01Rif-Stamm als unabhängiges Isolat und nicht als TT01-Mutante identifiziert werden und aufgrund dessen in P. luminescens subsp. laumondii DJC umbenannt. Mit dem korrekten DJC Genom konnte dann eine vergleichende Tanskriptomanalyse von P. luminescens DJC Primär- und Sekundärzellen durchgeführt werden welche beweisen konnte, dass primär-spezifische Merkmale wie z.B. Biolumineszenz, Pigmentierung, Antibiotikasynthese und Zellverklumpung auf Transkriptionsebene vermittelt werden. Außerdem zeigen die Daten dieser Arbeit, dass P. luminescens Sekundärzellen besser an ein Leben außerhalb des Wirts angepasst sind und sich vermutlich von Pflanzenwurzelexsudaten ernähren. Darüber hinaus konnten zwei neue Transkriptionsregulatoren, XreR1 und XreR2, identifiziert und erste Einblicke in ihre molekularen Mechanismen gewonnen werden

A luminescent whole-cell cyanobacterial bioreporter for measuring Fe availability in diverse marine environments

A Synechococcus sp. strain PCC 7002 Fe bioreporter was constructed containing the isiAB promoter fused to the Vibrio harveyi luxAB genes. Bioreporter luminescence was characterized with respect to the free ferric ion concentration in trace metal-buffered synthetic medium. The applicability of the Fe bioreporter to assess Fe availability in the natural environment was tested by using samples collected from the Baltic Sea and from the high-nutrient, low-chlorophyll subarctic Pacific Ocean. Parallel assessment of dissolved Fe and bioreporter response confirmed that direct chemical measurements of dissolved Fe should not be considered alone when assessing Fe availability to phytoplankton