Microbial Ecophysiology of Vibrio ruber

Bakterije se na različite načine prilagođavaju promjenama uvjeta okoline. U ovom su kratkom preglednom radu opisane različite strategije prilagodbe crveno pigmentirane bakterije Vibrio ruber, nedavno izolirane iz priobalja, na čimbenike stresa (tj. salinitet, viskoznost, UV svjetlost, mitomicin C, pristupačnost hranjiva i temperaturu). Bakterija Vibrio ruber se koristi različitim strategijama adaptacije kako bi se oduprla okolišnom stresu. Ovisno o koncentraciji soli, bakterija Vibrio ruber mijenja svoj lipidni sastav, te svojstva lipidne faze. Membrana se bakterije Vibrio ruber razlikuje od ostalih srodnih vrsta bakterije Vibrio po tome što ne sadržava hidroksi masne kiseline, ali zato ima izrazito velik udjel lizolipida. Nakupljanje anorganskih hranjivih tvari u bakteriji je selektivno i ovisi o uvjetima okoline. Bakterije se brzo prilagođavaju stresnim uvjetima i mijenjaju svoj proteinski sastav, metabolizam, tj. potrošnju ugljika i energije, te proizvodnju sekundarnih metabolita. Aktivnost glukoza-6-fosfat dehidrogenaze dobar je indikator stresa u Vibrio ruber. Bakterije mogu mijenjati viskozitet stanica kao odgovor na promjenu viskoziteta okoline. Imaju nekoliko virusnih elemenata u genomu koji se mogu inducirati mitomicinom C. Promjene u uvjetima okoline tijekom rasta bakterija bitno utječu na iskorištenje ugljika iz lizata mikrobnih stanica. Nedavno je otkrivena nova ekofiziološka funkcija sekundarnog metabolita prodigiozina, a to je da štiti stanicu od UV zračenja. Može se zaključiti da se u kratkom periodu istraživanja bakterije Vibrio ruber (kraćem od deset godina) dokazalo da se može upotrijebiti kao vrlo učinkovit model za ispitivanje ekofiziologije bakterija.Bacteria use different adaptation strategies to survive environmental perturbations. In this minireview, adaptation strategies of new red-pigmented Vibrio ruber isolated from coastal environments to different environmental stresses (i.e. salinity, viscosity, UV light, mitomycin C, nutrient availability and temperature) are reviewed. To cope with environmental stresses Vibrio ruber uses several different adaptive strategies. For example, lipid composition as well as phase behaviour are strongly dependent on salt concentration. Vibrio ruber membrane has no hydroxy fatty acids, but exceptionally high lysolipid content compared to other related Vibrio species. Inorganic nutrient uptake by bacteria is selective, depends on environmental conditions and varies several fold with environmental perturbations. Protein composition, carbon flow through the central metabolic pathways, energy generation as well as secondary metabolite production adapt readily to stress conditions. The activity of glucose-6-phosphate dehydrogenase proved to be a good indicator of Vibrio ruber stress. Cells are able to modulate their local viscosity in response to variations of environmental viscosity. The bacterium harbours several viral genetic elements in its genome, which could be induced by mitomycin C. Environmental conditions during growth of bacteria have a significant effect on lysate carbon turnover. Secondary metabolite prodigiosin confers protection against UV in the environment, which adds to the known repertoire of prodigiosin ecophysiological functions. In conclusion, Vibrio ruber in its short acquaintance with the scientific community (less than ten years) has proven to be an immensely valuable model system for ecophysiological studies of bacteria

The ComX Quorum Sensing Peptide of Bacillus subtilis Affects Biofilm Formation Negatively and Sporulation Positively

Quorum sensing (QS) is often required for the formation of bacterial biofilms and is a popular target of biofilm control strategies. Previous studies implicate the ComQXPA quorum sensing system of Bacillus subtilis as a promoter of biofilm formation. Here, we report that ComX signaling peptide deficient mutants form thicker and more robust pellicle biofilms that contain chains of cells. We confirm that ComX positively affects the transcriptional activity of the P$_{epsA}$ promoter, which controls the synthesis of the major matrix polysaccharide. In contrast, ComX negatively controls the P$_{tapA}$ promoter, which drives the production of TasA, a fibrous matrix protein. Overall, the biomass of the mutant biofilm lacking ComX accumulates more monosaccharide and protein content than the wild type. We conclude that this QS phenotype might be due to extended investment into growth rather than spore development. Consistent with this, the ComX deficient mutant shows a delayed activation of the pre-spore specific promoter, P$_{spoIIQ}$, and a delayed, more synchronous commitment to sporulation. We conclude that ComX mediated early commitment to sporulation of the wild type slows down biofilm formation and modulates the coexistence of multiple biological states during the early stages of biofilm development

Microbial Community Structure and Function in Peat Soil

Mnoga su tresetišta u Europi izlagana melioraciji i odvodnji, što je dovelo do promjena u procesima kruženja hranjivih tvari u tlu. Ovaj je rad sažetak objavljenih studija o mikrobnim procesima vezanim uz transformaciju ugljika i dušika u tlu Ljubljanskog barja. To je drenirano tresetište, smješteno nedaleko od Ljubljane, glavnoga grada Slovenije, poznato po bogatstvu biljnog i životinjskog svijeta. U radu je po prvi put dan širi pregled raznolikosti zajednice bakterija i arheja u tom organskoj tvari bogatom tlu, koje je izvor stakleničkih plinova, dušikovog oksida i ugljikovog dioksida, te ponor metana. U Ljubljanskom je barju metanogeneza ograničena velikim udjelom željeza, koje konkurira ostalim akceptorima elektrona. Osim toga, tlo je bogato vrlo aktivnim metanotrofima, naročito u slojevima tla s promjenjivom razinom podzemne vode. Denitrifikacija je ograničena akceptorima elektrona, a u dubljim slojevima tla i manjkom ugljičnih supstrata dostupnih za mikrobiološku razgradnju. Nitrifikacija je tla posljedica aktivnosti bakterija i arheja koje oksidiraju amonijak, pa je stupanj oksidacije amonijaka u Ljubljanskom barju među najvišim u svijetu. Zanimljivo, arheje iz odjeljka Thaumarchaeota u kiselim tresetištima uspijevaju samo na amonijaku što potječe iz organskog izvora i ne mogu oksidirati amonijak iz mineralnog izvora. U tlima je Ljubljanskoga barja pronađeno veliko bogatstvo gena što kodiraju bakterijske oksidoreduktaze slične lakazama. Uloga je tih enzima uglavnom nepoznata, a prema spoznajama o lakazama iz gljiva može se zaključiti da bakterijski enzimi sudjeluju u degradaciji lignina, oksidaciji različitih aromatskih i fenolnih spojeva, te oksidaciji metala. Budući su izazovi u ovom području istražiti specifične fiziološke uloge fenolnih oksidaza i ostalih enzima što sudjeluju u transformaciji tresetišta. Naše je poznavanje različitosti mikroorganizama u tresetištima, njihove funkcije i utjecaja na ekosustav još uvijek ograničeno, iako neophodno za učinkovito održavanje tresetišta, tih izvanrednih, ekološki značajnih, no osjetljivih staništa.Many peatlands in Europe have been subjected to land reclamation and systematic drainage, which have substantially affected nutrient cycles in the soil. This work reviews published studies on microbial processes linked to carbon and nitrogen transformations in the soils of the Ljubljana marsh, a drained peatland positioned close to Ljubljana, the capital of Slovenia. This region is known for its dramatic diversity of animal and plant life, but below ground it hides diverse bacterial and archaeal communities that are highly responsive to environmental changes and make the Ljubljana marsh soils a good source of N2O and CO2, and a sink for CH4. Methanogenesis is highly restricted in these soils due to competition for electron donors with iron reducers. In addition, methane is efficiently removed by methanotrophs, which are highly active, especially in the soil layers exposed to the changing water table. Denitrification is limited by electron acceptors and in deeper soil layers also by carbon, which becomes more recalcitrant with depth. Nitrification involves bacterial and archaeal ammonia oxidisers with ammonia oxidation rates being among the highest in the world. Interestingly, ammonia-oxidising Thaumarchaeota in acidic bog soils thrive only on ammonia released through mineralisation of organic matter and are incapable of oxidising added mineral ammonia. The soils of the Ljubljana marsh are rich in bacterial laccase-like genes, which may encode enzymes involved in lignin degradation and are therefore interesting for bioexploitations. Future challenges involve designing studies that will reveal specific physiological functions of phenol oxidases and other enzymes involved in peat transformations and address relations between microbial diversity, function and ecosystem responses to anthropogenic disturbances

Microbial Ecophysiology of Vibrio ruber

Bacteria use different adaptation strategies to survive environmental perturbations. In this minireview, adaptation strategies of new red-pigmented Vibrio ruber isolated from coastal environments to different environmental stresses (i.e. salinity, viscosity, UV light, mitomycin C, nutrient availability and temperature) are reviewed. To cope with environmental stresses Vibrio ruber uses several different adaptive strategies. For example, lipid composition as well as phase behaviour are strongly dependent on salt concentration. Vibrio ruber membrane has no hydroxy fatty acids, but exceptionally high lysolipid content compared to other related Vibrio species. Inorganic nutrient uptake by bacteria is selective, depends on environmental conditions and varies several fold with environmental perturbations. Protein composition, carbon flow through the central metabolic pathways, energy generation as well as secondary metabolite production adapt readily to stress conditions. The activity of glucose-6-phosphate dehydrogenase proved to be a good indicator of Vibrio ruber stress. Cells are able to modulate their local viscosity in response to variations of environmental viscosity. The bacterium harbours several viral genetic elements in its genome, which could be induced by mitomycin C. Environmental conditions during growth of bacteria have a significant effect on lysate carbon turnover. Secondary metabolite prodigiosin confers protection against UV in the environment, which adds to the known repertoire of prodigiosin ecophysiological functions. In conclusion, Vibrio ruber in its short acquaintance with the scientific community (less than ten years) has proven to be an immensely valuable model system for ecophysiological studies of bacteria

ComX-Induced Exoproteases Degrade ComX in Bacillus subtilis PS-216

Gram-positive bacteria use peptides as auto-inducing (AI) signals to regulate the production of extracellular enzymes (e.g., proteases). ComX is an AI peptide, mostly known for its role in the regulation of bacterial competence and surfactant production in Bacillus subtilis. These two traits are regulated accordingly to the bacterial population size, thus classifying ComX as a quorum sensing signal. ComX also indirectly regulates exoprotease production through the intermediate transcriptional regulator DegQ. We here use this peptide-based AI system (the ComQXPA system) as a model to address exoprotease regulation by ComX in biofilms. We also investigate the potential of ComX regulated proteases to degrade the ComX AI peptide. Results indicate that ComX indeed induces the expression of aprE, the gene for the major serine protease subtilisin, and stimulates overall exoprotease production in biofilms of B. subtilis PS-216 and several other B. subtilis soil isolates. We also provide evidence that these exoproteases can degrade ComX. The ComX biological activity decay is reduced in the spent media of floating biofilms with low proteolytic activity found in the comP and degQ mutants. ComX biological activity decay can be restored by the addition of subtilisin to such media. In contrast, inhibition of metalloproteases by EDTA reduces ComX biological activity decay. This suggests that both serine and metalloproteases, which are induced by ComX, are ultimately capable of degrading this signaling peptide. This work brings novel information on regulation of exoproteases in B. subtilis floating biofilms and reveals that these proteolytic enzymes degrade the AI signaling peptide ComX, which is also a major determinant of their expression in biofilms

ComX-induced exoproteases degrade ComX in Bacillus subtilis PS-216

Gram-positive bacteria use peptides as auto-inducing (AI) signals to regulate the production of extracellular enzymes (e.g., proteases). ComX is an AI peptide, mostly known for its role in the regulation of bacterial competence and surfactant production in Bacillus subtilis. These two traits are regulated accordingly to the bacterial population size, thus classifying ComX as a quorum sensing signal. ComX also indirectly regulates exoprotease production through the intermediate transcriptional regulator DegQ. We here use this peptide-based AI system (the ComQXPA system) as a model to address exoprotease regulation by ComX in biofilms. We also investigate the potential of ComX regulated proteases to degrade the ComX AI peptide. Results indicate that ComX indeed induces the expression of aprE, the gene for the major serine protease subtilisin, and stimulates overall exoprotease production in biofilms of B. subtilis PS-216 and several other B. subtilis soil isolates. We also provide evidence that these exoproteases can degrade ComX. The ComX biological activity decay is reduced in the spent media of floating biofilms with low proteolytic activity found in the comP and degQ mutants. ComX biological activity decay can be restored by the addition of subtilisin to such media. In contrast, inhibition of metalloproteases by EDTA reduces ComX biological activity decay. This suggests that both serine and metalloproteases, which are induced by ComX, are ultimately capable of degrading this signaling peptide. This work brings novel information on regulation of exoproteases in B. subtilis floating biofilms and reveals that these proteolytic enzymes degrade the AI signaling peptide ComX, which is also a major determinant of their expression in biofilms

Peptide signaling without feedback in signal production operates as a true quorum sensing communication system in Bacillus subtilis

Bacterial quorum sensing (QS) is based on signal molecules (SM), which increase in concentration with cell density. At critical SM concentration, a variety of adaptive genes sharply change their expression from basic level to maximum level. In general, this sharp transition, a hallmark of true QS, requires an SM dependent positive feedback loop, where SM enhances its own production. Some communication systems, like the peptide SM-based ComQXPA communication system of Bacillus subtilis, do not have this feedback loop and we do not understand how and if the sharp transition in gene expression is achieved. Based on experiments and mathematical modeling, we observed that the SM peptide ComX encodes the information about cell density, specific cell growth rate, and even oxygen concentration, which ensure power-law increase in SM production. This enables together with the cooperative response to SM (ComX) a sharp transition in gene expression level and this without the SM dependent feedback loop. Due to its ultra-sensitive nature, the ComQXPA can operate at SM concentrations that are 100–1000 times lower than typically found in other QS systems, thereby substantially reducing the total metabolic cost of otherwise expensive ComX peptide

Prodigiosin - A Multifaceted Escherichia coli Antimicrobial Agent.

Despite a considerable interest in prodigiosin, the mechanism of its antibacterial activity is still poorly understood. In this work, Escherichia coli cells were treated with prodigiosin to determine its antimicrobial effect on bacterial physiology. The effect of prodigiosin was concentration dependent. In prodigiosin treated cells above MIC value no significant DNA damage or cytoplasmic membrane disintegration was observed. The outer membrane, however, becomes leaky. Cells had severely decreased respiration activity. In prodigiosin treated cells protein and RNA synthesis were inhibited, cells were elongated but could not divide. Pre-treatment with prodigiosin improved E. coli survival rate in media containing ampicillin, kanamycin and erythromycin but not phleomycin. The results suggest that prodigiosin acts as a bacteriostatic agent in E. coli cells. If prodigiosin was diluted, cells resumed growth. The results indicate that prodigiosin has distinct mode of antibacterial action in different bacteria