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Thiomargarita namibiensis: Giant microbe holding its breath

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... The functions and composition of their intracellular inclusions is not yet completely resolved. So far, the storage of S 0 , polyhydroxyalkanoates (PHA), polyphosphate and nitrate has been demonstrated (McHatton et al., 1996;Schulz et al., 1999;Schulz, 2002;Schulz and Schulz, 2005;Dahl and Prange, 2006;Schwedt et al., 2012). Many species are motile and use their storage capabilities to transport nitrate to deeper, more sulfidic sediment layers during sulfide oxidation (Schulz, 2002;Teske and Nelson, 2006). ...
... So far, the storage of S 0 , polyhydroxyalkanoates (PHA), polyphosphate and nitrate has been demonstrated (McHatton et al., 1996;Schulz et al., 1999;Schulz, 2002;Schulz and Schulz, 2005;Dahl and Prange, 2006;Schwedt et al., 2012). Many species are motile and use their storage capabilities to transport nitrate to deeper, more sulfidic sediment layers during sulfide oxidation (Schulz, 2002;Teske and Nelson, 2006). ...
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... Bacteria live in most habitats, as well as in symbiotic and parasitic relationships with plants and animals. [241]. So far, more than 1500 types of fungi have been identified in marine environments [238]. ...
... Bacteria are known to undergo filamentous shift when coping with other environmental stress, such as cold, UV radiation, chromium, and BTEX (benzene, toluene, ethylbenzene, and o-xylene) (1,(20)(21)(22). It is believed that filamentation has been implicated in bacterial survival under environmental stresses with several benefits (23)(24)(25)(26). First, stretched growth of a cell increases its uptake-proficient surface without changing its surface/volume ratio appreciably. ...
Article
Keeping toxic organic pollutants (TOPs) in tolerable levels is a huge challenge for bacteria in extremely unfavorable environments since TOPs could serve as energy substitutes but also as survival stresses when they are beyond some thresholds. This study focused on the underlying adaptive mechanisms of ecologically successful bacterium Shewanella decolorationis S12 when exposed to amaranth, a typical toxic organic pollutant, as the extracellular electron acceptor. Our results suggest that filamentous shift is a flexible and valid way to solve the dilemma between the energy resource and toxic stress. Filamentous cells regulate gene expression to enhance their degradation and detoxification capabilities, resulting in a strong viability. These novel adaptive responses to TOPs are believed to be an evolutionary achievement to succeed in harsh habitats and thus have great potential to be applied to environment engineering or synthetic biology if we could picture every unknown node in this pathway.
... An understanding of how bacteria respond to nutrient gradients has important consequences for microbial ecology (2,3) and nutrients cycles (4,5). The challenges of living in nutrient gradients have driven many sulfur-oxidizing bacteria to evolve remarkable morphologies (6)(7)(8)(9) and behaviors such as magnetotaxis (10) and symbioses (11,12). Here we show how the response of the bacterium Thiovulum majus (13)(14)(15)(16) to nutrient gradients leads to the formation of a bacterial front that efficiently draws nutrient-rich water from its surroundings. ...
Article
The ecology and dynamics of many microbial systems, particularly in mats and soils, are shaped by how bacteria respond to evolving nutrient gradients and microenvironments. Here we show how the response of the sulfur-oxidizing bacterium Thiovulum majus to changing oxygen gradients causes cells to organize into large-scale fronts. To study this phenomenon, we develop a technique to isolate and enrich these bacteria from the environment. Using this enrichment culture, we observe the formation and dynamics of T. majus fronts in oxygen gradients. We show that these dynamics can be understood as occurring in two steps. First, chemotactic cells moving up the oxygen gradient form a front that propagates with constant velocity. We then show, through observation and mathematical analysis, that this front becomes unstable to changes in cell density. Random perturbations in cell density create oxygen gradients. The response of cells magnifies these gradients and leads to the formation of millimeter-scale fluid flows that actively pull oxygenated water through the front. We argue that this flow results from a nonlinear instability excited by stochastic fluctuations in the density of cells. Finally, we show that the dynamics by which these modes interact can be understood from the chemotactic response of cells. These results provide a mathematically tractable example of how collective phenomena in ecological systems can arise from the individual response of cells to a shared resource.
... contrasts with the ecophysiology of its recently discovered relative Thiomargarita namibiensis. This immotile, giant sulfur oxidizer is the largest known prokaryote by volume; it relies completely on its enormous storage capacity for sulfur and nitrate to carry it through irregular natural fluctuations of sulfide and nitrate concentration in its sedimentary habitat Schulz, 2002a). In contrast to the very oxygen-sensitive Chilean Thioploca spp., Thiomargarita namibiensis tolerates prolonged oxygen exposure and, in addition to nitrate, appears to be able to use oxygen for sulfide oxidation if acetate is provided. ...
... It has been hypothesized that sediment resuspension allows Thiomargarita to regenerate their NO À 3 reservoir from the sea water (Schulz and Jørgensen, 2001). The surface sediments at this site have been described as 'unusually fluid' (Schulz, 2002) and regular stirring of these layers by currents may allow Thiomargarita to contact the sea water. We were only able to create sufficient NO À 3 penetration into the sediment in the absence of additional non-local transport (Eq. ...
Article
In this study the sulfur cycle in the organic-rich mud belt underlying the highly productive upwelling waters of the Namibian shelf is quantified using a 1D reaction-transport model. The model calculates vertical concentration and reaction rate profiles in the top 500 cm of sediment which are compared to a comprehensive dataset which includes carbon, sulfur, nitrogen and iron compounds as well as sulfate reduction (SR) rates and stable sulfur isotopes (32S, 34S). The sulfur dynamics in the well-mixed surface sediments are strongly influenced by the activity of the large sulfur bacteria Thiomargaritanamibiensis which oxidize sulfide (H2S) to sulfate () using sea water nitrate () as the terminal electron acceptor. Microbial sulfide oxidation (SOx) is highly efficient, and the model predicts intense cycling between and H2S driven by coupled SR and SOx at rates exceeding 6.0 mol S m−2 y−1. More than 96% of the SR is supported by SOx, and only 2–3% of the pool diffuses directly into the sediment from the sea water. A fraction of the produced by Thiomargarita is drawn down deeper into the sediment where it is used to oxidize methane anaerobically, thus preventing high methane concentrations close to the sediment surface. Only a small fraction of total H2S production is trapped as sedimentary sulfide, mainly pyrite (FeS2) and organic sulfur (Sorg) (∼0.3 wt.%), with a sulfur burial efficiency which is amongst the lowest values reported for marine sediments (<1%). Yet, despite intense SR, FeS2 and Sorg show an isotope composition of ∼5 ‰ at 500 cm depth. These heavy values were simulated by assuming that a fraction of the solid phase sulfur exchanges isotopes with the dissolved sulfide pool. An enrichment in H2S of 34S towards the sediment-water interface suggests that Thiomargarita preferentially remove H232S from the pore water. A fractionation of 20–30‰ was estimated for SOx (εSOx) with the model, along with a maximum fractionation for SR (εSR–max) of 100‰. These values are far higher than previous laboratory-based estimates for these processes. Mass balance calculations indicate negligible disproportionation of autochthonous elemental sulfur; an explanation routinely cited in the literature to account for the large fractionations in SR. Instead, the model indicates that repeated multi-stepped sulfide oxidation and intracellular disproportionation by Thiomargarita could, in principle, allow the measured isotope data to be simulated using much lower fractionations for εSOx (5‰) and εSR (78‰).
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We have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology‐literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513‐1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public‐health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well‐being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of ‘germs’ and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination‐capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision‐making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology‐centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre‐occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom. The ubiquity of microbes, their manifold activities and pervasive influence on the health of all life, local environments and the planet, necessitate an understanding of relevant microbial processes for informed, evidence‐based decision‐making at all levels of society – i.e. Microbiology Literacy. While teaching microbiology topics in school is key to this objective, a strategic program to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics, and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organisations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policy makers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.
Thesis
In recent years, advances in computer architecture and lipid force field parameters have made Molecular Dynamics (MD) a powerful tool for gaining atomistic resolution of biological membranes on timescales that other tools simply cannot explore. With many key biological processes involving membranes occurring on the nanosecond timescale, MD allows us to probe the dynamics and energetics of these interactions in molecular detail. Specifically, we can observe the interactions taking place as a peptide or protein comes into contact with a lipid bilayer, and how this may shape or alter the bilayer either locally (changes in headgroup orientation, lipid fluidity) or in bulk (lipid demixing, membrane curvature). The resolution achieved through atomistic MD can be directly compared with other tools such as NMR and EPR to gain a full perspective of how these biological systems behave over different timescales. As my background is in computational physics, this thesis not only looks into broadening our understanding of various interactions with biological membranes, but also into the development of construction and analytical software to assist in my research and benefit others in the field. One aspect of biological membranes that could vastly benefit from MD simulations is that of antimicrobial peptides (AMPs). These peptides primarily target and destroy microbes by permeabilising the cell membrane through a variety of proposed mechanisms, where each mechanism relies on the AMP to adopt specific conformations upon contact with bacterial membranes. In this thesis, I present an investigation into the interactions between a synthetic AMP and an inhibitor peptide designed to regulate antimicrobial activity through the formation of a coiled coil structure, which restricts the AMP from adopting new conformations. Simulations captured the spontaneous formation of coiled coils between these peptides, and specific residues in their sequences were identified that promote unfolding. This knowledge may lead to better design of coiled coil forming peptides. Another aspect of biological membranes that can be explored with MD is the interactions between model bacterial membranes and amphipathic helices, such as the MinD membrane targeting sequence (MinD-MTS). This 11-residue helix is responsible for anchoring the MinD protein to the inner membrane of Bacillus subtilis and plays a crucial role in bacterial cell division. MinD is known to exhibit sensitivity to transmembrane potentials (TMVs), whereby its localisation and binding affinity to bacterial membranes are disrupted upon removal of the TMV. Simulations revealed rapid insertions of MinD-MTS peptides into the headgroup region of a model bacterial membrane. Analytical software was constructed to measure the membrane properties of the lipids surrounding inserted MinDMTS peptides, which revealed splayed lipid tails and suggests the MinD-MTS may be capable of inducing membrane curvature. Additional simulations were conducted to investigate the influence of a TMV on model bacterial membranes, where software was constructed to measure changes in membrane properties. An analysis of these simulations suggests that a TMV is capable of lowering the transition temperature of a model bacterial membrane by a few degrees, yielding increased fluidity in the lipids and increased perturbations on the membrane surface. Finally, another aspect of biological membranes that can be explored through MD is that of electroporation. This induction of transient water pores in cell membrane provides an exciting aspect for drug delivery applications into cells, whereby electric fields are applied to cells to increase the uptake of therapeutic drugs. Simulations of membranes with high voltage TMVs were conducted that sought to investigate the implications of electroporation across a variety of bilayer compositions at different temperatures. Software was constructed to measure changes in membrane and system properties, which revealed that pore formation occurred at the same threshold voltage for different bilayer compositions in the fluid phase (~1.9 V) and a higher voltage for DPPC bilayers in the gel phase (~2.4 V). The TMV was found to be highly dependent on the area per lipid (APL), implying that bilayers with bulkier lipids or those transitioning from gel to fluid will experience smaller TMVs and fewer pore formations. These simulations also revealed lipid flip-flopping through pores, where charged lipids tended to translocate in the direction of the electric field to produce an asymmetrically charged bilayer. Finally, simulations utilising charged peptides with membranes yielded electroporation effects, whereby the charged peptides generate an identical TMV to those produced by an ion imbalance of equal magnitude. This suggests that charged peptides, such as AMPs, may be capable of permeabilising cell membranes through electroporation mechanisms.
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Abundant sulphur is present in the Late Miocene evaporitic sequence of the lacustrine Hellín basin in SE Spain. Weathering of Triassic evaporites controlled the chemical composition of the Miocene lake. The lacustrine deposits comprise gypsum, marlstones, diatomites and carbonate beds. Sulphur-bearing carbonate deposits predominantly consist of early diagenetic dolomite. Abundant dolomite crystals with a spheroidal habit are in accordance with an early formation and point to a microbial origin. The carbon isotopic composition of the dolomite (δ13C values between −10 and −4‰) indicates mixing of lake water carbonate and carbonate derived from the remineralization of organic matter by heterotrophic bacteria. Dolomite precipitated syngenetically under evaporitic conditions as indicated by high oxygen isotope values (δ18O between +6 and +11‰). Nodules of native sulphur are found in gypsum, carbonate beds and marlstone layers. Sulphur formed in the course of microbial sulphate reduction, as reflected by its strong depletion in 34S (δ34S values as low as −17‰). Near to the surface many of the sulphur nodules were in part or completely substituted by secondary gypsum, which still reflects the sulphur isotopic composition of native sulphur (−18 to −10‰). This study exemplifies the role of bacterial sulphate reduction in the formation of dolomite and native sulphur in a semi-enclosed lacustrine basin during Late Miocene time.
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MARINE species of Thioploca occur over 3,000 km along the continental shelf off Southern Peru and North and Central Chile(1-4). These filamentous bacteria live in bundles surrounded by a common sheath and form thick mats on the sea floor under the oxygen-minimum zone in the upwelling region, at between 40 and 280 m water depth. The metabolism of this marine bacterium(5,6) remained a mystery until long after its discovery(1,7). We report here that Thioploca cells are able to concentrate nitrate to up to 500 mM in a liquid vacuole that occupies >80% of the cell volume. Gliding filaments transport this nitrate 5-10 cm down into the sediment and reduce it, with concomitant oxidation of hydrogen sulphide, thereby coupling the nitrogen and sulphur cycles in the sediment.
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A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA sequence data, these bacteria are closely related to the marine filamentous sulfur bacteria Thioploca, abundant in the upwelling area off Chile and Peru. Similar to Thioploca, the giant bacteria oxidize sulfide with nitrate that is accumulated to </=800 millimolar in a central vacuole.
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A small number of prokaryotic species have a unique physiology or ecology related to their development of unusually large size. The biomass of bacteria varies over more than 10 orders of magnitude, from the 0.2 microm wide nanobacteria to the largest cells of the colorless sulfur bacteria, Thiomargarita namibiensis, with a diameter of 750 microm. All bacteria, including those that swim around in the environment, obtain their food molecules by molecular diffusion. Only the fastest and largest swimmers known, Thiovulum majus, are able to significantly increase their food supply by motility and by actively creating an advective flow through the entire population. Diffusion limitation generally restricts the maximal size of prokaryotic cells and provides a selective advantage for microm-sized cells at the normally low substrate concentrations in the environment. The largest heterotrophic bacteria, the 80 x 600 microm large Epulopiscium sp. from the gut of tropical fish, are presumably living in a very nutrient-rich medium. Many large bacteria contain numerous inclusions in the cells that reduce the volume of active cytoplasm. The most striking examples of competitive advantage from large cell size are found among the colorless sulfur bacteria that oxidize hydrogen sulfide to sulfate with oxygen or nitrate. The several-cm-long filamentous species can penetrate up through the ca 500-microm-thick diffusive boundary layer and may thereby reach into water containing their electron acceptor, oxygen or nitrate. By their ability to store vast quantities of both nitrate and elemental sulfur in the cells, these bacteria have become independent of the coexistence of their substrates. In fact, a close relative, T. namibiensis, can probably respire in the sulfidic mud for several months before again filling up their large vacuoles with nitrate.
Article
Thioploca spp. are multicellular, filamentous, colorless sulfur bacteria inhabiting freshwater and marine sediments. They have elemental sulfur inclusions similar to the phylogenetically closely related Beggiatoa, but in contrast to these they live in bundles surrounded by a common sheath. Vast communities of large Thioploca species live along the Pacific coast of South America and in other upwelling areas of high organic matter sedimentation with bottom waters poor in oxygen and rich in nitrate. Each cell of these thioplocas harbors a large liquid vacuole which is used as a storage for nitrate with a concentration of up to 500 mM. The nitrate is used as an electron acceptor for sulfide oxidation and the bacteria may grow autotrophically or mixotrophically using acetate or other organic molecules as carbon source. The filaments stretch up into the overlying seawater, from which they take up nitrate, and then glide down 5-15 cm deep into the sediment through their sheaths to oxidize sulfide formed by intensive sulfate reduction. New major occurrences have been found in recent years, both in lakes and in the ocean, and have stimulated the interest in these fascinating bacteria.
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A recently isolated strain of Beggiatoa, MS-81-6 (cf. alba), was tested for chemoautotrophic growth in semi-solid (0.2% agar) sulfide/oxygen gradient cultures. The organism grew in a horizontal layer, the distance from the air/medium interface depending on sulfide concentrations and changing with time. Optimal growth as a gradient organism was based on a preference for reduced oxygen concentrations and a limited sulfide tolerance in combination with gliding motility. In gradient cultures chemoautotrophic growth was demonstrated by the following criteria: (1) biomass yield (protein) increased with increasing sulfide concentration, and estimated molar growth yields agreed with those for other sulfide-grown chemoautotrophs; (2) approximately 90% of total cell carbon and protein carbon were fixed from carbon dioxide; (3) the CO2-fixing enzyme, ribulosebisphosphate carboxylase, was present in cell-free extracts at a level typical of chemoautotrophs; (4) acidification of the medium, apparently linked to utilization of internal So granules, accompanied the later phase of growth. The ability to grow on acetate in the absence of a source of reduced sulfur renders the organism facultatively chemoautotrophic.
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WHITE web-like 'mats' of the filamentous sulphur-oxidizing bacterium Beggiatoa are commonly observed on the surface of anoxic sediments1-3. As a typical interface organism Beggiatoa requires a source of inorganic reduced sulphur and dissolved free oxygen. The first pure cultures of marine strains of Beggiatoa were recently obtained by artificially reconstructing an O2-H2S interface in a semi-solid medium that supports the gliding mobility of the filaments4,5. The maximal thickness of these Beggiatoa mats in culture was 1.0 mm. We now report the discovery of dense layers of filamentous sulphur-oxidizing bacteria up to 3 cm thick on the sediment surface, and up to 30 cm thick between stands of vestimen-tiferan tube worms at the Guaymas Basin hydrothermal vent site in the Gulf of California at a depth of 2,010 m. The mats are essentially monocultures of Beggiatoa-type organisms containing filaments of three width classes, the largest filaments being 116-122 μm in diameter. Freshly collected filaments showed chemoautotrophic metabolism and active gliding motility. The phenomenon of a natural mass growth of a bacterium is of great physiological and ecological interest, and could also be of biotechnical importance considering the difficulties of mass cultivation of interface organisms such as Beggiatoa and the other 'large' sulphur-oxidizing bacteria such as Thiovulum6 and Thioploca7.