Magnetite compensates for the lack of a pilin‐associated c‐type cytochrome in extracellular electron exchange

Nanoscale magnetite can facilitate microbial extracellular electron transfer that plays an important role in biogeochemical cycles, bioremediation and several bioenergy strategies, but the mechanisms for the stimulation of extracellular electron transfer are poorly understood. Further investigation revealed that magnetite attached to the electrically conductive pili of Geobacter species in a manner reminiscent of the association of the multi‐heme c‐type cytochrome OmcS with the pili of Geobacter sulfurreducens. Magnetite conferred extracellular electron capabilities on an OmcS‐deficient strain unable to participate in interspecies electron transfer or Fe(III) oxide reduction. In the presence of magnetite wild‐type cells repressed expression of the OmcS gene, suggesting that cells might need to produce less OmcS when magnetite was available. The finding that magnetite can compensate for the lack of the electron transfer functions of a multi‐heme c‐type cytochrome has implications not only for the function of modern microbes, but also for the early evolution of microbial electron transport mechanisms.     

Seeing is believing: novel imaging techniques help clarify microbial nanowire structure and function

Novel imaging approaches have recently helped to clarify the properties of ‘microbial nanowires’. Geobacter sulfurreducens pili are actual wires. They possess metallic‐like conductivity, which can be attributed to overlapping pi‐pi orbitals of key aromatic amino acids. Electrostatic force microscopy recently confirmed charge propagation along the pili, in a manner similar to carbon nanotubes. The pili are essential for long‐range electron transport to insoluble electron acceptors and interspecies electron transfer. Previous claims that Shewanella oneidensis also produce conductive pili have recently been recanted, based on novel live‐imaging studies. The putative pili are, in fact, long extensions of the cytochrome‐rich outer membrane and periplasm that, when dried, collapse to form filaments with dimensions similar to pili. It has yet to be demonstrated whether the cytochrome‐to‐cytochrome electron hopping documented in the dried membrane extensions takes place in intact hydrated membrane extensions or whether the membrane extensions enhance electron transport to insoluble electron acceptors such as Fe(III) oxides or electrodes. These findings demonstrate that G. sulfurreducens conductive pili and the outer membrane extensions of S. oneidensis are fundamentally different in composition, mechanism of electron transport and physiological role. New methods for evaluating filament conductivity will facilitate screening the microbial world for nanowires and elucidating their function.     

A tree-based method for the rapid screening of chemical fingerprints

Background  

The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase of drug development for identifying novel drug candidates by screening large databases for molecules with fingerprints similar to a query fingerprint.     

Breeding system, colony and population structure in the weaver ant Oecophylla smaragdina

Weaver ants ( Oecophylla smaragdina ) are dominant ants in open forests from India, Australia, China and Southeast Asia, whose leaf nests are held together with larval silk. The species, together with its sole congener O. longinoda , has been important in research on biological control, communication, territoriality and colony integration. Over most of the range, only one queen has been found per colony, but the occurrence of several queens per nest has been reported for the Australian Northern Territory. The number of males mating with each queen is little known. Here we report on the colony structure of O. smaragdina using published and new microsatellite markers. Worker genotype arrays reflect the occurrence of habitual polygyny (more than one queen per colony) in 18 colonies from Darwin, Northern Australia, with up to five queens inferred per colony. Monogyny (one queen per colony) with occasional polygyny was inferred for 14 colonies from Queensland, Australia, and 20 colonies from Java, Indonesia. Direct genotyping of the sperm carried by 77 Queensland queens and worker genotypic arrays of established colonies yielded similar results, indicating that less than half of the queens mate only once and some mate up to five times. Worker genotype arrays indicated that queens from Java and the Northern Territory also often mate with more than one male, but less often than those from Queensland. A strong isolation-by-distance effect was found for Queensland samples. The variation uncovered means that O. smaragdina is a more versatile study system than previously supposed.     

Centimeter-long electron transport in marine sediments via conductive minerals

Centimeter-long electron conduction through marine sediments, in which electrons derived from sulfide in anoxic sediments are transported to oxygen in surficial sediments, may have an important influence on sediment geochemistry. Filamentous bacteria have been proposed to mediate the electron transport, but the filament conductivity could not be verified and other mechanisms are possible. Surprisingly, previous investigations have never actually measured the sediment conductivity or its basic physical properties. Here we report direct measurements that demonstrate centimeter-long electron flow through marine sediments, with conductivities sufficient to account for previously estimated electron fluxes. Conductivity was lost for oxidized sediments, which contrasts with the previously described increase in the conductivity of microbial biofilms upon oxidation. Adding pyrite to the sediments significantly enhanced the conductivity. These results suggest that the role of conductive minerals, which are more commonly found in sediments than centimeter-long microbial filaments, need to be considered when modeling marine sediment biogeochemistry.To evaluate the conductivity of coastal anaerobic marine sediments, gold electrodes separated by a 50-μm nonconductive gap were inserted at different depths in intact sediment cores collected from Nantucket Bay, Massachusetts (Figure 1a). Conductivity of the sediments was measured with techniques comparable to those previously used to document the conductivity of microbial pili networks and biofilms (Malvankar et al., 2011, 2012a). This approach to measure in situ dc conductivity is substantially different from previous attempts to probe the conductivity of soils and sediments that either used self-potential monitoring (Ntarlagiannis et al., 2007) or measurements over small timescales (<1 s) (Regberg et al., 2011), which primarily measure the ionic contribution and not electron conductivity (Du et al., 2009; Patra et al., 2010). Direct conductivity measurements revealed values that were low in oxidized surficial sediments (<1 μS cm⁻¹); however, conductivities were significantly higher (P<0.05, t-test) in deeper, highly reduced sediments (Figure 1b). Along with intact sediment cores, experiments were also performed with mixed sediment subsamples. Comparable values of 7±0.15 μS cm⁻¹ (mean±s.e.; n=3) were obtained using this alternative approach, in which reduced sediments were placed on a four-probe electrode array under anaerobic conditions (Figure 1c) and conductivities measured over the 1-cm span of the electrodes.Open in a separate windowFigure 1Strategy to measure in situ sediment conductivity. (a) Schematic of setup to place intact cores of marine sediment. Gold electrodes with a 50-μm nonconductive spacing were inserted at different depths with respect to the overlying water. (b) Conductivity data of three independent sediment cores as a function of depth from the overlying water. Control setup was comprised of garden sand. Error bars represent s.d. These measurements were performed at 15 °C to mimic the physiological temperature of marine sediments. (c) Schematic of four-probe used to measure sediment conductivity. Current was injected using outer two gold electrodes and the voltage was measured using inner two gold electrodes using a high-impedance voltmeter.In previous studies (Nielsen et al., 2010) that led to the concept of long-range electron transport via conductive microbial filaments (Pfeffer et al., 2012), electric currents in the sediment were not actually measured, but rather inferred from rates of sediment oxygen consumption that were estimated from oxygen concentration profiles (Nielsen et al., 2010). In Aarhus Bay, estimated rates of oxygen consumption were 9.7 mmol O₂ per m² per day with 31% of this oxygen consumption attributed to electric current from deeper sediments (that is, 3 mmol O₂ per m² per day) and in Aarhus Harbor sediments 42% of the estimated 46 mmol O₂ per m² consumed per day (that is, 19.3 mmol O₂ per m² per day) was attributed to the inferred electric currents (Nielsen et al., 2010). Thus, given that four moles of electrons are required for each mole of oxygen reduced to water (O₂+4H⁺+4e⁻→2H₂O), the estimated electron flux through the sediments was 12–77 mmoles of electrons per m² per day. This electron flux through each m² of sediment can be converted to electric current as follows (calculations shown for maximum estimated flux): ((7.7 × 10⁻² moles of electrons per day) × (1.16 × 10⁻⁵ days s⁻¹) × (Amp/1.036 × 10⁻⁵ moles of electrons per second)=0.086 Amps or 86 mA for Aarhus Harbor sediments and 14 mA for the Aarhus Bay sediments). The proposed (Nielsen et al., 2010) reaction driving the electron flux is the oxidation of sulfide coupled to the reduction of oxygen, that is, a potential difference of ca. 1.1 V (HS⁻/S couple, −0.27 V; O₂/H₂O, +0.82 V; (Thauer et al., 1977)). The current (I) expected through 1 m² of sediment with the conductivity (σ) of 7 μS cm⁻¹ that was measured over 1 cm (approximate length of proposed conductive microbial filaments) of the Nantucket Bay sediments can be calculated from the relationship σ=G ×  l/A (l=length=1 cm; A=area=1 m² or 10⁴ cm²), where G is the conductance (G=I/V) and thus I=(V × A × σ)/l; (I=(1.1 V × 10⁴ cm² × 7 × 10⁻⁶ S cm⁻¹)/1 cm)=7.7 × 10⁻² V-S=77 mA. This compares well with the currents of 14–86 mA estimated from oxygen consumption in the sediments (Nielsen et al., 2010) in which it was proposed that microbial filaments were responsible for long-range electron transport (Pfeffer et al., 2012).To evaluate the contrast in conductivity between surficial oxidized sediments and deeper reduced sediments, reduced sediments were oxidized under air at 4 °C to preserve the biological components in the marine sediments such as bacterial c-type cytochromes and pili nanowires that have been hypothesized to confer conductivity to marine sediments (Nielsen et al., 2010; Reguera, 2012). Upon air-oxidation, conductivity of marine sediments declined ca. 90% (Figure 2a). Electrochemical oxidation of the sediments resulted in a similar conductivity loss (Figure 2b).Open in a separate windowFigure 2Effect of oxidation and mineral addition on sediment conductivity. (a) Effect of air-oxidation over days on the conductivity of marine sediments. Error bars represent s.d. (n=3 biological replicates). (b) Effect of electrochemical oxidation on the conductivity of marine sediments as a function of gate voltage using electrolyte-gated field-effect transistor geometry. (c) Effect of the addition of pyrite mineral to the conductivity of marine sediments. (d) Effect of the addition of pyrite mineral to the conductivity of freshwater sediments. All error bars represent s.d.The decrease in sediment conductivity upon oxidation contrasts with the two orders of magnitude increase in conductivity following oxidation of Geobacter sulfurreducens biofilms (Malvankar et al., 2011, 2012b), which are the only microbial system in which centimeter-long electron conduction has been directly documented. It is likely that oxidation increases conduction in G. sulfurreducens biofilms because the networks of pili that are thought to mediate long-range electron transport exhibit p-type conduction in which holes are majority carriers (Malvankar et al., 2011). The conductivity of p-type materials increases upon oxidation because the oxidation process increases the density of hole carriers (Heeger et al., 2010; Malvankar and Lovley, 2012). The suppression of sediment conductivity with oxidation indicated that long-range electron transport through the sediments is significantly different than that through G. sulfurreducens biofilms. It is unknown how oxidizing conditions might have an impact on the previously proposed conductivity through filamentous bacteria (Pfeffer et al., 2012; Malkin et al., 2014) because the hypothesized conductivity and the mechanisms for conduction have not been documented (Reguera, 2012).An abiological mechanism for electron transport through sediments that could potentially be eliminated with oxidation is conduction through iron–sulfur minerals. Dense assemblages of conductive iron–sulfur minerals in ore bodies (Sato and Mooney, 1960) or hydrothermal vents (Nakamura et al., 2010) may be capable of conducting electrons over distances of centimeters (Nakamura et al., 2010) to meters (Sato and Mooney, 1960). To determine whether lower abundances of an iron–sulfur mineral, comparable to those that might be found in reduced marine sediments, could contribute to conductivity, finely ground pyrite (10–100 μm diameters) was added to the reduced sediment. There was a significant increase in conductivity at higher pyrite concentrations (Figure 2c). The conductivity of freshwater sediment also increased upon addition of pyrite (Figure 2d).Although it has been suggested that filaments of cells closely related to Desulfobulbus species accounted for conductivity to reduced marine sediments from Aarhus Bay, it is, in fact, unknown whether this is possible because the conductivity of the filaments was not demonstrated (Pfeffer et al., 2012; Reguera, 2012; Malkin et al., 2014). No long bacterial filaments were observed in the Nantucket sediments used in these studies. The findings reported here, based on direct measurements of sediment conductivity, demonstrate that conductive minerals can confer substantial conductivity to anaerobic marine sediments and could potentially have an important role in sediment biogeochemistry. The simple method described here for assessing sediment conductivity is expected to be a useful tool for future studies of long-range electron conduction in a diversity of soils and sediments.     

CoaSim: A flexible environment for simulating genetic data under coalescent models

Background  

Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these.