Commensal symbiosis between agglutinated polychaetes and sulfate‐reducing bacteria

Pendant bioconstructions occur within submerged caves in the Plemmirio Marine Protected Area in SE Sicily, Italy. These rigid structures, here termed biostalactites, were synsedimentarily lithified by clotted‐peloidal microbial carbonate that has a high bacterial lipid biomarker content with abundant compounds derived from sulfate‐reducing bacteria. The main framework builders are polychaete serpulid worms, mainly Protula with subordinate Semivermilia and Josephella. These polychaetes have lamellar and/or fibrillar wall structure. In contrast, small agglutinated terebellid tubes, which are a minor component of the biostalactites, are discontinuous and irregular with a peloidal micritic microfabric. The peloids, formed by bacterial sulfate reduction, appear to have been utilized by terebellids to construct tubes in an environment where other particulate sediment is scarce. We suggest that the bacteria obtained food from the worms in the form of fecal material and/or from the decaying tissue of surrounding organisms and that the worms obtained peloidal micrite with which to construct their tubes, either as grains and/or as tube encompassing biofilm. Peloidal worm tubes have rarely been reported in the recent but closely resemble examples in the geological record that extend back at least to the early Carboniferous. This suggests a long‐lived commensal relationship between some polychaete worms and heterotrophic, especially sulfate‐reducing, bacteria.     

Controllable extracellular biosynthesis of bismuth sulfide nanostructure by sulfate‐reducing bacteria in water–oil two‐phase system

Due to strong hydrolysis of Bi³⁺ as precursor in aqueous media, there are no reports on biosynthesis of bismuth sulfide (Bi₂S₃) nanomaterials. In this work, the water–oil two‐phase system was used to biosynthesize the Bi₂S₃ nanomaterials based on the coupling reaction of biological reduction and chemical precipitation process for the first time. The results showed that the water–oil two‐phase system successfully eliminated hydrolysis of the Bi³⁺ and controllably and extracellularly fabricated the Bi₂S₃ crystal with high purity. The nanorods with diameter of about 100 nm and length of about 1.0 μm were attained under high dose of lactic acid and SO₄^2?; while low dose obtained the nanobundles consisted of nanoneedles with tip diameter of 10–20 nm and length of about 5.0–10.0 μm. The Bi₂S₃ nanorods as photocatalyst almost completely degraded methylene blue from solution within 12 h; whereas the Bi₂S₃ nanobundles removed about 87% of the dye. The amount of the Bi₂S₃ nanorods decreased by 48% due to photocorrosion, whereas 52% with the nanobundles. The Bi₂S₃ nanorods had relatively higher photocatalysis activity and slightly stronger photocorrosion resistance than the Bi₂S₃ nanobundles. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:960–966, 2014     

Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate‐reducing Deltaproteobacterium N47

Anaerobic degradation of polycyclic aromatic hydrocarbons (PAHs) is an important process during natural attenuation of aromatic hydrocarbon spills. However, knowledge about metabolic potential and physiology of organisms involved in anaerobic degradation of PAHs is scarce. Therefore, we introduce the first genome of the sulfate‐reducing Deltaproteobacterium N47 able to catabolize naphthalene, 2‐methylnaphthalene, or 2‐naphthoic acid as sole carbon source. Based on proteomics, we analysed metabolic pathways during growth on PAHs to gain physiological insights on anaerobic PAH degradation. The genomic assembly and taxonomic binning resulted in 17 contigs covering most of the sulfate reducer N47 genome according to general cluster of orthologous groups (COGs) analyses. According to the genes present, the Deltaproteobacterium N47 can potentially grow with the following sugars including d ‐mannose, d ‐fructose, d ‐galactose, α‐d ‐glucose‐1P, starch, glycogen, peptidoglycan and possesses the prerequisites for butanoic acid fermentation. Despite the inability for culture N47 to utilize NO₃^‐ as terminal electron acceptor, genes for nitrate ammonification are present. Furthermore, it is the first sequenced genome containing a complete TCA cycle along with the carbon monoxide dehydrogenase pathway. The genome contained a significant percentage of repetitive sequences and transposase‐related protein domains enhancing the ability of genome evolution. Likewise, the sulfate reducer N47 genome contained many unique putative genes with unknown function, which are candidates for yet‐unknown metabolic pathways.     

Low potential manganese ions as efficient electron donors in native anoxygenic bacteria

Systematic control over molecular driving forces is essential for understanding the natural electron transfer processes as well as for improving the efficiency of the artificial mimics of energy converting enzymes. Oxygen producing photosynthesis uniquely employs manganese ions as rapid electron donors. Introducing this attribute to anoxygenic photosynthesis may identify evolutionary intermediates and provide insights to the energetics of biological water oxidation. This work presents effective environmental methods that substantially and simultaneously tune the redox potentials of manganese ions and the cofactors of a photosynthetic enzyme from native anoxygenic bacteria without the necessity of genetic modification or synthesis. A spontaneous coordination with bis-tris propane lowered the redox potential of the manganese (II) to manganese (III) transition to an unusually low value (~400?mV) at pH?9.4 and allowed its binding to the bacterial reaction center. Binding to a novel buried binding site elevated the redox potential of the primary electron donor, a dimer of bacteriochlorophylls, by up to 92?mV also at pH?9.4 and facilitated the electron transfer that is able to compete with the wasteful charge recombination. These events impaired the function of the natural electron donor and made BTP-coordinated manganese a viable model for an evolutionary alternative.     

Development and comparison of SYBR Green quantitative real‐time PCR assays for detection and enumeration of sulfate‐reducing bacteria in stored swine manure

Aims: To develop and evaluate primer sets targeted to the dissimilatory sulfite reductase gene (dsrA) for use in quantitative real‐time PCR detection of sulfate‐reducing bacteria (SRB) in stored swine manure. Methods and Results: Degenerate primer sets were developed to detect SRB in stored swine manure. These were compared with a previously reported primer set, DSR1F+ and DSR‐R, for their coverage and ability to detect SRB communities in stored swine manure. Sequenced clones were most similar to Desulfovibrio sp. and Desulfobulbus sp., and these SRB populations differed within different manure ecosystems. Sulfur content of swine diets was shown to affect the population of Desulfobulbus‐like Group 1 SRB in manure. Conclusions: The newly developed assays were able to enumerate and discern different groups of SRB, and suggest a richly diverse and as yet undescribed population of SRB in swine manure. Significance and Impact of the Study: The PCR assays described here provide improved and efficient molecular tools for quantitative detection of SRB populations. This is the first study to show population shifts of SRB in swine manure, which are a result of either the effects of swine diets or the maturity of the manure ecosystem.     

The genome of the Gram‐positive metal‐ and sulfate‐reducing bacterium Desulfotomaculum reducens strain MI‐1

Spore‐forming, Gram‐positive sulfate‐reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens strain MI‐1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three‐ and four‐carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram‐positive SRB suggests a distinct sulfate‐reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H₂‐evolving and H₂‐consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H₂ cycling in the bacterium. The mechanism of metal reduction remains unknown.     

Analysis of copper corrosion in compacted bentonite clay as a function of clay density and growth conditions for sulfate‐reducing bacteria

Aims: To investigate the relationships between sulfate‐reducing bacteria (SRB), growth conditions, bentonite densities and copper sulfide generation under circumstances relevant to underground, high‐level radioactive waste repositories. Methods and Results: Experiments took place 450 m underground, connected under in situ pressure to groundwater containing SRB. The microbial reduction of sulfate to sulfide and subsequent corrosion of copper test plates buried in compacted bentonite were analysed using radioactive sulfur (³⁵SO₄^2?) as tracer. Mass distribution of copper sulfide on the plates indicated a diffusive process. The relationship between average diffusion coefficients (D_s) and tested density (ρ) was linear. D_s (m² s^?1) = ?0·004 × ρ (kg m^?3) + 8·2, decreasing by 0·2 D_s units per 50 kg m^?3 increase in density, from 1·2 × 10^?11 m² s^?1 at 1750 kg m^?3 to 0·2 × 10^?11 m² s^?1 at 2000 kg m^?3. Conclusions: It is possible that sulfide corrosion of waste canisters in future radioactive waste repositories depends mainly on sulfide concentration at the boundary between groundwater and the buffer, which in turn depends on SRB growth conditions (e.g., sulfate accessibility, carbon availability and electron donors) and geochemical parameters (e.g., presence of ferrous iron, which immobilizes sulfide). Maintaining high bentonite density is also important in mitigating canister corrosion. Significance and Impact of the Study: The sulfide diffusion coefficients can be used in safety calculations regarding waste canister corrosion. The work supports findings that microbial activity in compacted bentonite will be restricted. The study emphasizes the importance of growth conditions for sulfate reduction at the groundwater boundary of the bentonite buffer and linked sulfide production.     

Microbial diversity and community structure of a highly active anaerobic methane‐oxidizing sulfate‐reducing enrichment

Anaerobic oxidation of methane (AOM) is an important methane sink in the ocean but the microbes responsible for AOM are as yet resilient to cultivation. Here we describe the microbial analysis of an enrichment obtained in a novel submerged‐membrane bioreactor system and capable of high‐rate AOM (286 μmol g_{dry weight}^?1 day^?1) coupled to sulfate reduction. By constructing a clone library with subsequent sequencing and fluorescent in situ hybridization, we showed that the responsible methanotrophs belong to the ANME‐2a subgroup of anaerobic methanotrophic archaea, and that sulfate reduction is most likely performed by sulfate‐reducing bacteria commonly found in association with other ANME‐related archaea in marine sediments. Another relevant portion of the bacterial sequences can be clustered within the order of Flavobacteriales but their role remains to be elucidated. Fluorescent in situ hybridization analyses showed that the ANME‐2a cells occur as single cells without close contact to the bacterial syntrophic partner. Incubation with ¹³C‐labelled methane showed substantial incorporation of ¹³C label in the bacterial C₁₆ fatty acids (bacterial; 20%, 44% and 49%) and in archaeal lipids, archaeol and hydroxyl‐archaeol (21% and 20% respectively). The obtained data confirm that both archaea and bacteria are responsible for the anaerobic methane oxidation in a bioreactor enrichment inoculated with Eckernförde bay sediment.     

Consortium diversity of a sulfate‐reducing biofilm developed at acidic pH influent conditions in a down‐flow fluidized bed reactor

Sulfate reduction is an appropriate approach for the treatment of effluents with sulfate and dissolved metals. In sulfate‐reducing reactors, acetate may largely contribute to the residual organic matter, because not all sulfate reducers are able to couple the oxidation of acetate to the reduction of sulfate, limiting the treatment efficiency. In this study, we investigated the diversity of a bacterial community in the biofilm of a laboratory scale down‐flow fluidized bed reactor, which was developed under sulfidogenic conditions at an influent pH between 4 and 6. The sequence analysis of the microbial community showed that the 16S rRNA gene sequence of almost 50% of the clones had a high similarity with Anaerolineaceae. At second place, 33% of the 16S rRNA phylotypes were affiliated with the sulfate‐reducing bacteria Desulfobacca acetoxidans and Desulfatirhabdium butyrativorans, suggesting that acetotrophic sulfate reduction was occurring in the system. The remaining bacterial phylotypes were related to fermenting bacteria found at the advanced stage of reactor operation. The results indicate that the acetotrophic sulfate‐reducing bacteria were able to remain within the biofilm, which is a significant result because few natural consortia harbor complete oxidizing sulfate‐reducers, improving the acetate removal via sulfate reduction in the reactor.     

Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate‐reducing bacterial lipids in cocultures and methane seeps

Correlation between hydrogen isotope fractionation in fatty acids and carbon metabolism in pure cultures of bacteria indicates the potential of biomarker D/H analysis as a tool for diagnosing carbon substrate usage in environmental samples. However, most environments, in particular anaerobic habitats, are built from metabolic networks of micro‐organisms rather than a single organism. The effect of these networks on D/H of lipids has not been explored and may complicate the interpretation of these analyses. Syntrophy represents an extreme example of metabolic interdependence. Here, we analyzed the effect of metabolic interactions on the D/H biosignatures of sulfate‐reducing bacteria (SRB) using both laboratory maintained cocultures of the methanogen Methanosarcina acetivorans and the SRB Desulfococcus multivorans in addition to environmental samples harboring uncultured syntrophic consortia of anaerobic methane‐oxidizing archaea (ANME) and sulfate‐reducing Deltaproteobacteria (SRB) recovered from deep‐sea methane seeps. Consistent with previously reported trends, we observed a ~80‰ range in hydrogen isotope fractionation (ε_{lipid–water}) for D. multivorans grown under different carbon assimilation conditions, with more D‐enriched values associated with heterotrophic growth. In contrast, for cocultures of D. multivorans with M. acetivorans, we observed a reduced range of ε_{lipid–water} values (~36‰) across substrates with shifts of up to 61‰ compared to monocultures. Sediment cores from methane seep settings in Hydrate Ridge (offshore Oregon, USA) showed similar D‐enrichment in diagnostic SRB fatty acids coinciding with peaks in ANME/SRB consortia concentration suggesting that metabolic associations are connected to the observed shifts in ε_{lipid–water} values.     

Modeling the electron transport chain of purple non‐sulfur bacteria

Purple non‐sulfur bacteria (Rhodospirillaceae) have been extensively employed for studying principles of photosynthetic and respiratory electron transport phosphorylation and for investigating the regulation of gene expression in response to redox signals. Here, we use mathematical modeling to evaluate the steady‐state behavior of the electron transport chain (ETC) in these bacteria under different environmental conditions. Elementary‐modes analysis of a stoichiometric ETC model reveals nine operational modes. Most of them represent well‐known functional states, however, two modes constitute reverse electron flow under respiratory conditions, which has been barely considered so far. We further present and analyze a kinetic model of the ETC in which rate laws of electron transfer steps are based on redox potential differences. Our model reproduces well‐known phenomena of respiratory and photosynthetic operation of the ETC and also provides non‐intuitive predictions. As one key result, model simulations demonstrate a stronger reduction of ubiquinone when switching from high‐light to low‐light conditions. This result is parameter insensitive and supports the hypothesis that the redox state of ubiquinone is a suitable signal for controlling photosynthetic gene expression.     

Redox signaling mediates the expression of a sulfate‐deprivation‐inducible microRNA395 in Arabidopsis

MicroRNA395 (miR395) is a conserved miRNA that targets a low‐affinity sulfate transporter (AST68) and three ATP sulfurylases (APS1, APS3 and APS4) in higher plants. In this study, At2g28780 was confirmed as another target of miR395 in Arabidopsis. Interestingly, several dicots contained genes homologous to At2g28780 and a cognate miR395 complementary site but possess a gradient of mismatches at the target site. It is well established that miR395 is induced during S deprivation in Arabidopsis; however, the signaling pathways that mediate this regulation are unknown. Several findings in the present study demonstrate that redox signaling plays an important role in induction of miR395 during S deprivation. These include the following results: (i) glutathione (GSH) supplementation suppressed miR395 induction in S‐deprived plants (ii) miR395 is induced in Arabidopsis seedlings exposed to Arsenate or Cu²⁺, which induces oxidative stress (iii), S deprivation‐induced oxidative stress, and (iv) compromised induction of miR395 during S deprivation in cad2 mutant (deficient in GSH biosynthesis) that is defective in glutaredoxin‐dependent redox signaling and ntra/ntrb (defective in thioredoxin reductases a and b) double mutants that are defective in thioredoxin‐dependent redox signaling. Collectively, these findings strongly support the involvement of redox signaling in inducing the expression of miR395 during S deprivation in Arabidopsis.     

Photosynthetic electron transport activity in heat-treated barley leaves: the role of internal alternative electron donors to photosystem II

Electron transport processes were investigated in barley leaves in which the oxygen-evolution was fully inhibited by a heat pulse (48 degrees C, 40 s). Under these circumstances, the K peak (approximately F(400 micros)) appears in the chl a fluorescence (OJIP) transient reflecting partial Q(A) reduction, which is due to a stable charge separation resulting from the donation of one electron by tyrozine Z. Following the K peak additional fluorescence increase (indicating Q(A)(-) accumulation) occurs in the 0.2-2 s time range. Using simultaneous chl a fluorescence and 820 nm transmission measurements it is demonstrated that this Q(A)(-) accumulation is due to naturally occurring alternative electron sources that donate electrons to the donor side of photosystem II. Chl a fluorescence data obtained with 5-ms light pulses (double flashes spaced 2.3-500 ms apart, and trains of several hundred flashes spaced by 100 or 200 ms) show that the electron donation occurs from a large pool with t(1/2) approximately 30 ms. This alternative electron donor is most probably ascorbate.     

The impact of electron donors and anode potentials on the anode-respiring bacteria community

Both anode potentials and substrates can affect the process of biofilm formation in bioelectrochemical systems, but it is unclear who primarily determine the anode-respiring bacteria (ARB) community structure and composition. To address this issue, we divided microbial electrolysis cells (MECs) into groups, feeding them with different substrates and culturing them at various potentials. Non-turnover cyclic voltammetry indicated that the extracellular electron transfer components were uniform when feeding acetate, because the same oxidation peaks occurred at − 0.36 ± 0.01 and − 0.17 ± 0.01 V (vs. Ag/AgCl). Illumina MiSeq sequencing revealed that the dominating ARB was Geobacter, which did not change with different potentials. When the MECs were cultured with sucrose and mixed substrates, oxidation peak P3 (− 0.29 ± 0.015 V) occurred at potentials of − 0.29 and 0.01 V. This may be because of the appearance of Unclassified_AKYG597. In addition, oxidation peak P4 (− 0.99 ± 0.01 V) occurred at high and low potentials (0.61 and − 0.45 V, respectively), and the maximum current densities were far below those of the middle potentials. Illumina MiSeq sequencing showed that fermentation microorganisms (Lactococcus and Sphaerochaeta) dominated the biofilms. Consequently, substrate primarily determined the dominating ARB, and Geobacter invariably dominated the acetate-fed biofilms with potentials changed. Conversely, different potentials mainly affected fermentable substrate-fed biofilms, with dominating ARB turning into Unclassified_AKYG59.