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Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway., (© 2023. Springer Nature Limited.)

Smut fungi comprise one of the largest groups of fungal plant pathogens causing disease in all cereal crops. They directly penetrate host tissues and establish a biotrophic interaction. To do so, smut fungi secrete a wide range of effector proteins, which suppress plant immunity and modulate cellular functions as well as development of the host, thereby determining the pathogen's lifestyle and virulence potential. The conserved effector Erc1 (enzyme required for cell-to-cell extension) contributes to virulence of the corn smut Ustilago maydis in maize leaves but not on the tassel. Erc1 binds to host cell wall components and displays 1,3-β-glucanase activity, which is required to attenuate β-glucan-induced defense responses. Here we show that Erc1 has a cell type-specific virulence function, being necessary for fungal cell-to-cell extension in the plant bundle sheath and this function is fully conserved in the Erc1 orthologue of the barley pathogen Ustilago hordei., (© 2022. The Author(s).)

Oil and gas development can result in natural gas migration into shallow groundwater. Methane (CH 4 ), the primary component of natural gas, can subsequently react with solutes and minerals in the aquifer to create byproducts that affect groundwater chemistry. Hydro-biogeochemical processes induced by fugitive gas from leaky oil and gas wells are currently not well understood. We monitored the hydro-biogeochemical responses of a controlled natural gas release into a well-studied Pleistocene beach sand aquifer (Canadian Forces Base Borden, Ontario, Canada). Groundwater samples were collected before, during, and up to 700 days after gas injection and analyzed for pH, major and minor ions, alkalinity, dissolved gases, stable carbon isotope ratios of CO 2 and CH 4 , and microbial community composition. Gas injection resulted in a dispersed plume of free and dissolved phase natural gas, affecting groundwater chemistry in two distinct temporal phases. Initially (i.e. during and immediately after gas injection), pH declined and major ions and trace elements fluctuated; at times increasing above baseline concentrations. Changes in the short-term were due to invasion of deep groundwater with elevated total dissolved solids entrained with the upward migration of free phase gas and, reactions that were instigated through the introduction of constituents other than CH 4 present in the injected gas (e.g. CO 2 ). At later times, more pronounced aerobic and anaerobic CH 4 oxidation led to subtle increases in major ions (e.g. Ca 2+ , H 4 SiO 4 ) and trace elements (e.g. As, Cr). Microbial community profiling indicated a persistent perturbation to community composition with a conspicuous ingrowth of taxa implicated in aerobic CH 4 oxidation as well anaerobic S, N and Fe species metabolism., (Copyright © 2019 Elsevier B.V. All rights reserved.)

We developed an efficient, scalable and inexpensive method for recovering cellular biomass from complex fluid matrices that cannot be processed using conventional filtration methods. The method uses chemical flocculation with iron oxyhydroxides, is capable of recovering greater than 90% of cellular biomass from fluids with more than 10 3 cells ml -1 , and was validated using both mock communities and field samples. High quality DNA can be readily extracted from iron flocs using standard soil extraction kits. We applied chemical flocculation to fracing fluids from British Columbia, Canada and recovered a diversity of microbial taxa including abundant members of the Epsilon- and Deltaproteobacteria previously recovered from shale gas operations in the United States. Application of chemical flocculation presents new opportunities for scalable time-series monitoring and experimentation on complex fluid matrices including microbial community profiling and shotgun metagenomics over gas production well completion cycles., (© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.)

The role of hydrogen, acetate, and lactate as electron donors for microbial manganese reduction was investigated in manganese-rich marine sediment from Gullmar Fjord (Sweden). Here, manganese reduction accounted for 50% of the anaerobic carbon oxidation at 0-15 cm sediment depth. In anoxic incubations from 0 to 5 cm depth, where manganese reduction dominated completely as terminal electron-accepting process, the combined contribution of acetate and lactate as electron donors for manganese reducers corresponded to < ¼ of the electron flow. The concentrations, ¹⁴C-radiotracer turnover rates, and contributions to carbon oxidation of acetate and lactate associated with manganese reduction were similar to those found in deeper horizons dominated by concomitant iron and sulfate reduction and sulfate reduction alone, respectively. By contrast, hydrogen concentrations increased considerably with sediment depth, indicating thermodynamic control of the competition between the electron-accepting processes, and hydrogen may have contributed substantially to the > 75% of the electron flow that did not involve acetate and lactate. Alternatively, the oxidation of more complex organic substrates could be involved. Our study provides the first direct evidence of substrate utilization by a natural manganese-reducing community and indicates similar mechanisms of thermodynamic control and competition for electron donors as known from sediments dominated by iron reduction, sulfate reduction, or methanogenesis., (© 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

While most oxygenic phototrophs harvest light only in the visible range (400-700 nm, VIS), anoxygenic phototrophs can harvest near infrared light (> 700 nm, NIR). To study interactions between the photosynthetic guilds we used microsensors to measure oxygen and gross oxygenic photosynthesis (gOP) in a hypersaline microbial mat under full (VIS + NIR) and VIS illumination. Under normal dissolved inorganic carbon (DIC) concentrations (2 mM), volumetric rates of gOP were reduced up to 65% and areal rates by 16-31% at full compared with VIS illumination. This effect was enhanced (reduction up to 100% in volumetric, 50% in areal rates of gOP) when DIC was lowered to 1 mM, but diminished at 10 mM DIC or lowered pH. In conclusion, under full-light illumination anoxygenic phototrophs are able to reduce the activity of oxygenic phototrophs by efficiently competing for inorganic carbon within the highly oxygenated layer. Anoxygenic photosynthesis, calculated from the difference in gOP under full and VIS illumination, represented between 10% and 40% of the C-fixation. The DIC depletion in the euphotic zone as well as the significant C-fixation by anoxygenic phototrophs in the oxic layer influences the carbon isotopic composition of the mat, which needs to be taken into account when interpreting isotopic biosignals in geological records., (© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.)

Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetate-utilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 10(6) acetate-utilizing manganese-reducing cells cm(-3) in Gullmar Fjord sediment. A 16S rRNA gene clone library that was established from the highest MPN dilutions was dominated by sequences of Colwellia and Arcobacter species and members of the Oceanospirillaceae, supporting the obtained RNA-SIP results. In conclusion, these findings strongly suggest that (i) acetate-dependent manganese reduction in manganese oxide-rich sediments is catalyzed by members of taxa (Arcobacter, Colwellia and Oceanospirillaceae) previously not known to possess this physiological function, (ii) similar acetate-utilizing manganese reducers thrive in geographically distinct regions and (iii) the identified manganese reducers differ greatly from the extensively explored iron reducers in marine sediments.

Deposition of dredged harbor sediments in relatively undisturbed ecosystems is often considered a viable option for confinement of pollutants and possible natural attenuation. This study investigated the effects of deposition of heavy-metal-polluted sludge on the microbial diversity of sandy sediments during 12 months of mesocosm incubation. Geochemical analyses showed an initial increase in pore-water metal concentrations, which subsided after 3 months of incubation. No influence of the deposited sediment was observed in denaturing gradient gel electrophoresis (DGGE) profiles of bacterial 16S rRNA genes, whereas a minor, transient impact on the archaeal community was revealed. Phylogenetic analyses of bacterial 16S rRNA clone libraries showed an abundance of members of the Flavobacteriaceae, the alpha- and gamma-Proteobacteria, in both the muddy and the sandy sediments. Despite the finding that some groups of clones were shared between the metal-impacted sandy sediment and the harbor control, comparative analyses showed that the two sediments were significantly different in community composition. Consequences of redeposition of metal-polluted sediment were primarily underlined with cultivation-dependent techniques. Toxicity tests showed that the percentage of Cd- and Cu-tolerant aerobic heterotrophs was highest among isolates from the sandy sediment with metal-polluted mud on top.

Anaerobic degradation of organic material generally proceeds through a sequence of steps, including polymer hydrolysis, fermentation and respiration or methanogenesis. The intermediates, such as volatile fatty acids (VFA) or H(2), are generally maintained at low concentration, showing a close coupling of the terminal oxidation to fermentation. We exposed marine sediments to extreme temperature perturbations to study the nature and robustness of this coupling. Bacterial sulfate reduction and its dependence on fermentation were studied experimentally over a broad temperature range of -0.3 to 40 degrees C in sediments from temperate and permanently cold environments. In an Arctic sediment from Svalbard, the apparent optimum temperature for sulfate reduction decreased with prolonged incubation, whereas sulfate reduction rates increased. In a temperate sediment from the North Sea, the apparent optimum temperature was higher and did not change with incubation time. Up to a critical temperature, the concentrations of VFA remained low, <3 microM for acetate and <1 microM for the other VFA, the H(2) concentration showed thermodynamic control by sulfate-reducing bacteria, revealing a close coupling of fermentation and sulfate reduction. Above the critical temperature, the concentrations of VFA and H(2) increased transiently by 100-1000-fold. According to the different in situ temperatures of the samples, the critical temperature was lower for sediments from the Arctic than from the North Sea. The H(2) concentrations decreased again upon prolonged incubation to values typical for sulfate-depleted methanogenic sediments. This suggests that fermentative bacteria and methanogenic archaea in both sediments tolerated higher temperatures than the sulfate-reducing community.

We have designed and built an apparatus for real-time acoustic imaging of convective flow patterns in optically opaque fluids. This apparatus takes advantage of recent advances in two-dimensional ultrasound transducer array technology; it employs a modified version of a commercially available ultrasound camera, similar to those employed in nondestructive testing of solids. Images of convection patterns are generated by observing the lateral variation of the temperature dependent speed of sound via refraction of acoustic plane waves passing vertically through the fluid layer. The apparatus has been validated by observing convection rolls in both silicone oil and ferrofluid.

The effect of variations in H2 concentrations on methanogenesis from the non-competitive substrates methanol and methylamine (used by methanogens but not by sulfate reducers) was investigated in methanogenic marine sediments. Imposed variations in sulfate concentration and temperature were used to drive systematic variations in pore water H2 concentrations. Specifically, increasing sulfate concentrations and decreasing temperatures both resulted in decreasing H2 concentrations. The ratio of CO2 and CH4 produced from 14C-labelled methylamine and methanol showed a direct correlation with the H2 concentration, independent of the treatment, with lower H2 concentrations resulting in a shift towards CO2. We conclude that this correlation is driven by production of H2 by methylotrophic methanogens, followed by loss to the environment with a magnitude dependent on the extracellular H2 concentrations maintained by hydrogenotrophic methanogens (in the case of the temperature experiment) or sulfate reducers (in the case of the sulfate experiment). Under sulfate-free conditions, the loss of reducing power as H2 flux out of the cell represents a loss of energy for the methylotrophic methanogens while, in the presence of sulfate, it results in a favourable free energy yield. Thus, hydrogen leakage might conceivably be beneficial for methanogens in marine sediments dominated by sulfate reduction. In low-sulfate systems such as methanogenic marine or freshwater sediments it is clearly detrimental--an adverse consequence of possessing a hydrogenase that is subject to externally imposed control by pore water H2 concentrations. H2 leakage in methanogens may explain the apparent exclusion of acetoclastic methanogenesis in sediments dominated by sulfate reduction.

The contribution of volatile fatty acids (VFA) as e(-)-donors for anaerobic terminal oxidation of organic carbon through iron and sulfate reduction was studied in Arctic fjord sediment. Dissolved inorganic carbon, Fe(2+), VFA concentrations, and sulfate reduction were monitored in slurries from the oxidized (0-2 cm) and the reduced (5-9 cm) zone. In the 0-2 cm layer, 2/3 of the mineralization could be attributed to sulfate reduction and 1/3 to iron reduction. In the 5-9 cm layer, sulfate reduction was the sole mineralization process. Acetate and lactate turnover rates were measured by radiotracer. Inhibition of sulfate reduction with selenate resulted in the accumulation of acetate, propionate, and isobutyrate. The acetate turnover rates determined by radiotracer and accumulation after inhibition were similar. VFA turnover accounted for 21% and 52% of the mineralization through sulfate reduction in the 0-2 and 5-9 cm layer, respectively. Acetate and lactate turnover in the inhibited 0-2 cm slurry was attributed to iron reduction and accounted for 10% and 2% of the iron reduction. Therefore, 88% and 79% of the iron and sulfate reduction in the 0-2 cm layer, respectively, must be fueled by alternative e(-)-donors. The accumulation of VFA in the selenate-inhibited 0-2 cm slurry did not enhance iron reduction, indicating that iron reducers were not limited by VFA availability.

The benthic microbial mat community of the only permanent hypersaline natural inland lake of Western Europe, 'La Salada de Chiprana', northeastern Spain, was structurally and functionally analyzed. The ionic composition of the lake water is characterized by high concentrations of magnesium and sulfate, which were respectively 0.35 and 0.5 M at the time of sampling while the total salinity was 78 g l(-1). Community composition was analyzed by microscopy, high-performance liquid chromatography (HPLC) pigment analyses and by studying culturable bacteria from different functional groups. Therefore, denaturing gradient gel electrophoresis (DGGE) was applied on most probable number (MPN) dilution cultures. Microscopy revealed that a thin layer of Chloroflexus-like bacteria overlaid various cyanobacteria-dominated layers each characterized by different morphotypes. DGGE analysis of MPN dilution cultures from distinct mat layers showed that various phylotypes of anoxygenic phototrophic, aerobic heterotrophic, colorless sulfur-, and sulfate-reducing bacteria were present. The mats were furthermore functionally studied and attention was focussed on the relationship between oxygenic primary production and the flow of carbon through the microbial community. Microsensor techniques, porewater and sediment photopigment analysis were applied in order to estimate oxygenic photosynthetic rates, daily dynamics of (in)organic carbon porewater concentration and migration behavior of phototrophs. Chiprana microbial mats produced dissolved organic carbon (DOC) both during the day and night. It was estimated that 14% of the mats gross photosynthetic production and 49% of the mats net photosynthetic production diffused out of the mat in the form of low molecular mass fatty acids, although these compounds made up only 2% of the total DOC pool. The high flux of dissolved fatty acids from the microbial mat to the water column may explain why in this system Chloroflexus-like bacteria proliferate on top of the cyanobacterial layers since these photoheterotrophic bacteria grow preferably on organic phototrophic exudates. Furthermore it may also explain why high numbers of viable sulfate-reducing bacteria were found in the fully oxygenated sediment surface layers. These organisms apparently do not have to compete with aerobic heterotrophic community members due to the ample availability of organic substrates. Moreover, the high production of DOC strongly indicates that the mat community was nutrient limited in its growth. Photopigment analysis revealed furthermore that chlorophyll a (Chla) and three of its allomeres had a complementary depth distribution what suggests that the Chla allomeres are functional adaptations to differences in light quality and/or quantity and may be species specific.

Background: To evaluate the prevalence of thrombosis risk factors in a group of patients undergoing venous duplex scanning (VDS) and to design a risk factor stratification model with the ability to improve the diagnostic yield of VDS., Methods: Risk factor assessment and VDS were performed on 1,000 patients with clinically suspected lower extremity deep vein thrombosis (DVT) and patients were divided into two groups based upon the outcome of their scan: those with and those without confirmed DVT. Univariate and multivariate logistic regression analyses were performed in order to determine the significance of each risk factor in relation to having a confirmed DVT., Results: There were 181 patients (18.1%) with confirmed DVT. A prior history of DVT/pulmonary embolism, malignancy, prior immobilization, and age over 70 were the most important risk factors associated with having a DVT confirmed on VDS. A novel risk factor stratification model was created utilizing the odds ratios of those factors found to be significant and the prevalence of DVT was found to be 92.4% in the high risk category, 11.5% in the moderate risk category, and 3.2% in the low risk category using this model., Conclusions: Venous duplex scanning is established as the screening test of choice when one suspects the diagnosis of DVT despite the significant cost of performing and interpreting the test. We suggest that a better clinical model utilizing risk factor assessment may be the key to increasing the yield rate and cost-effectiveness of VDS by excluding low-risk patients from undergoing unnecessary testing.

Purpose: The purpose of this study was to evaluate the rate of resolution of deep vein thrombosis (DVT) in the leg, by means of duplex imaging, in patients with symptoms during a 6-month period after initial diagnosis., Methods: Seventy-three limbs in 69 patients with acute DVT diagnosed by duplex imaging received conventional heparin and warfarin treatment and underwent subsequent duplex studies 1, 4, 12, and 24 weeks after the initial diagnosis. The objectives of the study were to document (1) the rate or complete resolution of DVT, (2) the proportion of unstable, floating thrombi, and (3) the development of chronic damage as a result of vessel wall scarring., Results: The rate of normalization of DVT 6 months after diagnosis was 78% in the common femoral vein, 70% in the superficial femoral vein, 75% in the popliteal vein, and 70% in the calf veins examined at the scheduled intervals. Twenty-six percent of thrombi were considered unstable on the baseline examination. The average number of days necessary for these thrombi to become stable was 10.7 days. Damage to the vessel wall or valves was documented in 44% of the patients., Conclusions: Rates of resolution of DVT were similar for the different veins of the leg studied. There was a high proportion of unstable thrombi, which present a high potential risk of embolization. Serial duplex scanning after DVT renders important information with regard to thrombus resolution, propagation, and attachment to the vein wall.