Boosting ethanol production rates from carbon dioxide in MES cells under optimal solventogenic conditions

Microbial Electrosynthesis (MES) has been widely applied for acetic acid (HA) production from CO₂ and electricity. Ethanol (EtOH) has a higher market value than HA, and wide application in industry and as a biofuel. However, it has only been obtained sporadically and at low concentrations, probably due to sub-optimal operating conditions. This study aimed at enhancing EtOH productivity in MES cells by jointly optimising key operation parameters, including pH, H₂ and CO₂ partial pressure (pH₂ and pCO₂), and HA concentration, to promote solventogenesis. Two H-type cells were operated in fed-batch mode at -0.8 V vs. SHE with CO₂ as the sole carbon source. A mixed culture, enriched with Clostridium ljungdahlii was used as the biocatalyst. The combination of low pH (<4.5) and pCO₂ (<0.3 atm), along with high HA concentration (about 6 g L^-1) and pH₂ (>3 atm), were mandatory conditions for maintaining an efficient solventogenic culture, dominated by Clostridium sp., capable of high-rate EtOH production. The maximum EtOH production rate was 10.95 g m^-2 d^-1, and a concentration of 5.28 g L^-1 was achieved. Up to 30 % of the electrons and 15.2 % of the carbon provided were directed towards EtOH production, and 28.1 kWh were required for the synthesis of 1 kg of EtOH from CO₂. These results highlight that strict conditions are required for a continuous, reliable, EtOH production in MES cells. Future investigation should focus on improving cell configuration to achieve EtOH production at higher current densities while minimizing the electric energy input.

Let's chat: Communication between electroactive microorganisms

Electroactive microorganisms can exchange electrons with other cells or conductive interfaces in their extracellular environment. This property opens the way to a broad range of practical biotechnological applications, from manufacturing sustainable chemicals via electrosynthesis, to bioenergy, bioelectronics or improved, low-energy demanding wastewater treatments. Besides, electroactive microorganisms play key roles in environmental bioremediation, significantly impacting process efficiencies. This review highlights our present knowledge on microbial interactions promoting the communication between electroactive microorganisms in a biofilm on an electrode in bioelectrochemical systems (BES). Furthermore, the immediate knowledge gaps that must be closed to develop novel technologies will also be acknowledged.

The core microbiome is responsible for volatile silicon and organic compounds degradation during anoxic lab scale biotrickling filter performance

Volatile silicon compounds present in the biogas of anaerobic digesters can cause severe problems in the energy recovery systems, inducing costly damages. Herein, the microbial community of a lab-scale biotrickling filter (BTF) was studied while testing its biodegradation capacity on octamethylcyclotetrasiloxane (D4) and decamethylcyclopentasiloxane (D5), in the presence of toluene, limonene and hexane. The reactor performance was tested at different empty bed residence times (EBRT) and packing materials. Community structure was analysed by bar-coded amplicon sequencing of the 16S rRNA gene. Microbial diversity and richness were higher in the inoculum and progressively decreased during BTF operation (Simpson's diversity index changing from 0.98-0.90 and Richness from 900 to 200 OTUs). Minimum diversity was found when reactor was operated at relatively low EBRT (7.3 min) using a multicomponent feed. The core community was composed of 36 OTUs (accounting for 55% of total sequences). Packing material played a key role in the community structure. Betaproteobacteriales were dominant in the presence of lava rock and were partially substituted by Corynebacteriales and Rhizobiales when activated carbon was added to the BTF. Despite these changes, a stable and resilient core microbiome was selected defining a set of potentially degrading bacteria for siloxane bioremoval as a complementary alternative to non-regenerative adsorption onto activated carbon.

Electro-bioremediation of nitrate and arsenite polluted groundwater

The coexistence of different pollutants in groundwater is a common threat. Sustainable and resilient technologies are required for their treatment. The present study aims to evaluate microbial electrochemical technologies (METs) for treating groundwater contaminated with nitrate (NO₃^-) while containing arsenic (in form of arsenite (As(III)) as a co-contaminant. The treatment was based on the combination of nitrate reduction to dinitrogen gas and arsenite oxidation to arsenate (exhibiting less toxicity, solubility, and mobility), which can be removed more easily in further post-treatment. We operated a bioelectrochemical reactor at continuous-flow mode with synthetic contaminated groundwater (33 mg N-NO₃^- L^-1 and 5 mg As(III) L^-1) identifying the key operational conditions. Different hydraulic retention times (HRT) were evaluated, reaching a maximum nitrate reduction rate of 519 g N-NO₃^- m³_{Net Cathodic Compartment} d^-1 at HRT of 2.3 h with a cathodic coulombic efficiency of around 100 %. Simultaneously, arsenic oxidation was complete at all HRT tested down to 1.6 h reaching an oxidation rate of up to 90 g As(III) m^-3_{Net Reactor Volume} d ^-1. Electrochemical and microbiological characterization of single granules suggested that arsenite at 5 mg L^-1 did not have an inhibitory effect on a denitrifying biocathode mainly represented by Sideroxydans sp. Although the coexistence of abiotic and biotic arsenic oxidation pathways was shown to be likely, microbial arsenite oxidation linked to denitrification by Achromobacter sp. was the most probable pathway. This research paves the ground towards a real application for treating groundwater with widespread pollutants.

Hydrological variations shape diversity and functional responses of streambed microbes

Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.

Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW

In constructed wetlands (CW), denitrification usually accounts for > 60% of nitrogen removal and is supposedly affected by wetland management practices, such as dredging (and plant removal). These practices cause an impact in sediment properties and microbial communities living therein. We have quantified the effects of a sediment dredging event on dissimilatory nitrite reduction by analysing the structure and activities of the microbial community before and after the event. Potential rates for nitrate reduction to ammonia and denitrification were in accordance with changes in the physicochemical conditions. Denitrification was the predominant pathway for nitrite removal (> 60%) and eventually led to the complete removal of nitrate. On the contrary, dissimilatory nitrite reduction to ammonia (DNRA) increased from 5 to 18% after the dredging event. Both actual activities and abundances of 16S rRNA, nirK and nirS significantly decreased after sediment dredging. However, genetic potential for denitrification (qnirS + qnirK/q16S rRNA) remained unchanged. Analyses of the 16S rRNA gene sequences revealed the importance of vegetation in shaping microbial community structures, selecting specific phylotypes potentially contributing to the nitrogen cycle. Overall, we confirmed that sediment dredging and vegetation removal exerted a measurable effect on the microbial community, but not on potential nitrite + nitrate removal rates. According to redundancy analysis, nitrate concentration and pH were the main variables affecting sediment microbial communities in the Empuriabrava CWs. Our results highlight a high recovery of the functionality of an ecosystem service after a severe intervention and point to metabolic redundancy of denitrifiers. We are confident these results will be taken into account in future management strategies in CWs.

Potential use of Methylibium sp. as a biodegradation tool in organosilicon and volatile compounds removal for biogas upgrading

Organosilicon compounds are the most undesirable compounds for the energy recovery of biogas. These compounds are still resistant to biodegradation when biotechnologies are considered for biogas purification. Herein we isolated 52 bacterial species from anaerobic batch enrichment cultures (BEC) saturated with D4 and from an anaerobic lab-scale biotrickling filter (BTF) fed with a gas flow containing D4 as unique carbon source. Among those Methylibium sp. and Pseudomonas aeruginosa showed the highest capacity to remove D4 (53.04% ± 0.03 and 24.42% ± 0.02, respectively). Contrarily, co-culture evaluation treatment for the biodegradation of siloxanes together with volatile organic compounds removed a lower concentration of D4 compared to toluene and limonene, which were completely removed. Remarkably, the siloxane D5 proved to be more biodegradable than D4. Substrates removal values achieved by Methylibium sp. suggested that this bacterial isolate could be used in biological removal technologies of siloxanes.

Specific detection of "Clostridium autoethanogenum", Clostridium ljungdahlii and Clostridium carboxidivorans in complex bioreactor samples

The high genetic similarity between some carboxydotrophic bacteria does not allow for the use of common sequencing techniques targeting the 16S rRNA gene for species identification. 16S rRNA sequencing fails to discriminate among Clostridium ljungdahlii and 'Clostridium autoethanogenum', despite this two species exhibit significant differences in CO2 assimilation and alcohol production. In this work we designed PCR primers targeting for the DNA gyrase subunit A (gyrA) and a putative formate/nitrite transporter (fnt) to specifically detect the presence of 'C. autoethanogenum', C. ljungdahlii or Clostridium carboxidivorans. We could confirm the simultaneous presence of C. ljungdahlii and 'C. autoethanogenum' in different bioreactors, and a preference of the latter for high CO2 content.

Isotope and microbiome data provide complementary information to identify natural nitrate attenuation processes in groundwater

Natural attenuation processes alleviate the impact of fertilization practices on groundwater resources. Therefore, identifying the occurrence of denitrification has become a requirement for water quality management. Several approaches are useful for this purpose, such as isotopic and microbiological methods, each of them providing distinct but complementary information about denitrification reactions, attenuation rates and their occurrence in the aquifer. In this paper, we investigate the contribution of both approaches to describe denitrification in a consolidated rock aquifer (limestone and marls), with a porosity related to fracture networks located in the northeastern sector of the Osona basin (NE Spain). Isotopic methods indicated the origin of nitrate (fertilization using manure) and that denitrification occurred, reaching a reduction of near 25% of the nitrate mass in groundwater. The studied area could be divided in two zones with distinct agricultural pressures and, consequently, nitrate concentrations in groundwater. Denitrification occurred in both zones and at different levels, indicating that attenuation processes took place all along the whole hydrogeological unit, and that the observed levels could be attributed to a larger flow path or, in a minor extent, to mixing processes that mask the actual denitrification rates. Microbiological data showed a correlation between denitrifier genes and the isotopic composition. However, the groundwater microbiome and the distribution of denitrifying bacteria did not reveal a major influence on the denitrification level observed by isotopic methods. This focuses the interest of microbiological analysis to identify functional genes within the bacteria present in the aquifer. Results indicated that isotopic methods provide information of the overall denitrification ability of the hydrogeological unit, and that genomic data represent the processes actually acting nearby the well. A combination of both approaches is advised to support induced in situ attenuation actions in polluted sites.

Tracking bio-hydrogen-mediated production of commodity chemicals from carbon dioxide and renewable electricity

This study reveals that reduction of carbon dioxide (CO₂) to commodity chemicals can be functionally compartmentalized in bioelectrochemical systems. In the present example, a syntrophic consortium composed by H₂-producers (Rhodobacter sp.) in the biofilm is combined with carboxidotrophic Clostridium species, mainly found in the bulk liquid. The performance of these H₂-mediated electricity-driven systems could be tracked by the activity of a biological H₂ sensory protein identified at cathode potentials between -0.2V and -0.3V vs SHE. This seems to point out that such signal is not strain specific, but could be detected in any organism containing hydrogenases. Thus, the findings of this work open the door to the development of a biosensor application or soft sensors for monitoring such systems.

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Impact of formate on the growth and productivity of Clostridium ljungdahlii PETC and Clostridium carboxidivorans P7 grown on syngas

The current energy model based on fossil fuels is coming to an end due to the increase in global energy demand. Biofuels such as ethanol and butanol can be produced through the syngas fermentation by acetogenic bacteria. The present work hypothesizes that formate addition would positively impact kinetic parameters for growth and alcohol production in Clostridium ljungdahlii PETC and Clostridium carboxidivorans P7 by diminishing the need for reducing equivalents. Fermentation experiments were conducted using completely anaerobic batch cultures at different pH values and formate concentrations. PETC cultures were more tolerant to formate concentrations than P7, specially at pH 5.0 and 6.0. Complete growth inhibition of PETC occurred at sodium formate concentrations of 30.0 mM; however, no differences in growth rates were observed at pH 7.0 for the two strains. Incubation at formate concentrations lower than 2.0 mM resulted in increased growth rates for both strains. The most recognizable effects of formate addition on the fermentation products were the increase in the total carbon fixed into acids and alcohols at pH 5.0 and pH 6.0, as well as, a higher ethanol to total products ratio at pH 7.0. Taken all together, these results show the ability of acetogens to use formate diminishing the energy demand for growth, and enhancing strain productivity.

Incubation at 25 °C prevents acid crash and enhances alcohol production in Clostridium carboxidivorans P7

Incubation of carboxydotrophs at 37 °C provides optimal conditions for their growth. However, a fast accumulation of organic acids, specifically acetate, during the exponential growth phase may result in low alcohol production and substrate consumption due to a phenomenon known as "acid crash". The present work investigates growth and productivity of Clostridium carboxidivorans P7 at two incubation temperatures. At 37 °C the culture was not able to override the "acid crash", resulting in low ethanol titers (1.56 mM). On the other hand, lower metabolic rates at 25 °C enhanced ethanol and butanol production (32.1 and 14.5 mM, respectively). Moreover, at low temperatures, hexanol and caproic acid were also produced at significant concentrations, 8.21 and 9.02 mM respectively, among the highest values reported for P7. Our results demonstrate that production of biofuels with longer carbon chains molecules may be enhanced incubating syngas-fermenting acetogenic bacteria at sub-optimal temperatures.

Microbiome characterization of MFCs used for the treatment of swine manure

Conventional swine manure treatment is performed by anaerobic digestion, but nitrogen is not treated. Microbial Fuel Cells (MFCs) allow organic matter and nitrogen removal with concomitant electricity production. MFC microbiomes treating industrial wastewaters as swine manure have not been characterized. In this study, a multidisciplinary approach allowed microbiome relation with nutrient removal capacity and electricity production. Two different MFC configurations (C-1 and C-2) were used to treat swine manure. In C-1, the nitrification and denitrification processes took place in different compartments, while in C-2, simultaneous nitrification-denitrification occurred in the cathode. Clostridium disporicum and Geobacter sulfurreducens were identified in the anode compartments of both systems. C. disporicum was related to the degradation of complex organic matter compounds and G. sulfurreducens to electricity production. Different nitrifying bacteria populations were identified in both systems because of the different operational conditions. The highest microbial diversity was detected in cathode compartments of both configurations, including members of Bacteroidetes, Chloroflexiaceae and Proteobacteria. These communities allowed similar removal rates of organic matter (2.02-2.09 kg COD m(-3)d(-1)) and nitrogen (0.11-0.16 kg Nm(-3)d(-1)) in both systems. However, they differed in the generation of electric energy (20 and 2 mW m(-3) in C-1 and C-2, respectively).

Conversion of sewage sludge to commodity chemicals via syngas fermentation

Gasification of sewage sludge allows the recovery of energy, and produces a mix of CO, CO₂and H₂called synthesis gas (or syngas), which can be fermented by acetogenic bacteria to added-value products. This work presents the conversion of syngas to organic acids and alcohols using both pure and mixed cultures. Pure culture kinetic experiments with Clostridium carboxidivorans P7 resulted in the production of high concentrations of acetate (454 mgC/L) and ethanol (167 mgC/L). The pH was the main factor driving solventogenesis, with about 50% of the products in the form of alcohols at pH 5. Conversely, laboratory-scale experiments using a carboxydotrophic mixed culture of the genus Clostridium enriched from anaerobic digester sludge of a municipal wastewater treatment plant was capable of producing mainly butyrate, with maximum concentration of 1,184 mgC/L.

Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell

The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m⁻³ NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m⁻³ NCC in the case of nitrite. Contrarily, nitrous oxide (N₂O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N₂O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N₂O accumulation.

Changes of the phenol-degrading bacterial community during the decomposition of submersed Platanus acerifolia leaves

Microorganisms are responsible for the decomposition of plant litter due to their enhanced enzyme capabilities. Among extracellular enzymes, those involved in lignin decomposition are especially relevant in leaf degradation. However, the knowledge of the bacterial contribution to the decomposition of phenol-derived compounds in submerged leaf litter is limited. We have used the large unit of the multicomponent bacterial phenol hydroxylase (LmpH) as a genetic proxy to describe changes in the phenol-degrading bacterial community during the decomposition of Platanus acerifolia leaves in a forested stream. Significant differences were found in the phenol-degrading community when three decomposition stages, initial (day 7), midterm (day 58), and late (day 112), were compared. Estimated Shannon's diversity values decreased significantly from 1.93 (initial) to 0.98 (late). According to the deduced amino acid sequences and the corresponding theoretical kinetic parameters of phenol hydroxylases, the initial community showed a low degree of specialization, presumably resulting from random colonization of leaves. At the late decomposition stage, the bacterial community became more specialized, and LmpH genes similar to high-affinity phenol hydroxylases of Comamonas sp. and Burkholderia cepacia increased. The observed changes in the bacterial community suggested an active role of bacteria during litter decomposition in aquatic environments.

Abundance and composition of epiphytic bacterial and archaeal ammonia oxidizers of marine red and brown macroalgae

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for O. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions.

Genetic potential for N2O emissions from the sediment of a free water surface constructed wetland

Removal of nitrogen is a key aspect in the functioning of constructed wetlands. However, incomplete denitrification may result in the net emission of the greenhouse gas nitrous oxide (N(2)O) resulting in an undesired effect of a system supposed to provide an ecosystem service. In this work we evaluated the genetic potential for N(2)O emissions in relation to the presence or absence of Phragmites and Typha in a free water surface constructed wetland (FWS-CW), since vegetation, through the increase in organic matter due to litter degradation, may significantly affect the denitrification capacity in planted areas. Quantitative real-time PCR analyses of genes in the denitrification pathway indicating capacity to produce or reduce N(2)O were conducted at periods of different water discharge. Genetic potential for N(2)O emissions was estimated from the relative abundances of all denitrification genes and nitrous oxide reductase encoding genes (nosZ). nosZ abundance was invariably lower than the other denitrifying genes (down to 100 fold), and differences increased significantly during periods of high nitrate loads in the CW suggesting a higher genetic potential for N(2)O emissions. This situation coincided with lower nitrogen removal efficiencies in the treatment cell. The presence and the type of vegetation, mainly due to changes in the sediment carbon and nitrogen content, correlated negatively to the ratio between nitrate and nitrite reducers and positively to the ratio between nitrite and nitrous oxide reducers. These results suggest that the potential for nitrous oxide emissions is higher in vegetated sediments.

The microbiota of an unpolluted calcareous soil faces up chlorophenols: Evidences of resistant strains with potential for bioremediation

To highlight the effects of a variety of chlorophenols (CP) in relation to the response of an indigenous bacterial community, an agricultural Mediterranean calcareous soil has been studied in microcosms incubated under controlled laboratory conditions. Soil samples were artificially polluted with 2-monochlorophenol (MCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP), at concentrations ranging from 0.1 up to 5000 mg kg(-1). Both activity and composition of the microbial community were assessed during several weeks, respectively, by respirometric methods and PCR-DGGE analysis of extracted DNA and RNA. Significant decreases in soil respirometric values and changes in the bacterial community composition were observed at concentrations above 1000 mg kg(-1) MCP and TCP, and above 100 mg kg(-1) PCP. However, the persistence of several active bacterial populations in soil microcosms contaminated with high concentration of CP, as indicated by DGGE fingerprints, suggested the capacity of these native bacteria to survive in the presence of the pollutants, even without a previous adaptation or contact with them. The isolation of potential CP degraders was attempted by culture plating from microcosms incubated with high CP concentrations. Twenty-three different isolates were screened for their resistance to TCP and PCP. The most resistant isolates were identified as Kocuria palustris, Lysobacter gummosus, Bacillus sp. and Pseudomonas putida, according to 16S rRNA gene homology. In addition, these four isolates also showed the capacity to reduce the concentration of TCP and PCP from 15% to 30% after 5d of incubation in laboratory assays (initial pollutant concentration of 50 mg L(-1)). Isolate ITP29, which could be a novel species of Bacillus, has been revealed as the first known member in this bacterial group with potential for CP bioremediation applications, usually wide-spread in the soil natural communities, which has not been reported to date as a CP degrader.

Autotrophic nitrite removal in the cathode of microbial fuel cells

Nitrification to nitrite (nitritation process) followed by reduction to dinitrogen gas decreases the energy demand and the carbon requirements of the overall process of nitrogen removal. This work studies autotrophic nitrite removal in the cathode of microbial fuel cells (MFCs). Special attention was paid to determining whether nitrite is used as the electron acceptor by exoelectrogenic bacteria (biologic reaction) or by graphite electrodes (abiotic reaction). The results demonstrated that, after a nitrate pulse at the cathode, nitrite was initially accumulated; subsequently, nitrite was removed. Nitrite and nitrate can be used interchangeably as an electron acceptor by exoelectrogenic bacteria for nitrogen reduction from wastewater while producing bioelectricity. However, if oxygen is present in the cathode chamber, nitrite is oxidised via biological or electrochemical processes. The identification of a dominant bacterial member similar to Oligotropha carboxidovorans confirms that autotrophic denitrification is the main metabolism mechanism in the cathode of an MFC.

Off-odor compounds produced in cork by isolated bacteria and fungi: a gas chromatography-mass spectrometry and gas chromatography-olfactometry study

The risk of development of specific olfactory profiles in cork was evaluated after inoculation of cork granules and agglomerated and natural cork stoppers with isolated bacteria and fungi. The highest incidence of off-odor development was found in assays when fungi were inoculated. Cork granules with musty-earthy, musty-earthy-TCA, and vegetative deviations were inspected by gas chromatography-olfactometry (GC-O) and gas chromatography-mass spectrometry (GC-MS). Sixteen odor zones were clearly recognized in the GC-O analyses. Among these, octanal, 2-methoxy-3,5-dimethylpyrazine (MDMP), Z-2-nonenal, 2-methylisoborneol, 2,4,6-trichloroanisole (TCA), geosmin, and guaiacol were the most significant odorants and helped in the discrimination of sensory deviations. Only TCA and guaiacol were detected above their respective detection limits by HS-SPME-GC-MS. The fungi Cryptococcus sp. isolate F020, Rhodotorula sp. isolate F025, Penicillium glabrum isolate F001, and Pennicillium variabile F003A and the bacterium Pseudomonas jessenii isolate A1 were found to produce TCA to a greater extent. Additionally, 13 of 38 isolated microorganisms (2 bacteria and 11 fungi) proved able to produce unpleasant musty-earthy or vegetative odors that were not related to a significant TCA accumulation.

Lactic acid bacteria from fresh fruit and vegetables as biocontrol agents of phytopathogenic bacteria and fungi

This study evaluated the efficacy of lactic acid bacteria (LAB) isolated from fresh fruits and vegetables as biocontrol agents against the phytopathogenic and spoilage bacteria and fungi, Xanthomonas campestris, Erwinia carotovora, Penicillium expansum, Monilinia laxa, and Botrytis cinerea. The antagonistic activity of 496 LAB strains was tested in vitro and all tested microorganisms except P. expansum were inhibited by at least one isolate. The 496 isolates were also analyzed for the inhibition of P. expansum infection in wounds of Golden Delicious apples. Four strains (TC97, AC318, TM319, and FF441) reduced the fungal rot diameter of the apples by 20%; only Weissella cibaria strain TM128 decreased infection levels by 50%. Cell-free supernatants of selected antagonistic bacteria were studied to determine the nature of the antimicrobial compounds produced. Organic acids were the preferred mediators of inhibition but hydrogen peroxide was also detected when strains BC48, TM128, PM141 and FF441 were tested against E. carotovora. While previous reports of antifungal activity by LAB are scarce, our results support the potential of LAB as biocontrol agents against postharvest rot.

New phylotypes of mesophilic filamentous anoxygenic phototrophic bacteria enriched from sulfide-containing environments

Agar-based solid media with increasing concentrations of organic matter were used to isolate new members of the Chloroflexaceae (phylum Chloroflexi) from mesophilic environments containing sulfide. Inorganic media yielded less than 10% positive enrichments, which were not able to be maintained after repetitive inoculations in fresh medium. The use of casaminoacids and complex organic acid mixtures increased the number of positive enrichments (up to 45%) from both water and sediment samples. Two different green filamentous bacteria, SisoF2 and SalF, could be stably maintained as co-cultures for long periods and their phylogeny inferred from the analysis of complete sequences of the 16S rRNA gene. Ribotype SalF showed a high homology (95-98%) to previously isolated Oscillochloris trichoides strains. The 16S rRNA gene sequence retrieved from culture SisoF2 was largely divergent (< 92% similarity) from any sequence derived from either cultured representatives or environmental samples, suggesting that ribotype SisoF2 may constitute a new genus within the phylum. The presence of the new morphotypes in the environment from where they were enriched was analysed by high-resolution phylogenetic fingerprinting.

Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark

We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal carbon biogeochemistry.

Bioprotection of Golden Delicious apples and Iceberg lettuce against foodborne bacterial pathogens by lactic acid bacteria

Lactic acid bacteria were isolated from fresh vegetables and fruit and its ability to inhibit the growth of foodborne human pathogens (Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella typhimurium, and Staphylococcus aureus) was tested using the agar spot assay. Eighteen isolates showed a strong antagonistic capacity and were further characterised and identified using 16S rDNA sequencing and API 50CH. Most of them pertained to Leuconostoc spp. and Lactobacillus plantarum, and a few corresponded to Weissella spp. and Lactococcus lactis. Growth and efficacy of control of foodborne pathogen test bacteria by selected strains were tested in wounded Golden Delicious apples and Iceberg lettuce leaf cuts. The strains grew on the substrates and did not cause negative effects on the general aspect of tissues of apple or lettuce. Treatment of apple wounds and lettuce cuts with the antagonistic strains reduced the cell count of S. typhimurium and E .coli by 1 to 2 log cfu/wound or g, whereas the growth of L. monocytogenes was completely inhibited. Results support the potential use of lactic acid bacteria as bioprotective agents against foodborne human pathogens in ready-to-eat fresh fruit and vegetable products.

Diversity of the nitrite reductase gene nirS in the sediment of a free-water surface constructed wetland

The diversity of the nitrite reductase gene nirS was studied in the bulk sediment of a free-water surface constructed wetland (FWS-CW) located next to the Empuriabrava wastewater treatment plant (WWTP), in Castelló d'Empúries (Girona, NE Spain). The study period extended from the inception of the treatment wetland, in June 1998, until March 1999 and comprised periods of relatively high nitrate and ammonium concentrations at the influent and low nitrate-removal efficiencies. To evaluate nirS diversity, partial gene sequences were obtained by cloning of the respective PCR products. Rarefaction curves based on DOTUR analyses of the deduced amino-acid sequences predicted a greater diversity of nirS genes in samples containing higher ammonium concentrations. Estimated Shannon-Weaver indices of the four cloned samples showed a positive relationship with the N-NH4 +/N-NO3 - ratios measured at the FWS-CW inlet. Identities between the deduced amino-acid sequences and those previously deposited in public databases ranged from 72 to 97%. Phylogenetic analysis based on these deduced sequences grouped 165 nirS clones in seven main clusters according to high similarity indices. Up to 60% of the clones clustered together in a highly homogeneous group with little homologies to any sequence retrieved from cultured representatives. Moreover, prevailing environmental conditions appeared to select for particular denitrifying populations, e.g., with respect to ammonium load and nitrogen removal efficiencies. This observation is of particular interest for the management of treatment wetlands, in which only slight variations in the theoretical denitrification potential of the system can occur.

Fast energy transfer between BChl d and BChl c in chlorosomes of the green sulfur bacterium Chlorobium limicola

We have studied energy transfer in chlorosomes of Chlorobium limicola UdG6040 containing a mixture of about 50% bacteriochlorophyll (BChl) c and BChl d each. BChl d-depleted chlorosomes were obtained by acid treatment. The energy transfer between the different pigment pools was studied using both steady-state and time-resolved fluorescence spectroscopy at room temperature and low temperature. The steady-state emission of the intact chlorosome originated mainly from BChl c, as judged by comparison of fluorescence emission spectra of intact and BChl d-depleted chlorosomes. This indicated that efficient energy transfer from BChl d to BChl c takes place. At room temperature BChl c/d to BChl a excitation energy transfer (EET) was characterized by two components of 27 and 74 ps. At low temperature we could also observe EET from BChl d to BChl c with a time constant of approximately 4 ps. Kinetic modeling of the low temperature data indicated heterogeneous fluorescence kinetics and suggested the presence of an additional BChl c pool, E790, which is more or less decoupled from the baseplate BChl a. This E790 pool is either a low-lying exciton state of BChl c which acts as a trap at low temperature or alternatively represents the red edge of a broad inhomogeneous absorption band of BChl c. We present a refined model for the organization of the spatially separated pigment pools in chlorosomes of Cb. limicola UdG6040 in which BChl d is situated distal and BChl c proximal with respect to the baseplate.

Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis

The microbial assemblages of Lake Cisó and Lake Vilar (Banyoles, northeast Spain) were analyzed in space and time by microscopy and by performing PCR-denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 16S rRNA gene fragments. Samples obtained from different water depths and at two different times of the year (in the winter during holomixis and in the early spring during a phytoplankton bloom) were analyzed. Although the lakes have the same climatic conditions and the same water source, the limnological parameters were different, as were most of the morphologically distinguishable photosynthetic bacteria enumerated by microscopy. The phylogenetic affiliations of the predominant DGGE bands were inferred by performing a comparative 16S rRNA sequence analysis. Sequences obtained from Lake Cisó samples were related to gram-positive bacteria and to members of the division Proteobacteria. Sequences obtained from Lake Vilar samples were related to members of the Cytophaga-Flavobacterium-Bacteroides phylum and to cyanobacteria. Thus, we found that like the previously reported differences between morphologically distinct inhabitants of the two lakes, there were also differences among the community members whose morphologies did not differ conspicuously. The changes in the species composition from winter to spring were also marked. The two lakes both contained sequences belonging to phototrophic green sulfur bacteria, which is consistent with microscopic observations, but these sequences were different from the sequences of cultured strains previously isolated from the lakes. Euryarchaeal sequences (i.e., methanogen- and thermoplasma-related sequences) also were present in both lakes. These euryarchaeal group sequences dominated the archaeal sequences in Lake Cisó but not in Lake Vilar. In Lake Vilar, a new planktonic population related to the crenarchaeota produced the dominant archaeal band. The phylogenetic analysis indicated that new bacterial and archaeal lineages were present and that the microbial diversity of these assemblages was greater than previously known. We evaluated the correspondence between the abundances of several morphotypes and DGGE bands by comparing microscopy and sequencing results. Our data provide evidence that the sequences obtained from the DGGE fingerprints correspond to the microorganisms that are actually present at higher concentrations in the natural system.