Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments

Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments

Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.

Chlordecone-contaminated epilithic biofilms show increased adsorption capacities

The rivers of Guadeloupe and Martinique (French West Indies) show high levels of chlordecone (CLD) contamination. This persistent molecule has a dramatic impact on both aquatic ecosystems and human health. In these rivers, epilithic biofilms are the main endogenous primary producers and represent a central food source for fish and crustaceans. Recently, their viscoelastic properties have been shown to be effective in bio-assessing pollution in tropical environments. As these properties are closely related to the biochemical composition of the biofilms, biochemical (fatty acids, pigments, extracellular polymeric substances (EPS) monosaccharides) and molecular markers (T-RFLP fingerprints of bacteria, archaea and eukaryotes) were investigated. Strong links between CLD pollution and both biofilm biochemistry and microbial community composition were found. In particular, high levels of CLD were linked with modified exo-polysaccharides corresponding to carbohydrates with enhanced adsorption and adhesion properties. The observed change probably resulted from a preferential interaction between CLD and sugars and/or a differential microbial secretion of EPS in response to the pollutant. These changes were expected to impact viscoelastic properties of epilithic biofilms highlighting the effect of CLD pollution on biofilm EPS matrix. They also suggested that microorganisms implement a CLD scavenging strategy, providing new insights on the role of EPS in the adaptation of microorganisms to CLD-polluted environments.

A critical analysis of research methods and experimental models to study irrigants and irrigation systems

Irrigation plays an essential role in root canal treatment. The purpose of this narrative review was to critically appraise the experimental methods and models used to study irrigants and irrigation systems and to provide directions for future research. Studies on the antimicrobial effect of irrigants should use mature multispecies biofilms grown on dentine or inside root canals and should combine at least two complementary evaluation methods. Dissolution of pulp tissue remnants should be examined in the presence of dentine and, preferably, inside human root canals. Micro-omputed tomography is currently the method of choice for the assessment of accumulated dentine debris and their removal. A combination of experiments in transparent root canals and numerical modeling is needed to address irrigant penetration. Finally, models to evaluate irrigant extrusion through the apical foramen should simulate the periapical tissues and provide quantitative data on the amount of extruded irrigant. Mimicking the in vivo conditions as close as possible and standardization of the specimens and experimental protocols are universal requirements irrespective of the surrogate endpoint studied. Obsolete and unrealistic models must be abandoned in favour of more appropriate and valid ones that have more direct application and translation to clinical Endodontics.

Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane

A method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was controlled by adjusting reaction temperature and urea concentration in the mixture. Then, the mixture was filtered through the MWCOM. The rRNA and hybridized probes collected on the MWCOM were recovered and quantified using spectrophotometer and fluorospectrometer, respectively. The method showed high accuracy in detecting specific microbial rRNA in a defined nucleic acid mixture. Furthermore, the method was capable of simultaneous detection and quantification of multiple target rRNAs in a sample with sensitivity up to a single-base mismatch. The SCOPE method was tested and benchmarked against the reverse transcription-quantitative PCR (RT-qPCR) for the quantification of Bacteria, Archaea and some key methanogens in anaerobic sludge samples. It was observed that the SCOPE method produced comparatively more reliable and coherent results. In this way, the SCOPE method allows a simple and rapid detection and quantification of target microbial rRNAs for environmental microbial population analysis without any need for enzymatic reactions. Importance Microorganisms play integral roles in the earth's ecosystem. Microbial population and their activities significantly affect the global nutrient cycles. Quantification of key microorganisms provides important information that is required to understand their roles in the environment. Sequence-based analysis of microbial population is a powerful tool, but it only provides information on relative abundance of microorganisms. Hence, the development of a simpler and quick method for the quantification of microorganisms is necessary. To address the shortcomings of a variety of molecular methods reported so far, we developed a simple, rapid, accurate and multiplexed microbial rRNA quantification method to evaluate the abundance of specific microbial population in complex ecosystems. The developed method demonstrated high specificity, reproducibility, and applicability to such samples. The method is useful for quantitative detection of particular microbial members in the environment.

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.

Bacterial and archaeal lipids trace chemo(auto)trophy along the redoxcline in Vancouver Island fjords

Marine oxygen minimum zones play a crucial role in the global oceanic carbon, nitrogen, and sulfur cycles as they harbor microbial communities that are adapted to the water column chemistry and redox zonation, and in turn control the water column chemistry and greenhouse gas release. These micro-organisms have metabolisms that rely on terminal electron acceptors other than O₂ and often benefit from syntrophic relationships (metabolic coupling). Here, we study chemo(auto)trophy along the redoxcline in two stratified fjords on Vancouver Island (Canada) using bacterial bacteriohopanepolyols and archaeal ether lipids. We analyze the distribution of these lipid classes in suspended particulate matter (SPM) to trace ammonia oxidation, anaerobic ammonium oxidation (anammox), sulfate reduction/sulfur oxidation, methanogenesis, and methane oxidation, and investigate ecological niches to evaluate potential links between their respective bacterial and archaeal sources. Our results show an unparalleled BHP and ether lipid structural diversity that allows tracing the major redox-driven metabolic processes at the time of sampling: Both fjords are dominated by archaeal ammonia oxidation and anammox; sulfate-reducing bacteria may be present in Deer Bay, but absent from Effingham Inlet; methanogenic Euryarchaeota and archaeal and bacterial methanotrophs are detectable at low abundance. Correlation analysis reveals distinct biomarker clusters that provide constraints on the biogeochemical niches of some orphan BHP and ether lipids such as in situ-produced adenosyl-BHPs or unsaturated archaeols.

The gut and feed residue microbiota changing during the rearing of Hermetia illucens larvae

Larvae of Hermetia illucens, commonly known as black soldier fly, efficiently convert organic waste into nutrient-rich supplements for different applications. Here we performed a preliminary experiment to investigate the dynamics of the H. illucens gut microbiota and changes in the composition of the bacterial community in the residue of the larval feed during rearing. We furthermore quantified the presence of antibiotic resistance and disinfectant genes in the gut and feed microbiota during the rearing process to elucidate if rearing leads to a reduction, increase, and/or transfer of resistance genes from the feed to larvae and vice versa. We found that the gut and feed residue bacterial communities were distinct throughout the rearing process. The gut microbiome remained more stable compared to the feed residue microbiome varying in both bacterial abundance and community structure during rearing. Antibiotic-resistance genes were present in both, gut and feed residues, with a significant increase in pupae and residue samples taken at the end of the rearing process. Disinfectant-resistance genes were present in the feed residue and even increased during the rearing process but were not transferred to the gut microbiome. We conclude that H. illucens larvae have a stable gut microbiome that does not change significantly over the course of larval development, whereas bacterial communities in the feed residue are strongly affected by rearing. If the presence of antibiotics and disinfectants during rearing, can promote the spread of antibiotic/disinfectant-resistance genes among feed and larvae needs to be evaluated in further experiments.

Chronic responses of aerobic granules to the presence of graphene oxide in sequencing batch reactors

The chronic responses of aerobic granular sludge (AGS) to the presence of graphene oxide nanoparticles (GO NPs) (5, 15, 25, 35, 45, 55, 65, 75, 85, and 95 mg/L of GO NPs for 7 days) during biological wastewater treatment processes were investigated. Bioreactor performance, extracellular polymeric substance (EPS) secretion, and microbial community characteristics were assessed. The results showed that the effects of GO NPs on bioreactor performances were dependent on the dose applied and the duration for which it was applied. At concentrations of 55, 75, and 95 mg/L, GO NPs considerably inhibited the efficiency of organic matter and ammonia removal; however, nitrite and nitrate removal rates were unchanged. Biological phosphorus removal decreased even when only low concentrations of GO NPs were used. The secretion of EPS, which could alleviate the toxicity of GO NPs, also changed. The increased amount of nanoparticles also resulted in significant changes to the bacterial community structure. Based on the amplicon sequencing of 16S rRNA genes, Paracoccus sp., Klebsiella sp., and Acidovorax species were identified as the most tolerant strains.

Prokaryotic Dynamics in the Meromictic Coastal Lake Faro (Sicily, Italy)

Lake Faro, in the North-Eastern corner of Sicily (Italy), shows the typical stratification of a meromictic tempered basin, with a clear identification of the mixolimnion and the monimolimnion, separated by an interfacial chemocline. In this study, an annual-scaled study on the space-time distribution of the microbial communities in water samples of Lake Faro was performed by both ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and CARD-FISH (Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization) approaches. A correlation between microbial parameters and both environmental variables (i.e., temperature, pH, dissolved oxygen, redox potential, salinity, chlorophyll-a) and mixing conditions was highlighted, with an evident seasonal variability. The most significative differences were detected by ARISA between the mixolimnion and the monimolimnion, and between Spring and Autumn, by considering layer and season as a factor, respectively.

Molecular biological tools in concrete biodeterioration - a mini review

Concrete structures develop biofilms when exposed to various environments. At a certain stage, the microbial films destroy the concrete structures leading to significant deterioration. Culture-dependent techniques give an incomplete picture of the microbial communities on the concrete surface. Culture-independent techniques or molecular biological tools pave a new way to analyse microbial communities involved in concrete biodeterioration. This study highlights the need to 'build' a database, for Microbiologically Influenced Concrete Corrosion (MICC) involving microbial groups that are being identified using culture-dependent and independent techniques. The role of molecular tools such as 16S rRNA sequencing, denaturing gradient gel electrophoresis (DGGE), Fluorescent in situ hybridization (FISH), Real-time Polymerase Chain Reaction (RT-PCR), microarray analysis, 2-Dimensional gel electrophoresis (2-DE) in analysing microbial communities on the concrete structures have been reviewed in this paper.

Microbial community response and migration of petroleum compounds during a sea-ice oil spill experiment in Svalbard

This paper concerns the migration of oil through sea-ice and the biodegradation of different hydrocarbons in sea-ice and seawater following in situ oil spills in megacosms exposed to winter and spring conditions in Svalbard (80°N). Hydrocarbon-degrading microbes were detected in ice cores and the analysis of metabolically active bacterial populations in the different layers of sea-ice indicate significant population shifts following oil exposure, whether dispersant addition or oil burning was carried out or not. The presence of dispersant in the system was associated with the most pronounced and fastest population shifts out of all exposures, as well as lower bacterial diversity as measured by the Shannon index. Microorganisms were metabolically most active in the bottom layer of the sea ice and our data confirmed the predominance of Oleispira and Colwellia aestuarii in sea-ice. Migration of polycyclic aromatics through the sea-ice layer was observed when dispersant was added to the oil, and the presence of oil degrading organisms below the ice-layer was consistent with biodegradation taking place. Given the thickness and concentration of the oil-layer frozen into the ice, the bioavailability of the hydrocarbons was nevertheless limited. Consequently, much of the bulk of the oil remained intact.

Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain)

The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.

Capturing Early Changes in the Marine Bacterial Community as a Result of Crude Oil Pollution in a Mesocosm Experiment

The results of marine bacterial community succession from a short-term study of seawater incubations at 4°C to North Sea crude oil are presented herein. Oil was used alone (O) or in combination with a dispersant (OD). Marine bacterial communities resulting from these incubations were characterized by a fingerprinting analysis and pyrosequencing of the 16S rRNA gene with the aim of 1) revealing differences in bacterial communities between the control, O treatment, and OD treatment and 2) identifying the operational taxonomic units (OTUs) of early responders in order to define the bacterial gene markers of oil pollution for in situ monitoring.

After an incubation for 1 d, the distribution of the individual ribotypes of bacterial communities in control and oil-treated (O and OD) tanks differed. Differences related to the structures of bacterial communities were observed at later stages of the incubation. Among the early responders identified (Pseudoalteromonas, Sulfitobacter, Vibrio, Pseudomonas, Glaciecola, Neptunomonas, Methylophaga, and Pseudofulvibacter), genera that utilize a disintegrated biomass or hydrocarbons as well as biosurfactant producers were detected. None of these genera included obligate hydrocarbonoclastic bacteria (OHCB). After an incubation for 1 d, the abundances of Glaciecola and Pseudofulvibacter were approximately 30-fold higher in the OD and O tanks than in the control tank. OTUs assigned to the Glaciecola genus were represented more in the OD tank, while those of Pseudofulvibacter were represented more in the O tank. We also found that 2 to 3% of the structural community shift originated from the bacterial community in the oil itself, with Polaribacter being a dominant bacterium.

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay

Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community.IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.

Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing

Next Generation Sequencing has been widely used to characterize the prevalence of fecal bacteria in many different species. In this study, we attempted to employ a low-cost and high-throughput sequencing model to discern information pertaining to the wolf microbiota. It is hoped that this model will allow researchers to elucidate potential protective factors in relation to endangered wolf species. We propose three high-throughput sequencing models to reveal information pertaining to the micro-ecology of the wolf. Our analyses advised that, among the three models, more than 100,000 sequences are more appropriate to retrieve the communities' richness and diversity of micro-ecology. In addition, the top five wolf microbiome OTUs (99%) were members of the following five phyla: Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria. While Alloprevotella, Clostridium_sensu_stricto_1, Anaerobiospirillum, Faecalibactreium and Streptococcus were shared by all samples, their relative abundances were differentially represented between domestic dogs and other wolves. Our findings suggest that altitude, human interference, age, and climate all contribute towards the micro-ecology of the wolf. Specifically, we observed that genera Succinivibrio and Turicibacter are significantly related to altitude and human interference (including hunting practices).

Scaling-up of a zero valent iron packed anaerobic reactor for textile dye wastewater treatment: a potential technology for on-site upgrading and rebuilding of traditional anaerobic wastewater treatment plant

Anaerobic digestion (AD) is a cost-effective technology for the treatment of textile dye wastewater with clear environmental benefits. However, the need to improve process feasibility of high treatment efficiency as well as to shorten hydraulic retention time has raised interest on several intensification techniques. Zero valent iron (ZVI) packed anaerobic digesters have the potential to become an on-site upgrading wastewater treatment technology through building a ZVI bed in a traditional AD plant. However, the experiences and knowledge of scale-up are limited. In this study, a pilot-scale ZVI packed upflow anaerobic sludge bed (ZVI-UASB) was built up and operated for actual dye wastewater treatment in a textile dye industrial park. Results showed that the treatment performance of this digester is higher than that of a traditional AD plant in terms of chemical oxygen demand (COD) removal and color removal. During 90 days of operation, the average COD removal and color removal in ZVI-UASB was maintained at around 19% and 40%, respectively, while it was only 10% and 20%, respectively, in the traditional AD plant.

Root isoflavonoids and hairy root transformation influence key bacterial taxa in the soybean rhizosphere

Rhizodeposits play a key role in shaping rhizosphere microbial communities. In soybean, isoflavonoids are a key rhizodeposit component that aid in plant defense and enable symbiotic associations with rhizobia. However, it is uncertain if and how they influence rhizosphere microbial communities. Isoflavonoid biosynthesis was silenced via RNA interference of isoflavone synthase in soybean hairy root composite plants. Rhizosphere soil fractions tightly associated with roots were isolated, and PCR amplicons from 16S rRNA gene variable regions V1-V3 and V3-V5 from these fractions were sequenced using 454. The resulting data was resolved using MOTHUR and vegan to identify bacterial taxa and evaluate changes in rhizosphere bacterial communities. The soybean rhizosphere was enriched in Proteobacteria and Bacteroidetes, and had relatively lower levels of Actinobacteria and Acidobacteria compared with bulk soil. Isoflavonoids had a small effect on bacterial community structure, and in particular on the abundance of Xanthomonads and Comamonads. The effect of hairy root transformation on rhizosphere bacterial communities was largely similar to untransformed plant roots with approximately 74% of the bacterial families displaying similar colonization underscoring the suitability of this technique to evaluate the influence of plant roots on rhizosphere bacterial communities. However, hairy root transformation had notable influence on Sphingomonads and Acidobacteria.

Microcystin Biosynthesis and mcyA Expression in Geographically Distinct Microcystis Strains under Different Nitrogen, Phosphorus, and Boron Regimes

Roles of nutrients and other environmental variables in development of cyanobacterial bloom and its toxicity are complex and not well understood. We have monitored the photoautotrophic growth, total microcystin concentration, and microcystins synthetase gene (mcyA) expression in lab-grown strains of Microcystis NIES 843 (reference strain), KW (Wangsong Reservoir, South Korea), and Durgakund (Varanasi, India) under different nutrient regimes (nitrogen, phosphorus, and boron). Higher level of nitrogen and boron resulted in increased growth (avg. 5 and 6.5 Chl a mg/L, resp.), total microcystin concentrations (avg. 1.185 and 7.153 mg/L, resp.), and mcyA transcript but its expression was not directly correlated with total microcystin concentrations in the target strains. Interestingly, Durgakund strain had much lower microcystin content and lacked microcystin-YR variant over NIES 843 and KW. It is inferred that microcystin concentration and its variants are strain specific. We have also examined the heterotrophic bacteria associated with cyanobacterial bloom in Durgakund Pond and Wangsong Reservoir which were found to be enriched in Alpha-, Beta-, and Gammaproteobacteria and that could influence the bloom dynamics.

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor

Sulfate reducing bacteria (SRB) oxidize a significant proportion of subseafloor organic carbon, but their metabolic activities and subsistence mechanisms are poorly understood. Here, we report in depth phylogenetic and metabolic analyses of SRB transcripts in the Peru Margin subseafloor and interpret these results in the context of sulfate reduction activity in the sediment. Relative abundance of overall SRB gene transcripts declines strongly whereas relative abundance of ribosomal protein transcripts from sulfate reducing δ-Proteobacteria peak at 90 m below seafloor (mbsf) within a deep sulfate methane transition zone. This coincides with isotopically heavy δ(34) S values of pore water sulfate (70‰), indicating active subseafloor microbial sulfate reduction. Within the shallow sulfate reduction zone (0-5 mbsf), a transcript encoding the beta subunit of dissimilatory sulfite reductase (dsrB) was related to Desulfitobacterium dehalogenans and environmental sequences from Aarhus Bay (Denmark). At 159 mbsf we discovered a transcript encoding the reversely operating dissimilatory sulfite reductase α-subunit (rdsrA), with basal phylogenetic relation to the chemolithoautotrophic SUP05 Group II clade. A diversity of SRB transcripts involved in cellular maintenance point toward potential subsistence mechanisms under low-energy over long time periods, and provide a detailed new picture of SRB activities underlying sulfur cycling in the deep subseafloor.

One-stage partial nitritation and anammox in membrane bioreactor

Partial nitritation and anammox (PN/A) was applied in a lab-scale membrane bioreactor (MBR) to investigate its technical feasibility for treating ammonium-rich wastewater with low C/N ratio. The bacterial community was analyzed by molecular cloning and 16S rRNA sequence analysis. Partial nitritation (PN) was first realized in MBR by seeding aerobic activated sludge. With dissolved oxygen control, a steady effluent mixture with NO2 (-)-N/NH4 (+)-N ratio of 1.13 ± 0.08 was generated from the PN process. Subsequently, the MBR was seeded with anammox biomass on day 59. After running 300 days, the one-stage PN/A achieved a maximum nitrogen removal rate of 1.45 kg N/m(3)/day at the nitrogen removal efficiency of 89.5 %. Microbial community analysis revealed that Nitrosomonas sp. HKU and Nitrosospira sp. YKU corresponded to nitritation; meanwhile, Candidatus Brocadia TKU sp. accounted for nitrogen removal of the PN/A system. Specifically, Nitrosomonas sp. were enriched in the reactor at the PN/A phase and then conquered Nitrosospira sp. to be the predominant ammonia oxidizers. Nitrite oxidizers and denitrifiers were detected in symbiosis with aforementioned microbes. Denitrification promised potential plus nitrogen depletion. The present one-stage PN/A process allows a significant decrease in operational costs compared with classical nitrification/denitrification.

Increasing sulfate concentrations result in higher sulfide production and phosphorous mobilization in a shallow eutrophic freshwater lake

Increasing sulfate input has been seen as an issue in management of aquatic ecosystems, but its influences on eutrophic freshwater lakes is not clear. In this study, it was observed that increasing sulfate concentration without additional cyanobacterial bloom biomass (CBB) addition did not have an obvious effect on element cycling during 1-year continuous flow mesocosm experiments in which water and sediments were taken from a shallow eutrophic lake with sulfate levels near 1 mM. However, following addition of CBB to mesocosms, sulfate-reducing bacteria (SRB) were observed in the water column, and increasing numbers of SRB in the water column were associated with higher sulfate input. Sulfate amendment (0-70 mg L(-1)) also resulted in a larger amount of total dissolved sulfide (peak values of 5.90 ± 0.36 to 7.60 ± 0.12 mg L(-1)) in the water column and acid volatile sulfide (1081.71 ± 69.91 to 1557.98 ± 41.72 mg kg(-1)) in 0-1 cm surface sediments due to sulfate reduction. During the period of CBB decomposition, increasing sulfate levels in the water column were positively correlated with increasing diffusive phosphate fluxes of 1.23 ± 0.32 to 2.17 ± 0.01 mg m(-2) d(-1) at the water-sediment interface. As increases in sulfide and phosphate release rates deteriorated the water quality/ecosystem and even spurred the occurrence of a black water problem in lakes, the control of sulfate input level should be considered for shallow eutrophic lake management, especially during cyanobacterial bloom periods.

Nitrogen removal properties in a continuous marine anammox bacteria reactor under rapid and extensive salinity changes

Salinity tolerance is one of the most important factors for the application of bioreactors to high-salinity wastewater. Although marine anammox bacteria (MAB) might be expected to tolerate higher salinities than freshwater anammox bacteria, there is little information on the effects of salinity on MAB activity. This study aimed to reveal the nitrogen removal properties in a continuous MAB reactor under conditions of rapid and extensive salinity changes. The reactor demonstrated stable nitrogen removal performance with a removal efficiency of over 85% under salinity conditions ranging from 0 to 50 g/L NaCl. The reactor performance was also well maintained, even though the salinity was rapidly changed from 30 to 50 g/L and from 30 to 0 g/L. Other evidence suggested that the seawater medium used contained components essential for effective MAB performance. Bacterial community analysis using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) showed that planctomycete UKU-1, the dominant MAB species in the inoculum, was the main contributor to anammox activity under all conditions. The PCR-DGGE using a universal bacterial primer set showed different DNA band patterns between the reactor biomass sample collected under conditions of 75 g/L NaCl and all other conditions (0, 30, 50 and freshwater-medium). All DNA sequences determined were very similar to those of bacterial species from marine environments, anaerobic environments, or wastewater-treatment facilities.

Effect of substrate characteristics on microbial community structure, function, resistance, and resilience; application to coupled photocatalytic-biological treatment

Advanced oxidation (AO) coupled with biodegradation is an emerging treatment technology for wastewaters containing biologically recalcitrant and inhibitory organics, including those containing chlorinated aromatic compounds. The composition of the AO effluent organics can vary significantly with reaction conditions, and this composition can affect the performance of subsequent biodegradation. Three synthetic effluents were used to mimic varying degrees of AO of 2,4,5-trichlorophenol: 4-chlorocatechol to mimic light transformation, 2-chloromuconic acid to mimic moderate transformation, and acetate to mimic extensive transformation. The substrates were fed to identical chemostats and analyzed at steady state for removal of chemical oxygen demand (COD) and dissolved organic carbon (DOC), biomass concentration, and bacterial diversity. The chemostat fed acetate performed best at steady state. The 2-chloromuconic acid chemostat was next in terms of steady-state performance, and the 4-chlorocatechol reactor performed worst, correlating with degree of AO transformation. A spike of 100 μM 2,4,5-trichlorophenol was then applied to each chemostat. The chemostat fed 4-chlorocatechol exhibited the best resistance to the perturbation in terms of maintaining consistent community structure and biomass concentration, whereas the performance of the acetate-fed chemostat was severely impaired in these categories, although it quickly regained capacity to remove organics near pre-perturbation levels demonstrating good resilience. The opposing trends for steady-state versus perturbed performance highlight tradeoffs inherent in coupled chemical-biological systems.

Effects of organic pollution on biological communities of marine biofilm on hard substrata

We examined the effect of organic enrichment on diatom and bacterial assemblages of marine epilithic biofilms on two locations in the Mediterranean, one situated in Spain and the other in Greece. Total organic carbon, total organic nitrogen, stable isotopes (δ(13)C and δ(15)N) and chlorophyll a indicated significant incorporation of organic wastes, increased primary production and trophic niche modifications on the biofilms close to the organic enrichment source. In Spain, where the organic load was higher than in Greece, diatom and, to some extent, bacterial assemblages varied following the organic enrichment gradient. The taxonomic richness of diatom and bacterial communities was not influenced by organic enrichment. Classical community parameters showed consistent patterns to organic pollution in both locations, whereas community assemblages were only influenced when organic pollution was greatest. The successional patterns of these communities were similar to other epilithic communities. The modification of community assemblages induced by organic pollution may affect ecological functions.

Growth of the obligate anaerobe Desulfovibrio vulgaris Hildenborough under continuous low oxygen concentration sparging: impact of the membrane-bound oxygen reductases

Although obligate anaerobe, the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) exhibits high aerotolerance that involves several enzymatic systems, including two membrane-bound oxygen reductases, a bd-quinol oxidase and a cc(b/o)o₃ cytochrome oxidase. Effect of constant low oxygen concentration on growth and morphology of the wild-type, single (Δbd, Δcox) and double deletion (Δcoxbd) mutant strains of the genes encoding these oxygen reductases was studied. When both wild-type and deletion mutant strains were cultured in lactate/sulfate medium under constant 0.02% O₂ sparging, they were able to grow but the final biomasses and the growth yield were lower than that obtained under anaerobic conditions. At the end of the growth, lactate was not completely consumed and when conditions were then switched to anaerobic, growth resumed. Time-lapse microscopy revealed that a large majority of the cells were then able to divide (over 97%) but the time to recover a complete division event was longer for single deletion mutant Δbd than for the three other strains. Determination of the molar growth yields on lactate suggested that a part of the energy gained from lactate oxidation was derived toward cells protection/repairing against oxidative conditions rather than biosynthesis, and that this part was higher in the single deletion mutant Δbd and, to a lesser extent, Δcox strains. Our data show that when DvH encounters oxidative conditions, it is able to stop growing and to rapidly resume growing when conditions are switched to anaerobic, suggesting that it enters active dormancy sate under oxidative conditions. We propose that the pyruvate-ferredoxin oxidoreductase (PFOR) plays a central role in this phenomenon by reversibly switching from an oxidative-sensitive fully active state to an oxidative-insensitive inactive state. The oxygen reductases, and especially the bd-quinol oxidase, would have a crucial function by maintaining reducing conditions that permit PFOR to stay in its active state.

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218 O

Current limitations in culture-based methods have lead to a reliance on culture-independent approaches, based principally on the comparative analysis of primary semantides such as ribosomal gene sequences. DNA can be remarkably stable in some environments, so its presence does not indicate live bacteria, but extracted ribosomal RNA (rRNA) has previously been viewed as an indicator of active cells. Stable isotope probing (SIP) involves the incorporation of heavy isotopes into newly synthesized nucleic acids, and can be used to separate newly synthesized from existing DNA or rRNA. H218 O is currently the only potential universal bacterial substrate suitable for SIP of entire bacterial communities. The aim of our work was to compare soil bacterial community composition as revealed by total versus SIP-labeled DNA and rRNA. Soil was supplemented with H218 O and after 38 days the DNA and RNA were co-extracted. Heavy nucleic acids were separated out by CsCl and CsTFA density centrifugation. The 16S rRNA gene pools were characterized by DGGE and pyrosequencing, and the sequence results analyzed using mothur. The majority of DNA (~60%) and RNA (~75%) from the microcosms incubated with H218 O were labeled by the isotope. The analysis indicated that total and active members of the same type of nucleic acid represented similar community structures, which suggested that most dominant OTUs in the total nucleic acid extracts contained active members. It also supported that H218 O was an effective universal label for SIP for both DNA and RNA. DNA and RNA-derived diversity was dissimilar. RNA from this soil more comprehensively recovered bacterial richness than DNA because the most abundant OTUs were less numerous in RNA than DNA-derived community data, and dominant OTU pools didn't mask rare OTUs as much in RNA.

Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism

Large sulfur-oxidizing bacteria in the family Beggiatoaceae are important players in the global sulfur cycle. This group contains members of the well-known genera Beggiatoa, Thioploca, and Thiomargarita but also recently identified and relatively unknown candidate taxa, including "Candidatus Thiopilula" spp. and "Ca. Thiophysa" spp. We discovered a population of "Ca. Thiopilula" spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to Thiomargarita spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 μm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados "Ca. Thiopilula" organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for "Ca. Thiopilula" and other sulfur-oxidizing microorganisms in the community. The novel observations of "Ca. Thiopilula" and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful Beggiatoaceae group and thus offer insight into the composition and ecology of deep cold seep microbial communities.

Spatio Temporal Influence of Isoflavonoids on Bacterial Diversity in the Soybean Rhizosphere

High bacterial density and diversity near plant roots has been attributed to rhizodeposit compounds that serve as both energy sources and signal molecules. However, it is unclear if and how specific rhizodeposit compounds influence bacterial diversity. We silenced the biosynthesis of isoflavonoids, a major component of soybean rhizodeposits, using RNA interference in hairy-root composite plants, and examined changes in rhizosphere bacteriome diversity. We used successive sonication to isolate soil fractions from different rhizosphere zones at two different time points and analyzed denaturing gradient gel electrophoresis profiles of 16S ribosomal RNA gene amplicons. Extensive diversity analysis of the resulting spatio temporal profiles of soybean bacterial communities indicated that, indeed, isoflavonoids significantly influenced soybean rhizosphere bacterial diversity. Our results also suggested a temporal gradient effect of rhizodeposit isoflavonoids on the rhizosphere. However, the hairy-root transformation process itself significantly altered rhizosphere bacterial diversity, necessitating appropriate additional controls. Gene silencing in hairy-root composite plants combined with successive sonication is a useful tool to determine the spatio temporal effect of specific rhizodeposit compounds on rhizosphere microbial communities.

Identification and quantification of microbial populations in activated sludge and anaerobic digestion processes

Eight different phenotypes were studied in an activated sludge process (AeR) and anaerobic digester (AnD) in a full-scale wastewater treatment plant by means of fluorescent in situ hybridization (FISH) and automated FISH quantification software. The phenotypes were ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, phosphate-accumulating organisms (PAO), glycogen-accumulating organisms (GAO), sulphate-reducing bacteria (SRB), methanotrophic bacteria and methanogenic archaea. Some findings were unexpected: (a) Presence of PAO, GAO and denitrifiers in the AeR possibly due to unexpected environmental conditions caused by oxygen deficiencies or its ability to survive aerobically; (b) presence of SRB in the AeR due to high sulphate content of wastewater intake and possibly also due to digested sludge being recycled back into the primary clarifier; (c) presence of methanogenic archaea in the AeR, which can be explained by the recirculation of digested sludge and its ability to survive periods of high oxygen levels; (d) presence of denitrifying bacteria in the AnD which cannot be fully explained because the nitrate level in the AnD was not measured. However, other authors reported the existence of denitrifiers in environments where nitrate or oxygen was not present suggesting that denitrifiers can survive in nitrate-free anaerobic environments by carrying out low-level fermentation; (e) the results of this paper are relevant because of the focus on the identification of nearly all the significant bacterial and archaeal groups of microorganisms with a known phenotype involved in the biological wastewater treatment.

Halophilic microorganisms are responsible for the rosy discolouration of saline environments in three historical buildings with mural paintings

A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory.

Depletion and biodegradation of hydrocarbons in dispersions and emulsions of the Macondo 252 oil generated in an oil-on-seawater mesocosm flume basin

Physically and chemically (Corexit 9500) generated Macondo 252 oil dispersions, or emulsions (no Corexit), were prepared in an oil-on-seawater mesocosm flume basin at 30-32 °C, and studies of oil compound depletion performed for up to 15 days. The use of Corexit 9500 resulted in smaller median droplet size than in a physically generated dispersion. Rapid evaporation of low boiling point oil compounds (C⩽15) appeared in all the experiments. Biodegradation appeared to be an important depletion process for compounds with higher boiling points in the dispersions, but was negligible in the surface emulsions. While n-alkane biodegradation was faster in chemically than in physically dispersed oil no such differences were determined for 3- and 4-ring PAH compounds. In the oil dispersions prepared by Corexit 9500, increased cell concentrations, reduction in bacterial diversity, and a temporary abundance of bacteria containing an alkB gene were associated with oil biodegradation.

Speciation and isotopic composition of sulfur in limestone soil and yellow soil in karst areas of southwest china: implications of different responses to Acid deposition

The contents and stable S isotope ratio (δS) values of total S, organic S, SO-S, and total reduced inorganic S (TRS) in typical limestone soil and yellow soil were analyzed in this study to examine the general distributions of S forms and their δS values in soils in karst areas of southwest China. Under a similar level of acid deposition, the vertical profiles of the S forms and their δS values differed in limesto\ne soil and yellow soil, indicating the different geochemical responses of these soils to acid deposition. The deposited SO was retained as organic S in both soils. The depletion in S of TRS relative to SO and the parallel increasing δS values of TRS and SO indicate a bacterial reduction process of sulfate in both soils. The different extents of C-bonded S mineralization and organic sulfate transport explain the different vertical profiles of total S and organic S contents in both soils. Sulfate adsorption in limestone soil was negligible because of high pH values. Sulfate adsorption in yellow soil was another important S retention process in addition to biological S retention to form organic S and TRS because of low pH values. The effect of acid deposition on yellow soil appeared more serious because of the accumulation and leaching of deposited SO, which can result in soil acidification and accelerate the loss of basic cations from yellow soil. However, compared with yellow soil, limestone soil released more S into rivers by organic S mineralization after a large decrease in annual S deposition rate.

Rhizosphere effects of PAH-contaminated soil phytoremediation using a special plant named Fire Phoenix

The rhizosphere effect of a special phytoremediating species known as Fire Phoenix on the degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated, including changes of the enzymatic activity and microbial communities in rhizosphere soil. The study showed that the degradation rate of Σ8PAHs by Fire Phoenix was up to 99.40% after a 150-day culture. The activity of dehydrogenase (DHO), peroxidase (POD) and catalase (CAT) increased greatly, especially after a 60-day culture, followed by a gradual reduction with an increase in the planting time. The activity of these enzymes was strongly correlated to the higher degradation performance of Fire Phoenix growing in PAH-contaminated soils, although it was also affected by the basic characteristics of the plant species itself, such as the excessive, fibrous root systems, strong disease resistance, drought resistance, heat resistance, and resistance to barren soil. The activity of polyphenoloxidase (PPO) decreased during the whole growing period in this study, and the degradation rate of Σ8PAHs in the rhizosphere soil after having planted Fire Phoenix plants had a significant (R(2)=0.947) negative correlation with the change in the activity of PPO. Using an analysis of the microbial communities, the results indicated that the structure of microorganisms in the rhizosphere soil could be changed by planting Fire Phoenix plants, namely, there was an increase in microbial diversity compared with the unplanted soil. In addition, the primary advantage of Fire Phoenix was to promote the growth of flora genus Gordonia sp. as the major bacteria that can effectively degrade PAHs.

Coupled photocatalytic-biodegradation of 2,4,5-trichlorophenol: effects of photolytic and photocatalytic effluent composition on bioreactor process performance, community diversity, and resistance and resilience to perturbation

Sequentially coupled advanced oxidation-biodegradation systems have proven effective for treating a variety of wastewaters, but in several cases the pretreatment did not improve, or even hindered, subsequent biodegradation. Therefore, investigating the relationship between advanced oxidation pretreated effluent and subsequent bioreactor performance can help to optimize these systems. Here, a photocatalytic reactor was used to produce four unique effluents from 2,4,5-trichlorophenol (TCP) by varying light wavelength, catalyst presence, and reaction time, demonstrating that the conditions of photocatalytic pretreatment can be tuned to achieve a variety of treatment objectives. The photocatalytic effluents were characterized for chemical oxygen demand (COD), chloride release, aromaticity, and residual TCP concentration. The four effluents were normalized to 40 mg COD/L, combined with biological medium components, and fed to continuous bioreactors. Bioreactors were assayed for COD removal, TCP removal, optical density (OD), and microbial diversity via denaturing gradient gel electrophoresis. In general COD removal in the bioreactors increased as aromatic character of the photoeffluent decreased, but the least aromatic effluent performed poorly indicating the nuanced relationship between photoreactor effluent composition and bioreactor performance. While neither indicator of community diversity, richness nor evenness, correlated with COD removal or biomass accumulation, each effluent produced a unique community as indicated through similarity indices. All conditions demonstrated strong overall TCP removal. After two weeks at steady state, the reactors were perturbed with a 120-μM spike of TCP. Overall the most aromatic photoeffluent produced the most resistant community to the perturbation, while the optimum effluents at steady state produced communities with poor resistance in terms of biomass accumulation and COD removal. These results highlight the tradeoffs between steady state performance and resistance to perturbation that are necessary to optimize a combined advanced oxidation-biodegradation treatment strategy.

Succession of cable bacteria and electric currents in marine sediment

Filamentous Desulfobulbaceae have been reported to conduct electrons over centimetre-long distances, thereby coupling oxygen reduction at the surface of marine sediment to sulphide oxidation in sub-surface layers. To understand how these 'cable bacteria' establish and sustain electric conductivity, we followed a population for 53 days after exposing sulphidic sediment with initially no detectable filaments to oxygen. After 10 days, cable bacteria and electric currents were established throughout the top 15 mm of the sediment, and after 21 days the filament density peaked with a total length of 2 km cm(-2). Cells elongated and divided at all depths with doubling times over the first 10 days of <20 h. Active, oriented movement must have occurred to explain the separation of O2 and H2S by 15 mm. Filament diameters varied from 0.4-1.7 μm, with a general increase over time and depth, and yet they shared 16S rRNA sequence identity of >98%. Comparison of the increase in biovolume and electric current density suggested high cellular growth efficiency. While the vertical expansion of filaments continued over time and reached 30 mm, the electric current density and biomass declined after 13 and 21 days, respectively. This might reflect a breakdown of short filaments as their solid sulphide sources became depleted in the top layers of the anoxic zone. In conclusion, cable bacteria combine rapid and efficient growth with oriented movement to establish and exploit the spatially separated half-reactions of sulphide oxidation and oxygen consumption.

Microscopic, chemical, and molecular-biological investigation of the decayed medieval stained window glasses of two Catalonian churches

We investigated the decayed historical church window glasses of two Catalonian churches, both under Mediterranean climate. Glass surfaces were studied by scanning electron microscopy (SEM), energy dispersive spectrometry (EDS), and X-ray diffraction (XRD). Their chemical composition was determined by wavelength-dispersive spectrometry (WDS) microprobe analysis. The biodiversity was investigated by molecular methods: DNA extraction from glass, amplification by PCR targeting the16S rRNA and ITS regions, and fingerprint analyses by denaturing gradient gel electrophoresis (DGGE). Clone libraries containing either PCR fragments of the bacterial 16S rDNA or the fungal ITS regions were screened by DGGE. Clone inserts were sequenced and compared with the EMBL database. Similarity values ranged from 89 to 100% to known bacteria and fungi. Biological activity in both sites was evidenced in the form of orange patinas, bio-pitting, and mineral precipitation. Analyses revealed complex bacterial communities consisting of members of the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Fungi showed less diversity than bacteria, and species of the genera Cladosporium and Phoma were dominant. The detected Actinobacteria and fungi may be responsible for the observed bio-pitting phenomenon. Moreover, some of the detected bacteria are known for their mineral precipitation capabilities. Sequence results also showed similarities with bacteria commonly found on deteriorated stone monuments, supporting the idea that medieval stained glass biodeterioration in the Mediterranean area shows a pattern comparable to that on stone.

Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments

BACKGROUND

The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30' N, 64°40' W), B (10°40' N, 64°45' W) and D (10°43'N, 64°32'W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands.

RESULTS

DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability.

CONCLUSIONS

In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.

Application of high OLR-fed aerobic granules for the treatment of low-strength wastewater: performance, granule morphology and microbial community

Aerobic granules, pre-cultivated at the organic loading rate (OLR) of 3.0 kg COD/(m3 x day), were used to treat low-strength wastewater in two sequencing batch reactors at low OLRs of 1.2 and 0.6 kg COD/(m3 x day), respectively. Reactor performance, evolution of granule morphology, structure and microbial community at low OLRs under long-term operation (130 days) were investigated. Results showed that low OLRs did not cause significant damage to granule structure as a dominant granule morphology with size over 540 microm was maintained throughout the operation. Aerobic granules at sizes of about 750 microm were finally obtained at the low OLRs. The granule reactors operated at low OLRs demonstrated effective COD and ammonia removals (above 90%), smaller granule sizes and less biomass. The contents of extracellular polymeric substances in the granules were decreased while the ratios of exopolysaccharide/exoprotein were increased (above 1.0). The granules cultivated at the low OLRs showed a smoother surface and more compact structure than the seeded granules. A significant shift in microbial community was observed but the microbial diversity remained relatively stable. Confocal Laser Scanning Microscopy observation showed that the live cells were spread throughout the whole granule, while the dead cells were mainly concentrated in the outer layer of the granule, and the proteins, polysaccharides and lipids were mainly located in the central regime of the granule. In conclusion, granules cultivated at high OLRs show potential for treating low-strength organic wastewater steadily under long-term operation.

Dissimilatory sulphate reduction in hypersaline coastal pans: an integrated microbiological and geochemical study

Here, we report on the spatial and temporal variation in sulphate-reducing bacterial community structure and activity in three hypersaline coastal pans. Community structure was determined using denaturing gradient gel electrophoresis (DGGE). Cluster analysis of DGGE patterns indicated that similar microbial populations were generally found in individual pans but varied from one pan to the other. Sulphate reducing bacteria (SRB) were quantified by competitive polymerase chain reaction based on the amplification of the dsrAB genes. Cell numbers and in situ sulphate reduction activities varied between seasons and pans but in general showed low variation in depth. Sulphate reduction activity was not correlated with microbial population size indicating that community composition is relevant for specific microbial processes. Principal component analysis coupled with correlation analyses suggested that salinity, sulphate concentration, C/N ratio and pH were the most important factors in explaining variations in SRB community composition. Most sequences derived from DGGE amplicons belonged to members of the Desulfobacteraceae and Desulfohalobiaceae families.

Biological sulfate reduction in the acidogenic phase of anaerobic digestion under dissimilatory Fe (III)--reducing conditions

In this study, a novel approach was developed for sulfate - containing wastewater treatment via dosing Fe₂O₃ in a two - stage anaerobic reactor (A1, S1). The addition of Fe₂O₃ in its second stage i.e. acidogenic sulfate-reducing reactor (S1) resulted in microbial reduction of Fe (III), which significantly enhanced the biological sulfate reduction. In reactor S1, increasing influent sulfate concentration to 1400 mg/L resulted in a higher COD removal (27.3%) and sulfate reduction (57.9%). In the reference reactor without using Fe₂O₃ (S2), the COD and sulfate removal were 15.6% and 29%, respectively. The combined performance of the two-stage anaerobic reactor (A1, S1) also showed a higher COD removal of 74.2%. Denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis showed that the dominant bacteria with high similarity to IRB species as well as sulfate reducer Desulfovibrio and acidogenic bacteria (AB) were enriched in S1. Quantitative Polymerase Chain Reaction (qPCR) analysis presented a higher proportion of sulfate reducer Desulfovibrio marrakechensis and Fe (III) reducer Iron-reducing bacteria HN54 in S1.