Changes in microbial diversity associated with two coral species recovering from a stressed state in a public aquarium system:Microbial diversity associated with aquarium corals

Coral diseases are a major factor in the decline of coral reefs worldwide, and a large proportion of studies focusing on disease causation use aquaria to control variables that affect disease occurrence and development. Public aquaria can therefore provide an invaluable resource to study the factors contributing to health and disease. In November 2010 the corals within the main display tank at the Horniman Museum and Gardens, London, UK, underwent a severe stress event due to reduced water quality, which resulted in death of a large number of coral colonies. Three separate colonies of two species of reef coral, Seritopora hystrix and Montipora capricornis showing signs of stress and acute tissue loss were removed from the display tank and placed in a research tank with improved water quality. Both coral species showed a significant difference in 16S rRNA gene bacterial diversity between healthy and stressed states (S. hystrix; ANOSIM, R=0.44, p=0.02 and M. capricornis; ANOSIM, R=0.33, p=0.01), and between the stressed state and the recovering corals. After four months the bacterial communities had returned to a similar state to that seen in healthy corals of the same species. The bacterial communities associated with the two coral species were distinct, despite them
being reared under identical environmental conditions. Despite the environmental perturbation being identical different visual signs were seen in each species and distinctly different bacterial communities associated with the stressed state occurred within them. Recovery of the visually healthy state was associated with a return of the bacterial community, within two months, to the pre-disturbance state. These observations suggest that coral-associated microbial communities are remarkably resilient and return to a very similar stable state following disturbance.

Biostratigraphic Evidence Relating to the Age-Old Question of Hannibal's Invasion of Italy, II: Chemical Biomarkers and Microbial Signatures

As discussed in Part I, a large accumulation of mammalian faeces at the mire site in the upper Guil Valley near Mt. Viso, dated to 2168cal ¹⁴C yr., provides the first evidence of the passage of substantial but indeterminate numbers of mammals within the time frame of the Punic invasion of Italia. Specialized organic biomarkers bound up in a highly convoluted and bioturbated bed constitute an unusual anomaly in a histosol comprised of fibric and hemist horizons that are usually expected to display horizontal bedding. The presence of deoxycholic acid and ethylcoprostanol derived from faecal matter, coupled with high relative numbers of Clostridia 16S rRNA genes, suggests a substantial accumulation of mammalian faeces at the site over 2000years ago. The results reported here constitute the first chemical and biological evidence of the passage of large numbers of mammals, possibly indicating the route of the Hannibalic army at this time. Combined with the geological analysis reported in Part I, these data provide a background supporting the need for further historical archaeological exploration in this area.

Gaining biological perspectives from schistosome genomes

Characterization of the genomic basis underlying schistosome biology is an important strategy for the development of future treatments and interventions. Genomic sequence is now available for the three major clinically relevant schistosome species, Schistosoma mansoni, S. japonicum and S. haematobium, and this information represents an invaluable resource for the future control of human schistosomiasis. The identification of a biologically important, but distinct from the host, schistosome gene product is the ultimate goal for many research groups. While the initial elucidation of the genome of an organism is critical for most biological research, continued improvement or curation of the genome construction should be an ongoing priority. In this review we will discuss prominent recent findings utilizing a systems approach to schistosome biology, as well as the increased use of interference RNA (RNAi). Both of these research strategies are aiming to place parasite genes into a more meaningful biological perspective.

Microbial metabolism mediates interactions between dissolved organic matter and clay minerals in streamwater

Sorption of organic molecules to mineral surfaces is an important control upon the aquatic carbon (C) cycle. Organo-mineral interactions are known to regulate the transport and burial of C within inland waters, yet the mechanisms that underlie these processes are poorly constrained. Streamwater contains a complex and dynamic mix of dissolved organic compounds that coexists with a range of organic and inorganic particles and microorganisms. To test how microbial metabolism and organo-mineral complexation alter amino acid and organic carbon fluxes we experimented with 13C-labelled amino acids and two common clay minerals (kaolinite and montmorillonite). The addition of 13C-labelled amino acids stimulated increased microbial activity. Amino acids were preferentially mineralized by the microbial community, concomitant with the leaching of other (non-labelled) dissolved organic molecules that were removed from solution by clay-mediated processes. We propose that microbial processes mediate the formation of organo-mineral particles in streamwater, with potential implications for the biochemical composition of organic matter transported through and buried within fluvial environments.

Microbial phylogenetic and functional responses within acidified wastewater communities exhibiting enhanced phosphate uptake

Acid stimulated accumulation of insoluble phosphorus within microbial cells is highly beneficial to wastewater treatment but remains largely unexplored. Using single cell analyses and next generation sequencing, the response of active polyphosphate accumulating microbial communities under conditions of enhanced phosphorus uptake under both acidic and aerobic conditions was characterised. Phosphorus accumulation activities were highest under acidic conditions (pH 5.5 > 8.5), where a significant positive effect on bioaccumulation was observed at pH 5.5 when compared to pH 8.5. In contrast to the Betaproteobacteria and Actinobacteria dominated enhanced biological phosphorus removal process, the functionally active polyP accumulators at pH 5.5 belonged to the Gammaproteobacteria, with key accumulators identified as members of the families Aeromonadaceae and Enterobacteriaceae. This study demonstrated a significant enrichment of key polyphosphate kinase and exopolyphosphatase genes within the community metagenome after acidification, concomitant with an increase in P accumulation kinetics.

Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.

The occurrence of PAHs and faecal sterols in Dublin Bay and their influence on sedimentary microbial communities

The source, concentration, and potential impact of sewage discharge and incomplete organic matter (OM) combustion on sedimentary microbial populations were assessed in Dublin Bay, Ireland. Polycyclic aromatic hydrocarbons (PAHs) and faecal steroids were investigated in 30 surface sediment stations in the bay. Phospholipid fatty acid (PLFA) content at each station was used to identify and quantify the broad microbial groups present and the impact of particle size, total organic carbon (%TOC), total hydrogen (%H) and total nitrogen (%N) was also considered. Faecal sterols were found to be highest in areas with historical point sources of sewage discharge. PAH distribution was more strongly associated with areas of deposition containing high %silt and %clay content, suggesting that PAHs are from diffuse sources such as rainwater run-off and atmospheric deposition. The PAHs ranged from 12 to 3072 ng/g, with 10 stations exceeding the suggested effect range low (ERL) for PAHs in marine sediments. PAH isomer pair ratios and sterol ratios were used to determine the source and extent of pollution. PLFAs were not impacted by sediment type or water depth but were strongly correlated to, and influenced by PAH and sewage levels. Certain biomarkers such as 10Me16:0, i17:0 and a17:0 were closely associated with PAH polluted sediments, while 16:1ω9, 16:1ω7c, Cy17:0, 18:1ω6, i16:0 and 15:0 all have strong positive correlations with faecal sterols. Overall, the results show that sedimentary microbial communities are impacted by anthropogenic pollution.

A Microbial Link to Weathering of Postglacial Rocks and Sediments, Mount Viso Area, Western Alps, Demonstrated through Analysis of a Soil/Paleosol Bio/Chronosequence

Understanding the mechanism associated with rates of weathering and evolution of rocks→sediment→soil→paleosol in alpine environments raises questions related to the impact of microbial mediation versus various diverse abiotic chemical/physical processes, even including the overall effect of cosmic impact/airburst during the early stage of weathering in Late Glacial (LG) deposits. This study is of a chronosequence of soils/paleosols, with an age range that spans the post–Little Ice Age (post-LIA; <150 yr), the Little Ice Age (LIA; AD 1500–1850), the middle Neoglacial (∼3 ka)–Younger Dryas (YD; <12.8 ka), and the LG (<15 ka). The goal is to elicit trends in weathering, soil morphogenesis, and related eubacterial population changes over the past 13–15 k.yr. The older LG/YD paleosols in the sequence represent soil morphogenesis that started during the closing stage of Pleistocene glaciation. These are compared with undated soils of midto late Neoglacial age, the youngest of LIA and post-LIA age. All profiles formed in a uniform parentmaterial ofmetabasalt composition and in moraine, rockfall, protalus, and alluvial fan deposits. Elsewhere in Europe,North America, and Asia, the cosmic impact/airburst event at 12.8 ka often produced a distinctive, carbon-rich “black mat” layer that shows evidence of high-temperature melting. At this alpine site, older profiles of similar LG age contain scorched and melted surface sediments that are otherwise similar in composition to the youngest/thinnest profiles developing in the catchment today. Moreover, microbial analysis of the sediments offers new insight into the genesis of these sediments: the C and Cu (u = unweathered) horizons in LG profiles present at 12.8 ka (now Ah/Bw) show bacterial population structures that differ markedly from recent alluvial/protalus sample bacterial populations. We propose here that these differences are, in part, a direct consequence of the age/cosmic impact/weathering processes that have occurred in the chronosequence. Of the several questions that emerge from these sequences, perhaps the most important involve the interaction of biotic-mineral factors, which need to be understood if we are to generally fully appreciate the role played by microbes in rock weathering.

Improving photofermentative hydrogen production through metabolic engineering and DOE (Design of Experiments)

A l’heure actuelle, les biocarburants renouvelables et qui ne nuit pas à l'environnement sont à l'étude intensive en raison de l'augmentation des problèmes de santé et de la diminution des combustibles fossiles. H2 est l'un des candidats les plus prometteurs en raison de ses caractéristiques uniques, telles que la densité d'énergie élevée et la génération faible ou inexistante de polluants. Une façon attrayante pour produire la H2 est par les bactéries photosynthétiques qui peuvent capter l'énergie lumineuse pour actionner la production H2 avec leur système de nitrogénase. L'objectif principal de cette étude était d'améliorer le rendement de H2 des bactéries photosynthétiques pourpres non sulfureuses utilisant une combinaison de génie métabolique et le plan des expériences. Une hypothèse est que le rendement en H2 pourrait être améliorée par la redirection de flux de cycle du Calvin-Benson-Bassham envers du système de nitrogénase qui catalyse la réduction des protons en H2. Ainsi, un PRK, phosphoribulose kinase, mutant « knock-out » de Rhodobacter capsulatus JP91 a été créé. L’analyse de la croissance sur des différentes sources de carbone a montré que ce mutant ne peut croître qu’avec l’acétate, sans toutefois produire d' H2. Un mutant spontané, YL1, a été récupéré qui a retenu l'cbbP (codant pour PRK) mutation d'origine, mais qui avait acquis la capacité de se développer sur le glucose et produire H2. Une étude de la production H2 sous différents niveaux d'éclairage a montré que le rendement d’YL1 était de 20-40% supérieure à la souche type sauvage JP91. Cependant, il n'y avait pas d'amélioration notable du taux de production de H2. Une étude cinétique a montré que la croissance et la production d'hydrogène sont fortement liées avec des électrons à partir du glucose principalement dirigés vers la production de H2 et la formation de la biomasse. Sous des intensités lumineuses faibles à intermédiaires, la production d'acides organiques est importante, ce qui suggère une nouvelle amélioration additionnel du rendement H2 pourrait être possible grâce à l'optimisation des processus. Dans une série d'expériences associées, un autre mutant spontané, YL2, qui a un phénotype similaire à YL1, a été testé pour la croissance dans un milieu contenant de l'ammonium. Les résultats ont montré que YL2 ne peut croître que avec de l'acétate comme source de carbone, encore une fois, sans produire de H2. Une incubation prolongée dans les milieux qui ne supportent pas la croissance de YL2 a permis l'isolement de deux mutants spontanés secondaires intéressants, YL3 et YL4. L'analyse par empreint du pied Western a montré que les deux souches ont, dans une gamme de concentrations d'ammonium, l'expression constitutive de la nitrogénase. Les génomes d’YL2, YL3 et YL4 ont été séquencés afin de trouver les mutations responsables de ce phénomène. Fait intéressant, les mutations de nifA1 et nifA2 ont été trouvés dans les deux YL3 et YL4. Il est probable qu'un changement conformationnel de NifA modifie l'interaction protéine-protéine entre NifA et PII protéines (telles que GlnB ou GlnK), lui permettant d'échapper à la régulation par l'ammonium, et donc d'être capable d'activer la transcription de la nitrogénase en présence d'ammonium. On ignore comment le nitrogénase synthétisé est capable de maintenir son activité parce qu’en théorie, il devrait également être soumis à une régulation post-traductionnelle par ammonium. Une autre preuve pourrait être obtenue par l'étude du transcriptome d’YL3 et YL4. Une première étude sur la production d’ H2 par YL3 et YL4 ont montré qu'ils sont capables d’une beaucoup plus grande production d'hydrogène que JP91 en milieu d'ammonium, qui ouvre la porte pour les études futures avec ces souches en utilisant des déchets contenant de l'ammonium en tant que substrats. Enfin, le reformage biologique de l'éthanol à H2 avec la bactérie photosynthétique, Rhodopseudomonas palustris CGA009 a été examiné. La production d'éthanol avec fermentation utilisant des ressources renouvelables microbiennes a été traitée comme une technique mature. Cependant, la plupart des études du reformage de l'éthanol à H2 se sont concentrés sur le reformage chimique à la vapeur, ce qui nécessite généralement une haute charge énergetique et résultats dans les émissions de gaz toxiques. Ainsi le reformage biologique de l'éthanol à H2 avec des bactéries photosynthétiques, qui peuvent capturer la lumière pour répondre aux besoins énergétiques de cette réaction, semble d’être plus prometteuse. Une étude précédente a démontré la production d'hydrogène à partir d'éthanol, toutefois, le rendement ou la durée de cette réaction n'a pas été examiné. Une analyse RSM (méthode de surface de réponse) a été réalisée dans laquelle les concentrations de trois facteurs principaux, l'intensité lumineuse, de l'éthanol et du glutamate ont été variés. Nos résultats ont montré que près de 2 moles de H2 peuvent être obtenus à partir d'une mole d'éthanol, 33% de ce qui est théoriquement possible.

Treatment of phenanthrene and benzene using microbial fuel cells operated continuously for possible in situ and ex situ applications

Bioelectrochemical systems could have potential for bioremediation of contaminants either in situ or ex situ. The treatment of a mixture of phenanthrene and benzene using two different tubular microbial fuel cells (MFCs) designed for either in situ and ex situ applications in aqueous systems was investigated over long operational periods (up to 155 days). For in situ deployments, simultaneous removal of the petroleum hydrocarbons (>90% in term of degradation efficiency) and bromate, used as catholyte, (up to 79%) with concomitant biogenic electricity generation (peak power density up to 6.75 mWm−2) were obtained at a hydraulic retention time (HRT) of 10 days. The tubular MFC could be operated successfully at copiotrophic (100 ppm phenanthrene, 2000 ppm benzene at HRT 30 days) and oligotrophic (phenanthrene and benzene, 50 ppb each, HRT 10 days) substrate conditions suggesting its effectiveness and robustness at extreme substrate concentrations in anoxic environments. In the MFC designed for ex situ deployments, optimum MFC performance was obtained at HRT of 30 h giving COD removal and maximum power output of approximately 77% and 6.75 mWm−2 respectively. The MFC exhibited the ability to resist organic shock loadings and could maintain stable MFC performance. Results of this study suggest the potential use of MFC technology for possible in situ/ex situ hydrocarbon-contaminated groundwater treatment or refinery effluents clean-up, even at extreme contaminant level conditions.

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition

Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils ( model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material.