Geochemistry and geomicrobiology profiles of ferruginous sediment, Lake Towuti, Indonesia

Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site - a feature we attribute to the availability of labile organic matter and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA provides information on aerobic and anaerobic heterotrophs related to Actinobacteria, Nitrospirae, Chloroflexi and Thermoplasmatales. These taxa apparently played a significant role in the degradation of sinking organic matter. However, extracellular DNA concentrations rapidly decrease with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales and Methanomicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments show that microbial populations perform successive metabolisms related to sulfur, iron and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.

Soil properties and microbial indicators of samples from Lake Wellman, Darwin Mountains, Antarctica

Four pedons on each of four drift sheets in the Lake Wellman area of the Darwin Mountains were sampled for chemical and microbial analyses. The four drifts, Hatherton, Britannia, Danum, and Isca, ranged from early Holocene (10 ka) to mid-Quaternary (c. 900 ka). The soil properties of weathering stage, salt stage, and depths of staining, visible salts, ghosts, and coherence increase with drift age. The landforms contain primarily high-centred polygons with windblown snow in the troughs. The soils are dominantly complexes of Typic Haplorthels and Typic Haploturbels. The soils were dry and alkaline with low levels of organic carbon, nitrogen and phosphorus. Electrical conductivity was high accompanied by high levels of water soluble anions and cations (especially calcium and sulphate in older soils). Soil microbial biomass, measured as phospholipid fatty acids, and numbers of culturable heterotrophic microbes, were low, with highest levels detected in less developed soils from the Hatherton drift. The microbial community structure of the Hatherton soil also differed from that of the Britannia, Danum and Isca soils. Ordination revealed the soil microbial community structure was influenced by soil development and organic carbon.

The relationship of E. coli and total coliform culture to the quantitative molecular detection of various fecal indicators, sources, and pathogens in private drinking water wells

Water remains a predominant vector for human enteric pathogens not just for developing countries but also developed nations, where numerous infectious disease outbreaks, linked to the contamination of drinking water have been documented. Private drinking water wells are a source of drinking water that is largely unstudied even though a significant percentage of the population in Ontario relies on wells as their primary water source. As there exists little to no systematic surveillance for enteric infections or outbreaks related to well water sources, these individuals may be at higher risk of waterborne infectious diseases. The relationships between various fecal indicators in the water of private drinking water wells, including E. coli, Total Coliforms (TC) and Bacteroides, and enteric pathogens, including Campylobacter jejuni, Salmonella spp., and Shiga toxin producing E. coli, were studied. Convenience private well water samples collected from various regions of interest during the summer of 2014 underwent membrane filtration and culture to determine quantities of E. coli and TC colony forming units. 289 E. coli positive and 230 TC-only waters were successfully analyzed by individual qPCR assays for the aforementioned enteric pathogens. Microbial source tracking methods targeted to specific Bacteroides were used to determine the source of fecal contamination as either human or bovine. The source of fecal contamination varied by geographic region and is thought to be due to such things as differences in septic tank density and underlying geology, among others. Fecal indicators, E. coli and Bacteroides, were significantly correlated. E. coli as measured by qPCR was more strongly correlated to both total and human-specific Bacteroides genetic markers than culturable E. coli. Lastly, 1.9% of samples showed molecular evidence of contamination with enteric pathogens. Although low, this finding is significant given the limited volume of water available for testing, and suggests a potential health risk to consumers. Knowing the extent of contamination, as well as the biologic source, can better inform risk assessment and the development of potential intervention strategies for private well water in specific regions of Ontario.

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.

Effect of time and diet change on the bacterial community structure throughout the gastrointestinal tract and in faeces of the northern brown bandicoot, Isoodon macrourus

A significant gap, in not only peramelid nutritional physiology but marsupial nutrition as a whole, is the lack of information relating to microorganisms of the gastrointestinal tract. This research is a preliminary investigation that will provide a baseline for comparisons among peramelids. The high degree of 16S rRNA gene clones identified in this research that are closely related to culturable bacteria suggests that additional research will enable a more complete description of the gastrointestinal bacteria of I. macrourus. Most identifiable clones belonged to Clostridium and Ruminococcus. This research has confirmed that the hindgut of I. macrourus, the caecum, proximal colon and distal colon, are the main sites for microbial activity.

Indoor air quality in Portuguese schools: levels and sources of pollutants

Indoor air quality (IAQ) parameters in 73 primary classrooms in Porto were examined for the purpose of assessing levels of volatile organic compounds (VOCs), aldehydes, particulate matter, ventilation rates and bioaerosols within and between schools, and potential sources. Levels of VOCs, aldehydes, PM2.5 , PM10 , bacteria and fungi, carbon dioxide (CO2 ), carbon monoxide, temperature and relative humidity were measured indoors and outdoors and a walkthrough survey was performed concurrently. Ventilation rates were derived from CO2 and occupancy data. Concentrations of CO2 exceeding 1000 ppm were often encountered, indicating poor ventilation. Most VOCs had low concentrations (median of individual species <5 μg/m(3) ) and were below the respective WHO guidelines. Concentrations of particulate matter and culturable bacteria were frequently higher than guidelines/reference values. The variability of VOCs, aldehydes, bioaerosol concentrations, and CO2 levels between schools exceeded the variability within schools. These findings indicate that IAQ problems may persist in classrooms where pollutant sources exist and classrooms are poorly ventilated; source control strategies (related to building location, occupant behavior, maintenance/cleaning activities) are deemed to be the most reliable for the prevention of adverse health consequences in children in schools.

Metagenômica comparativa de solo de regiões de mata atlântica e caatinga do estado do Rio Grande do Norte - Brasil

The microorganisms play very important roles in maintaining ecosystems, which explains the enormous interest in understanding the relationship between these organisms as well as between them and the environment. It is estimated that the total number of prokaryotic cells on Earth is between 4 and 6 x 1030, constituting an enormous biological and genetic pool to be explored. Although currently only 1% of all this wealth can be cultivated by standard laboratory techniques, metagenomic tools allow access to the genomic potential of environmental samples in a independent culture manner, and in combination with third generation sequencing technologies, the samples coverage become even greater. Soils, in particular, are the major reservoirs of this diversity, and many important environments around us, as the Brazilian biomes Caatinga and Atlantic Forest, are poorly studied. Thus, the genetic material from environmental soil samples of Caatinga and Atlantic Forest biomes were extracted by direct techniques, pyrosequenced, and the sequences generated were analyzed by bioinformatics programs (MEGAN MG-RAST and WEBCarma). Taxonomic comparative profiles of the samples showed that the phyla Proteobacteria, Actinobacteria, Acidobacteria and Planctomycetes were the most representative. In addition, fungi of the phylum Ascomycota were identified predominantly in the soil sample from the Atlantic Forest. Metabolic profiles showed that despite the existence of environmental differences, sequences from both samples were similarly placed in the various functional subsystems, indicating no specific habitat functions. This work, a pioneer in taxonomic and metabolic comparative analysis of soil samples from Brazilian biomes, contributes to the knowledge of these complex environmental systems, so far little explored

Organismos marinhos em estudo na Península Ibérica, com fins de utilização em saúde sensu lato: estado da arte em 2015

Dissertação para obtenção do grau de Mestre no Instituto Superior de Ciências da Saúde Egas Moniz

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats

Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Quorum Sensing and Microbial Interactions in Coral Black Band Disease and Coral-Associated Bacteria

The black band disease (BBD) microbial consortium often causes mortality of reef-building corals. Microbial chemical interactions (i.e., quorum sensing (QS) and antimicrobial production) may be involved in the BBD disease process. Culture filtrates (CFs) from over 150 bacterial isolates from BBD and the surface mucopolysaccharide layer (SML) of healthy and diseased corals were screened for acyl homoserine lactone (AHL) and Autoinducer-2 (AI-2) QS signals using bacterial reporter strains. AHLs were detected in all BBD mat samples and nine CFs. More than half of the CFs (~55%) tested positive for AI-2. Approximately 27% of growth challenges conducted among 19 isolates showed significant growth inhibition. These findings demonstrate that QS is actively occurring within the BBD microbial mat and that culturable bacteria from BBD and the coral SML are able to produce QS signals and antimicrobial compounds. This is the first study to identify AHL production in association with active coral disease.

Mineralisation of the fungicide 14C-labelled metalaxyl fungicide in Brazilian soils.

Laboratory incubation experiments were carried out to estimate the mineralisation of metalaxyl 14C {N-(2-6 dimethyphenyl)-N-(methoxyacetyl) alanine methyl ester} in four Brazilian soils with different physico-chemical properties, at 3 and 30 ?g a.i. g-1. In the Petrolina sandy soil the mineralisation presented higher 14CO2 production rates, at two essayed concentrations, after 70 days. Microbiological studies were done to determine the numbers of bacteria, actinobacteria and fungi (CFU g-1 soil). In relation with other microbial community, bacterial population demonstrated to be a major component of the cultivable heterotrophic community after the application.of the compound. No detectable metabolites were found in this study. The results suggest that soil properties and application history may have a strong influence on the fungicide behavior in these soil samples.

Intestinal microbiome in chronic intestinal failure and associations with intestinal failure associated liver disease

Background and Aims: Intestinal dysbiosis has been described in children with chronic intestinal failure (CIF) and in adults with short bowel syndrome (SBS), mostly with jejunocolic anastomosis (SBS-2) and jejuno-ileal anastomosis (SBS-3), linked to generic data with the pathogenesis of Intestinal Failure Associated Liver Disease (IFALD). Little is known about gut microbiome of adults with end-jejunostomy (SBS-1) and in CIF other than SBS and any specific associations with the onset of IFALD. We aimed to describe the fecal microbiome of adult patients with different mechanisms of CIF and any possible associations with the development of IFALD. Material and methods: Fecal samples from 61 patients with benign CIF. Phylogenetic characterization of the microbiome by amplification of the hypervariable regions V3 and V4 of the bacterial gene encoding 16S rRNA, and subsequent grouping of sequences in amplicon sequence variants (ASVs). Patient samples comparison to microbiome sequences from 61 healthy subjects, matched for sex and age, selected from the healthy subjects library of the Laboratory of the Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, of the University of Bologna. IFALD was assessed by the diagnostic criteria of IFALD-cholestasis, IFALD-steatosis, IFALD-fibrosis. Results: Decreased bacterial α-diversity in CIF patients (increase of Proteobacteria and Actinobacteria and decrease in Bacteroidetes). Identification of microbial family-level signatures specific for CIF mechanisms (increase in Actinomycetaceae and Streptococcaceae in SBS-1, Bifidobacteriaceae and Lactobacillaceae in SBS-2, Bacteroidaceae and Porphyromonadaceae in dysmotility). Abundance of Lactobacillus and Lactobacillaceae strongly associated with IFALD-cholestasis and IFALD–fibrosis for SBS-1; Peptostreptococcus, Prevotellaceae (Prevotella) and Pasteurellaceae (Haemophilus) significantly increased in IFALD-fibrosis for other CIF mechanisms. Conclusions: CIF patients had a marked intestinal dysbiosis with microbial family-level signatures specific to the pathophysiological mechanism. Specific characteristics of microbiome may contribute to the pathogenesis of IFALD. Intestinal microbiome could become a therapeutic target in patients with CIF.

Policitemia Vera: scoperta di saggi di biopsia liquida finalizzata a identificare i biomarcatori correlati al rischio trombotico

La Policitemia Vera (PV) è una neoplasia mieloproliferativa con un aumentato rischio di trombosi e di progressione verso la Mielofibrosi. L'infiammazione cronica è comunemente osservata nelle neoplasie mieloproliferative, compresa la PV. La rete infiammatoria, tra le varie componenti, comprende le vescicole extracellulari (EVs), che svolgono un ruolo nella comunicazione cellula-cellula. Inoltre, le componenti microbiche circolanti sono state recentemente indicate come potenziali modificatori dell'infiammazione, della coagulazione e dell’emopoiesi in generale. Qui abbiamo studiato il DNA microbico delle EVs circolanti attraverso. Sangue periferico e feci sono stati raccolti da pazienti con PV (n=38) e da donatori sani (n=30). Le EVs circolanti derivate da megacariociti (MK) e piastrine (PLT) sono state analizzate mediante citometria a flusso. Dopo l'estrazione del DNA microbico dalle feci e dalle EV isolate, è stata sequenziata la regione V3-V4 del 16S rDNA. La percentuale di EVs di MK era ridotta nei pazienti con PV rispetto ai donatori sani. Al contrario, la proporzione di EVs di PLT era aumentata. La PV è stata associata anche a una firma del DNA microbico delle EVs isolate con una maggiore diversità e una composizione microbica distinta rispetto alla controparte sana. Nei pazienti con PV c’è una maggiore proporzione di EVs associate al lipopolisaccaride. Il profilo del microbioma intestinale non differiva tra PV e doantori. Inoltre, l'aumento della proporzione di EVs di MK e la riduzione di EVs di piastre identificavano i pazienti con pregressa trombosi. Le EVs dei pazienti con trombosi erano impoverite di DNA di Staphylococcus ma arricchite di DNA di Actinobacteria e Anaerococcus. Inoltre, questi pazienti avevano livelli più bassi di EVs associate al lipopolisaccaride. I pazienti con fibrosi midollare avevano una maggiore proporzione di PE-EV ed erano arricchite in DNA di Collinsella e Flavobacterium. Questi dati possono contribuire a perfezionare la prognosi della PV e a identificare nuovi bersagli farmacologici.