Using genomics, metagenomics and other omics to assess valuable microbial ecosystem services and novel biotechnological applications

Metagenomics and other "omics" are among the fastest advancing scientific tools, underpinning the recent and unprecedented access to genetic and functional information of entire communities of bacteria, virus and fungi. These remarkable advances contribute greatly to expanding our understanding of the diversity, ecology, evolution and functioning of the microbial world. There is a continuous and dynamic development of faster and cheaper sequencing and other "omics" techniques. This, combined with the development of analytical tools to deal with the exponentially increasing amount of data generated, allows access to microbial communities from a wide range of habitats and environments. The synergy between metagenomics and other ?omics? is paving the path to functional, integrative, and wider analyses including systems biology. All these new developments are increasingly contributing to the understanding of the mechanisms and processes of essential microbial ecosystem services, and to the emergence of innovative applications in many different areas.Ecosystems support life on Earth, and human existence relies heavily on ecosystem goods and services. Although only recently recognized, most of these services and goods are provided by microbial populations and communities. Many of the provisioning services (e.g. food and enzymes for industrial processes); regulating services (e.g. water quality, contamination alleviation and biological processes such as pollination and symbioses); and supporting services (e.g. nutrient cycling, agricultural production and biodiversity), are produced or mediated by microbes. Indeed, for example, many of the nitrogen cycle pathways are known to be driven by different microbial guilds. For instance, atmospheric nitrogen fixation for plant crops utilization is a microbial process, which raises agricultural productivity while decreasing the use of nitrogen fertilizers. These, when used in excess, cause water eutrophication, decrease water quality and increase the emission of the greenhouse gas N2O. Recent functional metagenomic studies have shown in freshwater relationships between the microbial nitrogen cycle and the microbial cycle of methane, another source of global warming, thus revealing the intricacy of microbial ecosystem services.A recently discovered ecosystem service performed by microbial communities is based on their ability to metabolize halogenated organic compounds. These compounds, are diverse and widespread in nature, and come from both anthropogenic and natural origins. Metagenomics has revealed a high diversity and abundance of genes encoding for halogenating and dehalogenating enzymes in soil. These discoveries are highly relevant to industrial biotechnologies and to the development of bioremediation applications.Metagenomics and other "omics" methods are also playing pivotal roles in the following areas: the development of novel antibiotics, by accessing in situ antimicrobial biosynthesis and resistance within microbiomes; the identification of new enzymes like esterases with novel properties of industrial interest; the optimization of biogas-producing microbial reactors; the understanding of the implication of microbiomes in metal corrosion processes; the prevention of microbial food spoilage, not only dependent on microbiome composition but also on the interactions between the microorganisms present naturally or as contaminants in food; the development of culture-independent surveillance of commercially available probiotics. These are only a few examples as ?omics? technologies are continuously opening new areas of research.There is virtually no limitations to the investigation of the microbial world using metagenomics, other "omics" and/or integrative approaches like systems biology. Articles in this Frontiers Topic are expected to contribute to a better understanding of microbial ecosystem services and to expand the horizon for finding and developing new and more efficient biotechnological applications.Fil: Marco, Diana Elizabeth. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Matemáticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Florence Abram. National University Of Ireland; Irland

Absence of curli in soil-persistent Escherichia coli is mediated by a C-di-GMP signaling defect and suggests evidence of biofilm-independent niche specialization

peer-reviewedEscherichia coli is commonly viewed as a gastrointestinal commensal or pathogen although an increasing body of evidence suggests that it can persist in non-host environments as well. Curli are a major component of biofilm in many enteric bacteria including E. coli and are important for adherence to different biotic and abiotic surfaces. In this study we investigated curli production in a unique collection of soil-persistent E. coli isolates and examined the role of curli formation in environmental persistence. Although most soil-persistent E. coli were curli-positive, 10% of isolates were curli-negative (17 out of 170). Curli-producing E. coli (COB583, COB585, and BW25113) displayed significantly more attachment to quartz sand than the curli-negative strains. Long-term soil survival experiments indicated that curli production was not required for long-term survival in live soil (over 110 days), as a curli-negative mutant BW25113ΔcsgB had similar survival compared to wild type BW25113. Mutations in two genes associated with c-di-GMP metabolism, dgcE and pdeR, correlated with loss of curli in eight soil-persistent strains, although this did not significantly impair their survival in soil compared to curli-positive strains. Overall, the data indicate that curli-deficient and biofilm-defective strains, that also have a defect in attachment to quartz sand, are able to reside in soil for long periods of time thus pointing to the possibility that niches may exist in the soil that can support long-term survival independently of biofilm formation

Toward assessing farm-based anaerobic digestate public health risks : comparative investigation with slurry, effect of pasteurization treatments, and use of miniature bioreactors as proxies for pathogen spiking trials

Manure and slurry may contain a range of bacterial, viral, and parasitic pathogens and land application of these organic fertilizers typically occurs without prior treatment. In-situ treatment through farm-based anaerobic digestion (AD) of such organic fertilizers co-digested with food-production wastes is multi-beneficial due to energy recovery, increased farm incomes and noxious gas reduction. Before risk assessment can be carried out at field scale an investigation of the fate of relevant target pathogens during the actual AD process must be undertaken, requiring the development of practical test systems for evaluation of pathogen survival. The present study examines miniature (50 mL) and laboratory (10 L) scale AD systems. Treatments included slurry co-digested with fats, oils, and grease (FOG) under typical operating and pasteurization conditions used in farm-based AD, in batch-fed miniature and laboratory mesophilic (37°C) continuously stirred tank reactors. Biogas production, pH, chemical oxygen demand, volatile solids, and ammonia concentration were measured throughout the trial, as were fecal indicator bacteria (FIB) i.e., total coliforms, Escherichia coli, and Enterococcus species. The miniature and laboratory bioreactors performed similarly in terms of physicochemical parameters and FIB die-off. In the absence of pasteurization, after 28 days, enterococci numbers were below the <1,000 cfu g−1 threshold required for land application, while E. coli was no longer detectable in the digestate. For comparison, FIB survival in slurry was examined and after 60 days of storage, none of the FIB tested was <1,000 cfu g−1, suggesting that slurry would not be considered safe for land application if FIB thresholds required for AD digestate were to be applied. Taken together we demonstrate that (i) miniature-scale bioreactors are valid proxies of farm-based AD to carry out targeted pathogen survival studies and (ii) in situ AD treatment of slurry prior to land application reduces the level of FIB, independently of pasteurization, which in turn might be indicative of a decreased potential pathogen load to the environment and associated public health risks

Linking microbial community structure and function during the acidified anaerobic digestion of grass

This research was funded by the Irish Higher Education Authority Program for Research in Third Level Institutions Cycle 5: – PRTLI-5 ESI Ph.D. ENS Program. This work was also supported by the Wellcome Trust (grant number 094476/Z/10/Z for the TripleTOF 5600 mass spectrometer at the University of St Andrews), NERC (grant number NE/L011956/1), and a Royal Irish Academy Mobility Grant.Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g. carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilised as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilising, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analysed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e. grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored.Publisher PDFPeer reviewe

Financial leverage and stock returns: evidence from an emerging economy

The aim of this research was to examine the propositions of Campbell et al. and Mirza et al. on pricing of leverage in stock returns using a comprehensive set of firms listed on the Karachi Stock Exchange (KSE) over a period of 13 years. Our results suggest that while size, value and, more importantly, financial leverage are systematic in nature, market risk premium is not a relevant factor. The results confirm the notion of leverage premium and have important implications for financial managers, investment analysts and other market participants who use asset pricing frameworks for investment appraisals. These findings have global relevance, notably for other emerging and developing economies where default risk is of importance due to cyclical nature of cash flows and low recovery rates owing to weaknesses of legal structure

Back to the future: Using long-term observational and paleo-proxy reconstructions to improve model projections of antarctic climate

Quantitative estimates of future Antarctic climate change are derived from numerical global climate models. Evaluation of the reliability of climate model projections involves many lines of evidence on past performance combined with knowledge of the processes that need to be represented. Routine model evaluation is mainly based on the modern observational period, which started with the establishment of a network of Antarctic weather stations in 1957/58. This period is too short to evaluate many fundamental aspects of the Antarctic and Southern Ocean climate system, such as decadal-to-century time-scale climate variability and trends. To help address this gap, we present a new evaluation of potential ways in which long-term observational and paleo-proxy reconstructions may be used, with a particular focus on improving projections. A wide range of data sources and time periods is included, ranging from ship observations of the early 20th century to ice core records spanning hundreds to hundreds of thousands of years to sediment records dating back 34 million years. We conclude that paleo-proxy records and long-term observational datasets are an underused resource in terms of strategies for improving Antarctic climate projections for the 21st century and beyond. We identify priorities and suggest next steps to addressing this.The Antarctic Climate Change in the 21st Century (AntClim21) Scientific Research Programme of the Scientific Committee on Antarctic Research are thanked for supporting the international scientific workshop at which the writing of this manuscript was initiated. This is a contribution to the PAGES 2k Network (through the CLIVASH 2k project). NJA acknowledges support by the Australian Research Council through a Future Fellowship (FT160100029) and the Centre of Excellence for Climate Extremes (CE170100023). SJP was supported under the Australian Research Council’s Special Research Initiative for the Antarctic Gateway Partnership (Project ID SR140300001). JMJ acknowledges support from the Leverhulme Trust through a Research Fellowship (RF-2018-183). FC acknowledges support from the PNRA national Italian projects PNRA16_00016, “WHISPERS” and project PNRA_00002, “ANTIPODE”. TJB, LS, and ERT were supported by the Natural Environment Research Council (NERC) as part of the British Antarctic Survey Polar Science for Planet Earth Programme. TJB additionally acknowledges support for this work as a contribution to the NERC grant NE/N01829X/1. IW thanks FAPESP 2015/50686-1, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) Finance Code 001 and CNPq 300970/2018-8, CNPq INCT Criosfera 704222/200

Djelatnost Odsjeka za povijest hrvatske glazbe Zavoda za povijest hrvatske književnosti, kazališta i glazbe HAZU u 2016. godini

<i>Geobacter sulfurreducens</i> is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes. Here we employ for the first time comparative proteomics to identify key physiological changes involved in <i>G. sulfurreducens</i> adaptation from fumarate-respiring planktonic cells to electron-conducting biofilms. Increased levels of proteins involved in outer membrane biogenesis, cell motility, and secretion are expressed in biofilms. Of particular importance to the electron-conducting biofilms are proteins associated with secretion systems of Type I, II, V and Type IV pili. Furthermore, enzymes involved in lipopolysaccharide and peptidoglycan biosynthesis show increased levels of expression in electron-conducting biofilms compared with planktonic cells. These observations point to similarities in long-range electron-transfer mechanisms between <i>G. sulfurreducens</i> and <i>Shewanella oneidensis</i> while highlighting the wider significance of secretion systems beyond that of Type IV pili identified to date in the adaptation of <i>G. sulfurreducens</i> to electrode respiration

riboSeed:leveraging prokaryotic genomic architecture to assemble across ribosomal regions

The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only similar to 10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome's rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome