Microbial diversity of a disused copper mine site (Parys Mountain, UK), dominated by intensive eukaryotic filamentous growth

The Parys Mountain copper mine (Wales, UK) contains a wide range of discrete environmental microniches with various physicochemical conditions that shape microbial community composition. Our aim was to assess the microbial community in the sediments and overlying water column in an acidic mine drainage (AMD) site containing abundant filamentous biogenic growth via application of a combination of chemical analysis and taxonomic profiling using 16S rRNA gene amplicon sequencing. Our results were then compared to previously studied sites at Parys Mt. Overall, the sediment microbiome showed a dominance of bacteria over archaea, particularly those belonging to Proteobacteria (genera Acidiphilium and Acidisphaera), Acidobacteriota (subgroup 1), Chloroflexota (AD3 cluster), Nitrospirota (Leptospirillum) and the uncultured Planctomycetota/CPIa-3 termite group. Archaea were only present in the sediment in small quantities, being represented by the Terrestrial Miscellaneous Euryarchaeota Group (TMEG), Thermoplasmatales and Ca. Micrarchaeota (Ca. Micracaldota). Bacteria, mostly of the genera Acidiphilium and Leptospirillum, also dominated within the filamentous streamers while archaea were largely absent. This study found pH and dissolved solutes to be the most important parameters correlating with relative proportions of bacteria to archaea in an AMD environment and revealed the abundance patterns of native acidophilic prokaryotes inhabiting Parys Mt sites and their niche specificities

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome

Improving the health beneficial fatty acid content of meat and milk is a major challenge requiring an increased understanding of rumen lipid metabolism. In this study, we isolated and characterized rumen bacterial lipases/esterases using functional metagenomics. Metagenomic libraries were constructed from DNA extracted from strained rumen fluid (SRF), solid-attached bacteria (SAB) and liquid-associated rumen bacteria (LAB), ligated into a fosmid vector and subsequently transformed into an Escherichia coli host. Fosmid libraries consisted of 7,744; 8,448; and 7,680 clones with an average insert size of 30 to 35 kbp for SRF, SAB and LAB, respectively. Transformants were screened on spirit blue agar plates containing tributyrin for lipase/esterase activity. Five SAB and four LAB clones exhibited lipolytic activity, and no positive clones were found in the SRF library. Fosmids from positive clones were pyrosequenced and twelve putative lipase/esterase genes and two phospholipase genes retrieved. Although the derived proteins clustered into diverse esterase and lipase families, a degree of novelty was seen, with homology ranging from 40 to 78 % following BlastP searches. Isolated lipases/esterases exhibited activity against mostly short- to medium-chain substrates across a range of temperatures and pH. The function of these novel enzymes recovered in ruminal metabolism needs further investigation, alongside their potential industrial uses

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi-enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large-scale chronic pollution is yet to be defined, particularly in anaerobic and micro-aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen-depleted petroleum-polluted sediments

Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads

Uric acid is a promising hydrophobic nitrogen source for biostimulation of microbial activities in oil-impacted marine environments. This study investigated metabolic processes and microbial community changes in a series of microcosms using sediment from the Mediterranean and the Red Sea amended with ammonium and uric acid. Respiration, emulsification, ammonium and protein concentration measurements suggested a rapid production of ammonium from uric acid accompanied by the development of microbial communities containing hydrocarbonoclastic bacteria after 3 weeks of incubation. About 80 % of uric acid was converted to ammonium within the first few days of the experiment. Microbial population dynamics were investigated by Ribosomal Intergenic Spacer Analysis and Illumina sequencing as well as by culture-based techniques. Resulting data indicated that strains related to Halomonas spp. converted uric acid into ammonium, which stimulated growth of microbial consortia dominated by Alcanivorax spp. and Pseudomonas spp. Several strains of Halomonas spp. were isolated on uric acid as the sole carbon source showed location specificity. These results point towards a possible role of halomonads in the conversion of uric acid to ammonium utilized by hydrocarbonoclastic bacteria

ULIXES, unravelling and exploiting Mediterranean Sea microbial diversity and ecology for xenobiotics' and pollutants' clean up

The civilizations in the Mediterranean Sea have deeply changed the local environment, especially with the extraction of subsurface oil and gas, their refinery and transportation. Major environmental impacts are affecting all the sides of the basin with actual and potential natural and socio-economic problems. Events like the recent BP\u2019s oil disaster in the Gulf of Mexico would have a tremendous impact on a close basin like the Mediterranean Sea. The recently EU-funded project ULIXES (http://www.ulixes.unimi.it/) aims to unravel, categorize, catalogue, exploit and manage the microbial diversity available in the Mediterranean Sea for addressing bioremediation of polluted marine sites. The rationale of the project is based on the multiple diverse environmental niches of the Mediterranean Sea and the huge range of microorganisms inhabiting therein. Microbial consortia and their ecology, their components or products are used for designing novel pollutant- and site-tailored bioremediation approaches. ULIXES exploits microbial resource mining by the isolation of novel microorganisms as well as by novel advanced \u2018meta-omics\u2019 technologies for solving pollution of three major high priority pollutant classes, petroleum hydrocarbons, chlorinated compounds and heavy metals. A network of twelve European and Southern Mediterranean partners is exploring the microbial diversity and ecology associated to a large set of polluted environmental matrices including seashore sands, lagoons, harbors and deep-sea sediments, oil tanker shipwreck sites, as well as coastal and deep sea natural sites where hydrocarbon seepages occur. The mined collections are exploited for developing novel bioremediation processes to be tested in ex situ and in situ field bioremediation trials

Systems approaches to microbial communities and their functioning.

Recent advances in molecular microbial ecology and systems biology enhance insight into microbial community structure and functioning. They provide conceptual and technical bases for the translation of species-data and community-data into a model framework accounting for the functioning of and interactions between metabolic networks of species in multispecies environments. Function-directed and single cell-directed approaches supplement and improve metagenomics-derived community information. The topology of the metabolic network, reconstructed from a species' genome sequence, provides insight into its metabolic environments and interactions with other microorganisms. Progress in the theoretical and experimental analysis of flux through metabolic networks paves the way for their application at the community level, contributing to understanding of material flows between and within species and their resilience toward perturbations. © 2010 Elsevier Ltd

Bioreduction of Sheep Carcasses Effectively Contains and Reduces Pathogen Levels under Operational and Simulated Breakdown Conditions

Options for the storage and disposal of animal carcasses are extremely limited in the EU after the introduction of the EU Animal By-products Regulations (ABPR; EC/1774/2002), leading to animosity within the livestock sector and the call for alternative methods to be validated. Novel storage technologies such as bioreduction may be approved under the ABPR provided that they can be shown to prevent pathogen proliferation. We studied the survival of Enterococcus faecalis, Salmonella spp., E. coli O157 and porcine parvovirus in bioreduction vessels containing sheep carcasses for approximately 4 months. The vessels were operated under two different scenarios: (A) where the water within was aerated and heated to 40 °C, and (B) with no aeration or heating, to simulate vessel failure. Microbial analysis verified that pathogens were contained within the bioreduction vessel and indeed reduced in numbers with time under both scenarios. This study shows that bioreduction can provide an effective and safe on-farm storage system for livestock carcasses prior to ultimate disposal. The findings support a review of the current regulatory framework so that bioreduction is considered for approval for industry use within the EU

Corrigendum: High representation of archaea across all depths in oxic and low-pH sediment layers underlying an acidic stream

In the original article, there was a mistake. The incorrect Figure 1 was published..

Temperature and water controls on vegetation emergence, microbial dynamics, and soil carbon and nitrogen fluxes in a high Arctic tundra ecosystem

Arctic tundra ecosystems contain 14% of the global soil carbon (C) store which is becoming vulnerable to decomposition. Arctic soil organic matter (SOM) contains large amounts of old, recalcitrant, high molecular weight (MW) C compounds which are protected from decomposition whilst soils remain frozen. Climatic change alters soil temperature and water regimes in the Arctic, however, the impact of these changes on C decomposition and storage is poorly understood. We investigated vegetation emergence, microbial dynamics and nutrient fluxes in response to snow melt on the high Arctic Svalbard archipelago using field and laboratory studies. Using bacterial and archaeal genetic material (16S rRNA) and ammonia-oxidising genes, microbial communities were quantified in transects across the active snow melt front. The effects of soil temperature and water content on SOM decomposition rates were measured using 14C-labelled low and high MW compounds. Vegetation and below-ground microbial communities, in the field, responded rapidly with peaks in nutrient availability and soil respiration observed within 72 h of snowmelt. Temperature strongly drives early growing season C dynamics in the Arctic. We suggest the nutrient peaks following snowmelt, coupled with higher levels of DNA in the subniveal zone are due to the decomposition of bacteria and archaea from previous years. We show, in the laboratory, when soils thaw, mineralisation of recalcitrant C (high MW) compounds was sensitive to soil water but not to increasing temperatures. In contrast, low MW compounds exhibited sensitivity to both temperature and soil water. We suggest that if future soil water content increases under climate change, high MW compounds could become more susceptible to decomposition, releasing more C to the atmosphere