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Aroney, S.

Publications and source records attributed to Aroney, S..

4 recordsLinked to original sources

Mobile genetic elements that shape microbial diversity and functions inthawing permafrost soils

The worlds ecosystems are shaped by microbiota. Their niches and their impacts depend on functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, quantitative field data on the rates and impacts of MGE activity remains scarce. Here we leverage large-scale soil meta-omic data to develop and apply analytics for studying MGEs in complex natural systems. In our model permafrost-thaw ecosystem, Stordalen Mire, we identify [~]2.1 million MGE recombinases across 89 microbial phyla to assess ecological distributions, affected functions, past mobility, and current activity. This revealed MGEs shaping natural genetic diversity via differential impacts on major phyla; affecting a wide range of functions, including diverse regulatory and metabolic genes affecting carbon flux and nutrient cycling; and moving at rates that should significantly influence the realized functional profiles of natural microbiomes. These findings and this systematic meta-omic framework open new avenues to better investigate MGE diversity, activity, mobility, and impacts in nature.

microbiology↗

Microflora Danica: the atlas of Danish environmental microbiomes

The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes in natural and human associated environments. Recent large-scale metagenome surveys record the variety of microbial life in the oceans1, wastewater2, human gut3,4, and earth5,6, with compilations encompassing thousands of public datasets7-13. So far, large-scale microbiome studies either miss functional information or consistency in sample processing, and although they may cover thousands of locations, these are missing resolution, sparsely located, or lacking metadata. Here, we present Microflora Danica, an atlas of Danish environmental microbiomes, encompassing 10,686 shotgun metagenomes and 449 full-length 16S and 18S rRNA datasets linked to a detailed 5 level habitat classification scheme. We determine that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.

microbiology↗

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials

Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene also known as styrofoam, is among the most commonly produced plastics worldwide and is recalcitrant to microbial degradation. In this study, we assessed changes in the gut microbiome of superworms (Zophobas morio) reared on bran, polystyrene, or under starvation conditions over a three weeks time period. Superworms on all diets were able to complete their life cycle to pupae and imago, although superworms reared on polystyrene had minimal weight gains, resulting in lower pupation rates. The change in microbial gut communities from baseline differed considerably between diet groups, with polystyrene and starvation groups characterized by a loss of microbial diversity and the presence of opportunistic pathogens. Inferred microbial functions enriched in the polystyrene group included transposon movements, membrane restructuring, and adaptations to oxidative stress. We detected several encoded enzymes with reported polystyrene and styrene degradation abilities, supporting previous reports of polystyrene degrading bacteria in the superworm gut. By recovering metagenome-assembled genomes (MAGs) we linked phylogeny and functions and identified genera including Pseudomonas, Rhodococcus and Corynebacterium, that possess genes associated with polystyrene degradation. In conclusion, our results provide the first metagenomic insights into the metabolic pathways used by the gut microbiome of superworms to degrade polystyrene. Our results also confirm that superworms can survive on polystyrene feed, however, this diet has considerable negative impacts on host gut microbiome diversity and health. Impact StatementIncreasing plastic pollution is a major environmental problem, and a recently proposed way to counteract this trend is to embrace a circular economy, in which used materials are recycled, rather than disposed of. An important step to facilitate this process is to invent new approaches for upcycling of plastic waste to desirable consumer products. Microbial plastic degradation and conversion is likely to play a considerable part in shaping a circular economy, by engineering microbes or their enzymes to bio-upcycle plastic waste. A first step towards actualizing this goal is to identify microbes that can degrade polystyrene and to investigate the enzymes and pathways involved. Our study represents the first metagenomic analysis of an insect gut microbiome on a polystyrene diet. It identifies bacteria with polystyrene and styrene degrading abilities, and infers enzymes and pathways involved in these reactions. Therefore, our results contribute towards understanding microbial polystyrene degradation and will provide a base for future investigations into microbial upcycling of plastic waste.

microbiology↗

Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis

By analyzing successive lifestyle stages of a model Rhizobium-legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N2-fixing bacteroids and release from legume (pea) nodules. While only 27 genes are annotated as nif and fix in Rhizobium leguminosarum, we show 603 genetic regions (593 genes, 5 tRNAs and 5 RNA features) are required for the competitive ability to nodulate pea and fix N2. Of these, 146 are common to rhizosphere growth through to bacteroids. This large number of genes, defined as rhizosphere-progressive, highlights how critical successful competition in the rhizosphere is to subsequent infection and nodulation. As expected, there is also a large group (211) specific for nodule bacteria and bacteroid function. Nodule infection and bacteroid formation require genes for motility, cell envelope restructuring, nodulation signalling, N2 fixation, and metabolic adaptation. Metabolic adaptation includes urea, erythritol and aldehyde metabolism, glycogen synthesis, dicarboxylate metabolism and glutamine synthesis (GlnII). There are separate lifestyle adaptations specific to rhizosphere growth (17) and root colonization (23), distinct from infection and nodule formation. These results dramatically highlight the importance of competition at multiple stages of a Rhizobium-legume symbiosis. SignificanceRhizobia are soil-dwelling bacteria that form symbioses with legumes and provide biologically useable nitrogen as ammonium for the host plant. High-throughput DNA sequencing has led to a rapid expansion in publication of complete genomes for numerous rhizobia, but analysis of gene function increasingly lags gene discovery. Mariner-based transposon insertion sequencing (INSeq) has allowed us to characterize the fitness contribution of bacterial genes and determine those functionally important in a Rhizobium-legume symbiosis at multiple stages of development.

microbiology↗