Project description:Proteomics has become a popular method for investigating diet and cuisine in well-preserved ancient food remains, and calcified deposits like dental calculus. However, foodcrusts (the typically charred residues on the surface of pottery) have not been extensively explored as a source of dietary proteins. We remain ignorant of the impact of cooking and burial on the protein extractome, and crucially, the extent to which palaeoproteomic extractomes actually reflect the composition of input ingredients and cuisines. Therefore, through cooking and burial experiments we investigate the impact of these processes on protein preservation in foodcrusts and accompanying ceramics. Here, we aim to identify proteins that persist throughout the cooking process and become embedded in foodcrusts and ceramics, as well as those that persist through six months burial in soil, using ‘typical’ Mesolithic ingredients of Cervus elaphus (red deer), Salmo salar (Atlantic salmon) and Castanea sativa (sweet chestnut). Specifically, we seek to understand why particular proteins persist through cooking and burial. Hence we examine a range of physiochemical properties which have been theorised to aid protein preservation. The results reveal that proteins were much more likely to be detected in foodcrusts than ceramics using the methodology employed, with dietary proteins identified in all buried deer and salmon foodcrust replicates and most chestnut replicates, tentatively indicating that extraction of protein from ancient foodcrusts may be successful, while in contrast, dietary proteins were rarely identified in cooked or buried ceramics of any input ingredient. It was apparent that the input ingredient strongly influenced frequency of protein and peptide identifications, with chestnut surviving poorly compared to other ingredients, revealing that the detection of ingredients is biassed by the ingredients themselves. The results also reveal that degradation is not universal nor linear between proteins, indicating that protein physiochemical properties are at play. While certain properties appear to aid protein preservation such as hydrophobicity, none was seen to single-handedly explain why particular proteins/peptides survive in buried foodcrusts, with results indicating that certain properties act on protein preservation in complex ways requiring further investigation. These results have implications on archaeological analyses, by demonstrating the utility of foodcrusts as a good target sample for proteomics, while cautioning the interpretation of foodcrust extractomes: which should not be expected to reflect the initial input extractome.

Project description:Fire disturbances are becoming more common, more intense, and further-reaching across the globe, with consequences for ecosystem functioning. Importantly, fire can have strong effects on the soil microbiome, including community and functional changes after fire, but surprisingly little is known regarding the role of soil fire legacy in shaping responses to recent fire. To address this gap, we conducted a manipulative field experiment administering fire across 32 soils with varying fire legacies, including combinations of 1-7 historic fires and 1-33 years since most recent fire. We analyzed soil metatranscriptomes, determining for the first time how fire and fire legacy interactively affect metabolically-active soil taxa, the microbial regulation of important carbon (C), nitrogen (N) and phosphorus (P) cycling, expression of carbohydrate-cycling enzyme pathways, and functional gene co-expression networks. Experimental fire strongly downregulated fungal activity while upregulating many bacterial and archaeal phyla. Further, fire decreased soil capacity for microbial C and N cycling and P transport, and drastically rewired functional gene co-expression. Perhaps most importantly, we highlight a novel role of soil fire legacy in regulation of microbial C, N, and P responses to recent fire. We observed a greater number of functional genes responsive to the interactive effects of fire and fire legacy than those affected solely by recent fire, indicating that many functional genes respond to fire only under certain fire legacy contexts. Therefore, without incorporating fire legacy of soils, studies will miss important ways that fire shapes microbial roles in ecosystem functioning. Finally, we showed that fire caused significant downregulation of carbon metabolism and nutrient cycling genes in microbiomes under abnormal soil fire histories, producing a novel warning for the future: human manipulation of fire legacies, either indirectly through global change-induced fire intensification or directly through fire suppression, can negatively impact soil microbiome functional responses to new fires.

Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions. We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. We compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during exponential growth and at stationary phase, all in carefully controlled and replicated experimental conditions.

Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. we compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during lag phase, all in carefully controlled and replicated experimental conditions.

			Action	DRS
	SRR12354000_1.fastq.gz	Fastqsanger.gz
	SRR12354000_2.fastq.gz	Fastqsanger.gz
	SRR12354001_1.fastq.gz	Fastqsanger.gz
	SRR12354001_2.fastq.gz	Fastqsanger.gz
	SRR12354002_1.fastq.gz	Fastqsanger.gz

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