Cryopreservation of a soil microbiome using a Stirling 1 cycle approach - a genomic assessment

Soil microbiomes are dynamic systems that respond to biotic and abiotic environmental factors such as those presented at seasonal scales or due to long-term anthropogenic regime shifts. These can affect the composition and function of microbiomes. Investigation of microbiomes can uncover hidden microbial roles in health and disease and discover microbiome-based interventions. Collections of soil samples are kept by various institutions in either a refrigerated or occasionally frozen state, but conditions are not optimised to ensure the integrity of soil microbiome. In this manuscript, we describe cryopreservation with a controlled rate cooler and estimate the genomic content of an exemplar soil sample before and after cryopreservation. The first hypothesis was to test the genomic integrity of the microbiome. We also enriched the soil sample with a liquid medium to estimate the growth of bacteria and compared their growth before and after cryopreservation. Sequence-based rRNA metabarcoding was used to demonstrate that the controlled rate cooler maintains intact the DNA content of the microbiome. Two methods of cryopreservation were applied and compared with control aliquots of soil. An optimised cryopreservation of soil samples is essential for the development of microbiome research in order to retain stable, functionally intact microbiomes. Our results showed that metabarcoding of 16S and ITS rRNA were useful methods to estimate successful cryopreservation. The soil microbiome after enrichment with liquid medium exhibited a similar response of cryopreserved soil and this was estimated with the comparison of the ten most abundant bacterial taxa. These findings support a successful process of cryopreservation and are promising for future use of this technology. To the best of our knowledge, this study is the first report of cryopreservation of soil using a Stirling cycle cooling approach

The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research

Plant microbiomes are the microbial communities essential to the functioning of the phytobiome—the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure. The UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated and open-access resource to enable the development of solutions to improve soil and crop health. Six economically important crops (Barley, Fava Bean, Oats, Oil Seed Rape, Sugar Beet and Wheat) are targeted, and the methods as well as data outputs will underpin research activity both in the UK and internationally. This manuscript describes the approaches being taken, from characterisation, cryopreservation and analysis of the crop microbiome through to potential applications. We believe that the model research framework proposed is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production.The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I—“Slash-and-Burn”) the community structures detected by automated ribosomal intergenic spacer analysis (ARISA) revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II—“Anthropogenic Soil”), the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP) differed among an Amazonian Dark Earth (ADE), black carbon (BC) and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU) richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria—24% ADE, 15% BC; Acidobacteria—10% ADE, 21% BC; Actinobacteria—7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes—3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the microbes