Thrive or survive: prokaryotic life in hypersaline soils

Background: Soil services are central to life on the planet, with microorganisms as their main drivers. Thus, the evaluation of soil quality requires an understanding of the principles and factors governing microbial dynamics within it. High salt content is a constraint for life affecting more than 900 million hectares of land, a number predicted to rise at an alarming rate due to changing climate. Nevertheless, little is known about how microbial life unfolds in these habitats. In this study, DNA stable-isotope probing (DNA-SIP) with 18O-water was used to determine for the first time the taxa able to grow in hypersaline soil samples (EC e = 97.02 dS/m). We further evaluated the role of light on prokaryotes growth in this habitat. Results: We detected growth of both archaea and bacteria, with taxon-specific growth patterns providing insights into the drivers of success in saline soils. Phylotypes related to extreme halophiles, including haloarchaea and Salinibacter, which share an energetically efficient mechanism for salt adaptation (salt-in strategy), dominated the active community. Bacteria related to moderately halophilic and halotolerant taxa, such as Staphylococcus, Aliifodinibius, Bradymonadales or Chitinophagales also grew during the incubations, but they incorporated less heavy isotope. Light did not stimulate prokaryotic photosynthesis but instead restricted the growth of most bacteria and reduced the diversity of archaea that grew. Conclusions: The results of this study suggest that life in saline soils is energetically expensive and that soil heterogeneity and traits such as exopolysaccharide production or predation may support growth in hypersaline soils. The contribution of phototrophy to supporting the heterotrophic community in saline soils remains unclear. This study paves the way toward a more comprehensive understanding of the functioning of these environments, which is fundamental to their management. Furthermore, it illustrates the potential of further research in saline soils to deepen our understanding of the effect of salinity on microbial communities

Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing.

Background: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled “heavy” and the unlabelled “light” SIP fractions were sequenced. Results: An increase of the 16S rRNA copy numbers in the “heavy” fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified. Conclusions: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur

The effect of land-use change on soil CH4 and N2O fluxes: A global meta-analysis

Land-use change is a prominent feature of the Anthropocene. Transitions between natural and human-managed ecosystems affect biogeochemical cycles in many ways, but soil processes are among the least understood. We used a global meta-analysis (62 studies, 1670 paired comparisons) to examine effects of land conversion on soil–atmosphere fluxes of methane (CH4) and nitrous oxide (N2O) from upland soils, and determine soil and environmental factors driving these effects. Conversion from a natural ecosystem to any anthropogenic land use increased soil CH4 and N2O fluxes by 234 kg CO2-equivalents ha−1 y−1, on average. Reversion of managed ecosystems to that resembling natural ecosystems did not fully reverse those effects, even after 80 years. In general, neither the type of ecosystem converted, nor the type of subsequent anthropogenic land use, affected the magnitude of increase in soil emissions. Land-use changes in wetter ecosystems resulted in greater increases in CH4 fluxes, but reduced N2O fluxes. An interacting suite of soil variables influenced CH4 and N2O fluxes, with availability of inorganic nitrogen (that is, extractable ammonium and nitrate), pH, total carbon, and microclimate being strong mediators of effects of land-use change. In addition, time after a change in land use emerged as a critical factor explaining the effects of land-use change—with increased emissions of both greenhouse gases diminishing rapidly after conversion. Further research is needed to elucidate complex biotic and abiotic mechanisms that drive land-use change effects on soil greenhouse gas emissions, but particularly during this initial disturbance when emissions are greatest relative to native vegetation. Efforts to mitigate emissions will be severely hampered by this gap in knowledge

Soil bacterial community mediates the effect of labile carbon on methanogenic decomposition of soil organic matter

Input of plant material may strongly change decomposition rates of soil organic matter (SOM), i.e. causing priming effect (PE), but the underlying mechanisms are largely unknown. We found that rice straw addition in anoxic Fuyang (F) rice field soil stimulated CH4 production from SOM at the expense of CO2, whereas in Uruguay (U) soil it suppressed SOM degradation to CO2 plus CH4 (negative PE). Reciprocal inoculation experiments with non-sterile and sterile soils showed that the soils always displayed the effect of rice straw characteristic for the live microbial community rather than for the soil physicochemical properties. Pyrosequencing of 16S rRNA genes showed that bacterial communities in these soil samples were separated into two clusters (F and U). Symbiobacterium was abundant or dominant in microbiota from U soil, but negligible in those from F soil. Network analysis indicated that the bacterial populations involved in SOM decomposition were different between soils of F and U clusters; moreover, they were more tightly connected to methanogens in U than in F clusters. Ultimately, our results suggested that the PE of rice straw is mediated by the composition and activity of soil microbial community

Hypoxia induces dilated cardiomyopathy in the chick embryo: mechanism, intervention, and long-term consequences

Background: Intrauterine growth restriction is associated with an increased future risk for developing cardiovascular diseases. Hypoxia in utero is a common clinical cause of fetal growth restriction. We have previously shown that chronic hypoxia alters cardiovascular development in chick embryos. The aim of this study was to further characterize cardiac disease in hypoxic chick embryos. Methods: Chick embryos were exposed to hypoxia and cardiac structure was examined by histological methods one day prior to hatching (E20) and at adulthood. Cardiac function was assessed in vivo by echocardiography and ex vivo by contractility measurements in isolated heart muscle bundles and isolated cardiomyocytes. Chick embryos were exposed to vascular endothelial growth factor (VEGF) and its scavenger soluble VEGF receptor-1 (sFlt-1) to investigate the potential role of this hypoxia-regulated cytokine. Principal Findings: Growth restricted hypoxic chick embryos showed cardiomyopathy as evidenced by left ventricular (LV) dilatation, reduced ventricular wall mass and increased apoptosis. Hypoxic hearts displayed pump dysfunction with decreased LV ejection fractions, accompanied by signs of diastolic dysfunction. Cardiomyopathy caused by hypoxia persisted into adulthood. Hypoxic embryonic hearts showed increases in VEGF expression. Systemic administration of rhVEGF165 to normoxic chick embryos resulted in LV dilatation and a dose-dependent loss of LV wall mass. Lowering VEGF levels in hypoxic embryonic chick hearts by systemic administration of sFlt-1 yielded an almost complete normalization of the phenotype. Conclusions/Significance: Our data show that hypoxia causes a decreased cardiac performance and cardiomyopathy in chick embryos, involving a significant VEGF-mediated component. This cardiomyopathy persists into adulthood

A PALB2 mutation associated with high risk of breast cancer

Introduction: As a group, women who carry germline mutations in partner and localizer of breast cancer 2 susceptibility protein (PALB2) are at increased risk of breast cancer. Little is known about by how much or whether risk differs by mutation or family history, owing to the paucity of studies of cases unselected for family history.Methods: We screened 1,403 case probands for PALB2 mutations in a population-based study of Australian women with invasive breast cancer stratified by age at onset. The age-specific risk of breast cancer was estimated from the cancer histories of first- and second-degree relatives of mutation-carrying probands using a modified segregation analysis that included a polygenic modifier and was conditioned on the carrier case proband. Further screening for PALB2 c.3113G > A (W1038X) was conducted for 779 families with multiple cases of breast cancer ascertained through family cancer clinics in Australia and New Zealand and 764 population-based controls.Results: We found five independent case probands in the population-based sample with the protein-truncating mutation PALB2 c.3113G > A (W1038X); 2 of 695 were diagnosed before age 40 years and 3 of 708 were diagnosed when between ages 40 and 59 years. Both of the two early-onset carrier case probands had very strong family histories of breast cancer. Further testing found that the mutation segregated with breast cancer in these families. No c.3113G > A (W1038X) carriers were found in 764 population-based unaffected controls. The hazard ratio was estimated to be 30.1 (95% confidence interval (CI), 7.5 to 120; P A mutation appears to be associated with substantial risks of breast cancer that are of clinical relevance. © 2010 Southey et al.; licensee BioMed Central Ltd

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

Analysis of the microbial communities in soils of different ages following volcanic eruptions

Volcanism is a primary process of land formation. It provides a model for understanding soil-forming processes and the role of pioneer bacteria and/or archaea as early colonizers in those new environments. The objective of this study was to identify the microbial communities involved in soil formation. DNA was extracted from soil samples from the Llaima volcano in Chile at sites destroyed by lava in different centuries (1640, 1751, and 1957). Bacterial and archaeal 16S rRNA genes were analyzed using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing. Results showed that microbial diversity increased with soil age, particularly between the 1751 and 1640 soils. For archaeal communities, Thaumarchaeota was detected in similar abundances in all soils, but Euryarchaeota was rare in the older soils. The analysis of bacterial 16S rRNA genes showed high abundances of Chloroflexi (37%), Planctomycetes (18%), and Verrucomicrobia (10%) in the youngest soil. Proteobacteria and Acidobacteria were highly abundant in the older soils (16% in 1640 and 15% in 1751 for Acidobacteria; 38% in 1640 and 27% in 1751 for Proteobacteria). The microbial profiles in the youngest soils were unusual, with a high abundance of bacteria belonging to the order Ktedonobacterales (Chloroflexi) in the 1957 soil (37%) compared with the 1751 (18%) and 1640 (7%) soils. In this study, we show that there is a gradual establishment of the microbial community in volcanic soils following an eruption and that specific microbial groups can colonize during the early stages of recovery