The Dynamic Nature of Genomes Across the Tree of Life

Genomes are dynamic in lineages across the tree of life. Among bacteria and archaea, for example, DNA content varies through out life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. These observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual\u27s lifetime. Here, we synthesize information on three aspects of dynamic genomes from exemplars representing a diverse array of bacterial and archaeal lineages: 1) ploidy level variation, 2) epigenetic mechanisms, and 3) life cycle variation. For example, the Euryarchaeota analyzed to date are all polyploid, as is the bacterium Epulopiscium that contains up to tens of thousands of copies of its genome and reproduces by viviparity. The bacterium Deinococcus radiodurans and the archaeon Halobacterium sp. NRC-1 can repair a highly fragmented genome within a few hours. Moreover, bacterial genera such as Dermocarpella and Planctomyces reproduce by fission (i.e., generating many cells from one cell) and budding, respectively, highlighting the need for regulation of genome inheritance in these lineages. Combining these data with our previous work on widespread genome dynamics among eukaryotes, we hypothesize that dynamic genomes are a rule rather than the exception across the tree of life. Further, we speculate that all domains may have the ability to distinguish germline from somatic DNA and that this ability may have been present the last universal common ancestor

Are Microbes Fundamentally Different Than Macroorganisms? Convergence and a Possible Case for Neutral Phenotypic Evolution in Testate Amoeba (Amoebozoa: Arcellinida)

This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for ‘core Nebela’ species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses corroborate the prior ssu-rDNA findings of morphological convergence in test (shell) morphologies, as COI and ssu-rDNA phylogenies are concordant. Further, the monophyly of morphospecies is rejected using approximately unbiased tests. Given that testate amoebae are used as bioindicators in both palaeoecological and contemporary studies of threatened ecosystems such as bogs and fens, understanding the discordance between morphology and genetics in the hyalosphenids is essential for interpretation of indicator species. Further, while convergence is normally considered the result of natural selection, it is possible that neutrality underlies phenotypic evolution in these microorganisms

A global atlas of the dominant bacteria found in soil.

A global atlas of the dominant bacteria found in soil. Published in Science. http://science.sciencemag.org/content/359/6373/32

The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities.

Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.</div

Sleep behavior and daily activity levels in people with metabolic syndrome: effect of 1 year of metformin treatment

Impaired sleep and low daily activity levels increase the risk of developing metabolic syndrome (MS). Metformin (MET), an insulin sensitizer drug, is effective in regressing MS and has been recently studied as an adjuvant agent for managing sleep disorders. The present study aimed to assess whether 1,700 mg/day of MET treatment modifies sleep and daily activity levels in people with MS evaluated by Rest-Activity circadian Rhythm (RAR), which is the expression of 24 h of spontaneous activity parameters. A total of 133 subjects with MS, randomized into the MET (n = 65) or placebo (PLA, n = 68) group, underwent a clinical/anthropometric examination and carried out a continuous 7-day actigraphic monitoring to investigate sleep and RAR parameters at baseline and after 1 year of intervention. After 1 year of intervention, 105 subjects were analyzed. The MET group showed greater anthropometric and metabolic improvements compared with placebo, with a significant reduction in weight (p = 0.01), body mass index (p = 0.01), waist circumference (p = 0.03), and glucose (p &lt; 0.001). With regard to sleep parameters, the MET group showed a significant increase in actual sleep time (p = 0.01) and sleep efficiency (p = 0.04) compared with placebo. There were no significant changes reported in the RAR parameters. Our study suggests that MET might be used as an adjuvant treatment for sleep disorders in people with MS

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles

Transglutaminase 2 Contributes to Apoptosis Induction in Jurkat T Cells by Modulating Ca(2+) Homeostasis via Cross-Linking RAP1GDS1

BACKGROUND: Transglutaminase 2 (TG2) is a protein cross-linking enzyme known to be associated with the in vivo apoptosis program of T cells. However, its role in the T cell apoptosis program was not investigated yet. RESULTS: Here we report that timed overexpression of both the wild type (wt) and the cross-linking mutant of TG2 induced apoptosis in Jurkat T cells, the wt being more effective. Part of TG2 colocalised with mitochondria. WtTG2-induced apoptosis was characterized by enhanced mitochondrial Ca(2+) uptake. Ca(2+)-activated wtTG2 cross-linked RAP1, GTP-GDP dissociation stimulator 1, an unusual guanine exchange factor acting on various small GTPases, to induce a yet uncharacterized signaling pathway that was able to promote the Ca(2+) release from the endoplasmic reticulum via both Ins3P and ryanodine sensitive receptors leading to a consequently enhanced mitochondrial Ca(2+)uptake. CONCLUSIONS: Our data indicate that TG2 might act as a Ca(2+) sensor to amplify endoplasmic reticulum-derived Ca(2+) signals to enhance mitochondria Ca(2+) uptake. Since enhanced mitochondrial Ca(2+) levels were previously shown to sensitize mitochondria for various apoptotic signals, our data demonstrate a novel mechanism through which TG2 can contribute to the induction of apoptosis in certain cell types. Since, as compared to knock out cells, physiological levels of TG2 affected Ca(2+) signals in mouse embryonic fibroblasts similar to Jurkat cells, our data might indicate a more general role of TG2 in the regulation of mitochondrial Ca(2+) homeostasis

Bog-gling diversity : cryptic species of testate amoebae in local fens and bogs of western Massachusetts

Pt. 1. Microbes comprise most of the lineages in the tree of life, yet many are among the least understood organisms. Microbes include archaea, bacteria, and unicellular eukaryotes, and are important in understanding evolutionary history of life on Earth, and crucial sustaining many ecosystem processes. The morphological characters traditionally used to describe and characterize microbes, especially among lobose testate (shelled) amoebae, the focus organisms of this study, have often been found to not reflect genetic relatedness or evolutionary history. Thus, molecular analyses of gene sequences in combination with morphological descriptions are needed to assess phylogenetic and biogeographical patterns among testate amoebae within the order Arcellinda. Here, we assess (1) biogeography and distribution patterns at local sites, (2) the biodiversity within given taxa, and (3) the evolutionary relationships among the morphospecies. Our biogeographical analyses indicate there are complex distribution patterns both in terms of morphological and genetic species, including substantial short-term variability in testate community composition. In molecular analyses we use primers to target SSU-rDNA and actin genes of five morphospecies of testate amoebae. Seventy-eight individuals were used in building the SSU phylogeny (17 from Genbank, 33 from Nguyen (2011) and Lahr, unpublished, and 26 from this study). We compare reconstructions against previously published phylogenies of Arcellinda (namely, Hyalospheniidae). Our molecular results suggest that cryptic species exist within multiple Hyalospehniidae morphospecies and that morphospecies and genera are not monophyletic. Pt. 2. The perception of the bacterial and archaeal genomes as fixed within a species and throughout an individual\u27s lifetime still dominates textbooks and much of the literature. In contrast to this view, research increasingly shows that DNA content varies dramatically within individuals in a life cycle and among closely related individuals within a bacterial or archael species. In this review, we synthesize information on five categories of dynamic genome mechanisms within bacteria and archaea: (1) ploidy level variation, (2) repair of highly fragmented genomes, (3) epigenetics and genome rearrangement, and (4) life cycle variation. Model species with dynamic genomes are found in a diverse array of lineages within archaea and bacteria. For example, Escherichia coli is rarely monoploid, Epulopiscium contains up to tens of thousands of copies of its genome and reproduces by viviparity, and Deinococcus radiodurans can repair its shattered genome in a few hours. The number of discoveries of dynamic genome features is increasing rapidly as more genome analyses are undertaken in archaeal and bacterial domains. We hypothesize that (1) archaea and bacteria have the ability to distinguish germline from somatic DNA; (2) dynamic genomes are the rule rather than the exception across the tree of life; and (3) perhaps this is representative of the last universal common ancestor (LUCA)