Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation dependent and independent study of the grassland phyllosphere of a long-term warming field-experiment

Plant science

Crises and collective socio-economic phenomena: simple models and challenges

Financial and economic history is strewn with bubbles and crashes, booms and busts, crises and upheavals of all sorts. Understanding the origin of these events is arguably one of the most important problems in economic theory. In this paper, we review recent efforts to include heterogeneities and interactions in models of decision. We argue that the Random Field Ising model (RFIM) indeed provides a unifying framework to account for many collective socio-economic phenomena that lead to sudden ruptures and crises. We discuss different models that can capture potentially destabilising self-referential feedback loops, induced either by herding, i.e. reference to peers, or trending, i.e. reference to the past, and account for some of the phenomenology missing in the standard models. We discuss some empirically testable predictions of these models, for example robust signatures of RFIM-like herding effects, or the logarithmic decay of spatial correlations of voting patterns. One of the most striking result, inspired by statistical physics methods, is that Adam Smith's invisible hand can badly fail at solving simple coordination problems. We also insist on the issue of time-scales, that can be extremely long in some cases, and prevent socially optimal equilibria to be reached. As a theoretical challenge, the study of so-called "detailed-balance" violating decision rules is needed to decide whether conclusions based on current models (that all assume detailed-balance) are indeed robust and generic.Comment: Review paper accepted for a special issue of J Stat Phys; several minor improvements along reviewers' comment

<em>Rhodococcus pseudokoreensis</em> sp. nov. isolated from the rhizosphere of young M26 apple rootstocks.

The Gram-positive strain R79T, isolated from the rhizosphere of young M26 apple rootstocks, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the full-length 16S rRNA gene sequence revealed highest 16S rRNA gene sequence similarity to the type strains of Rhodococcus wratislaviensis (99.6%) and Rhodococcus opacus (99.2%) followed by Rhodococcus imtechensis (98.9%). All other 16S rRNA gene sequence similarities were below 98.65%. A phylogenomic tree calculated based on a whole-genome sequence also showed a distinct clustering with the type strain of Rhodococcus koreensis. Average nucleotide identity (ANI) values between whole-genome sequences of R79T and the closest related type strains were below 95% supported the novel species status. The DNA G + C content of R79T was 67.24% mol. Predominant fatty acids were C16:0, C15:0 and C17:1ω8c. The strain contained MK8-H2 as the major respiratory quinone. The polar lipid profile consists of diphosphatidylglycerol and phosphatidylethanolamine, as well as of some unidentified lipids. The peptidoglycan type of the strain is A1γ meso-diaminopimelic acid. Based on the obtained genotypic and phenotypic, including chemotaxonomic data, we conclude that R79T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus pseudokoreensis sp. nov. is proposed. The type strain is R79T (= DSM 113102T = LMG 32444T = CCM 9183T)

A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies

Yu J, Blom J, Glaeser SP, et al. A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. Journal of Biotechnology. 2017;261:2-9.The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics. In this manuscript, we review the most commonly used platforms and approaches for ortholog group analyses with a focus on their potential for phylogenetic and taxonomic research. Furthermore, we describe the latest improvements of the EDGAR platform for comparative genome analyses and present recent examples of its application for the phylogenomic analysis of different taxa. Finally, we illustrate the role of the EDGAR platform as part of the BiGi Center for Microbial Bioinformatics within the German network on Bioinformatics Infrastructure (de.NBI)

Paracoccus nototheniae sp. nov., isolated from a black rock cod fish (Notothenia coriiceps) from the Chilean Antarctic

An orange-pigmented, oxidase-positive bacterial strain (I-41R45(T)), isolated from the kidney of a black rock cod fish sampled in the Chilean Antarctic was studied in a polyphasic taxonomic investigation. Cells of the isolate were coccoid and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain I-41R45(T) with sequences of type strains of most closely related Paracoccus species showed highest sequence similarities to Paracoccus hibiscisoli (98.4 %), Paracoccus marcusii (98.3%), Paracoccus haeundaensis and Paracoccus carotinifaciens (both 98.2%). 16S rRNA gene sequence similarities to all other Paracoccus species were below 97%. The draft genome of strain I-41R45(T) had a size of 4.59 Mb with a DNA G+C content of 65.26 mol% and included the prediction and annotation of 4426 coding genes, 1973 protein-coding genes and 46 tRNAs. The fatty acid profile of strain I-41R45(T) consisted mainly of the major fatty acids C-18 : 1 omega 7c/omega 9t/omega 12t and C-18: 0, typical of the genus Paracoccus. DNA-DNA hybridizations between I-41R45(T) and type strains of P. hibiscisoli, P. marcusii and P. haeundaensis resulted in similarity values of 45% (reciprocal 26 %), 66% (reciprocal 61 %), and 29% (reciprocal 36 %), respectively. DNA-DNA hybridization results, together with the differentiating biochemical and chemotaxonomic properties, showed that strain I-41R45(T) represents a novel Paracoccus species, for which the name Paracoccus nototheniae sp. nov. (type strain I-41R45(T)=CCM 8875(T)=CIP 111632(T)), is proposed

Non-pathogenic <em>Rhizobium radiobacter</em> F4 deploys plant beneficial activity independent of its host <em>Piriformospora indica</em>.

The Alphaproteobacterium Rhizobium radiobacter F4 (RrF4) was originally characterized as an endofungal bacterium in the beneficial endophytic Sebacinalean fungus Piriformospora indica. Although attempts to cure P. indica from RrF4 repeatedly failed, the bacterium can easily be grown in pure culture. Here, we report on RrF4&rsquo;s genome and the beneficial impact the free-living bacterium has on plants. In contrast to other endofungal bacteria, the genome size of RrF4 is not reduced. Instead, it shows a high degree of similarity to the plant pathogenic R. radiobacter (formerly: Agrobacterium tumefaciens) C58, except vibrant differences in both the tumor-inducing (pTi) and the accessor (pAt) plasmids, which can explain the loss of RrF4&rsquo;s pathogenicity. Similar to its fungal host, RrF4 colonizes plant roots without host preference and forms aggregates of attached cells and dense biofilms at the root surface of maturation zones. RrF4-colonized plants show increased biomass and enhanced resistance against bacterial leaf pathogens. Mutational analysis showed that, similar to P. indica, resistance mediated by RrF4 was dependent on the plant&rsquo;s jasmonate-based induced systemic resistance (ISR) pathway. Consistent with this, RrF4- and P. indica-induced pattern of defense gene expression were similar. In clear contrast to P. indica, but similar to plant growth-promoting rhizobacteria, RrF4 colonized not only the root outer cortex but also spread beyond the endodermis into the stele. On the basis of our findings, RrF4 is an efficient plant growth-promoting bacterium