Haloviruses HF1 and HF2 were isolated from the same saltern pond and are adapted to hypersaline conditions, where they infect a broad range of haloarchaeal species. The HF2 genome has previously been reported. The complete sequence of the HF1 genome has now been determined, mainly by PCR and primer walking. It was 75,898 bp in length and was 94.4% identical to the HF2 genome but about 1.8 kb shorter. A total of 117 open reading frames and five tRNA-like genes were predicted, and their database matches and characteristics were similar to those found in HF2. A comparison of the predicted restriction digest patterns based on nucleotide sequence with the observed restriction digest patterns of viral DNA showed that, unlike the case for HF2, some packaged HF1 DNA had cohesive termini. Except for a single base change, HF1 and HF2 were identical in sequence over the first 48 kb, a region that includes the early and middle genes. The remaining 28 kb of HF1 showed many differences from HF2, and the similarity of the two genomes over this late gene region was 87%. The abrupt shift in sequence similarity around 48 kb suggests a recent recombination event between either HF1 or HF2 and another HF-like halovirus that has swapped most of the right-end 28 kb. This example indicates there is a high level of recombination among viruses that live in this extreme environment.Our understanding of viral and prokaryotic evolution has been radically changed over the last 10 years as a result of the ability to sequence whole genomes of organisms, including a large number of viruses (3). One of the most striking discoveries is that viral genomes are often mosaics (22), consisting of many small genetic fragments from different sources yet making up a functional whole (17,38). Despite this mosaicism, the arrangement and order of genes (synteny), particularly within functional modules such as DNA packaging and virus structural genes, are often well conserved (2,4,17,18,21).About 204 prokaryotic viruses have been fully sequenced (National Center for Biotechnology Information [NCBI] database, December 2003), and many are related (for example, the dairy bacteriophages and the lambdoid phages). Comparison of related viruses is important as it can shed light on their evolution and structure-function relationships, but to adequately assess the breadth of virus diversity and the degree of genetic exchange between viruses, novel viruses from across the two prokaryotic domains need to be isolated and sequenced (13). While thousands of bacteriophages are known, it is unfortunate that only a small number of archaeal viruses have been isolated and few of these have had their genomes completely sequenced (20,24,(33)(34)(35)38). Most of these genome sequences are very different from each other (and from those of other viruses), but some are sufficiently close that comparisons can be made (e.g., viruses of Sulfolobus [36] and Methanobacterium [24]), and these have given some indication about how archaeal viruses have evolved.The first haloarchaeal virus t...

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Background: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra model in research. However existing research fails to consider a biologically meaningful underlying mathematical model for MINs or to address the possibility of multiple solutions. Results: In this paper we present IMPARO, a method for inferring microbial interactions through parameter optimisation. We use biologically meaningful models for both the abundance profile, as well as the MIN. We show how multiple MINs could be inferred with similar reconstructed abundance profile accuracy, and argue that a unique solution is not always satisfactory. Using our method, we successfully inferred clear interactions in the gut microbiome which have been previously observed in in-vitro experiments. Conclusions: IMPARO was used to successfully infer microbial interactions in human microbiome samples as well as in a varied set of simulated data. The work also highlights the importance of considering multiple solutions for MINs.

The productivity of forests is often considered to be limited by the availability of phosphorus (P). Knowledge of the role of organic and inorganic P in humid subtropical forest soils is lacking. In this study, we used chemical fractionation and 31 P nuclear magnetic resonance (NMR) spectroscopy to characterize the form of P and its distribution in undisturbed perhumid Taiwan false cypress (Chamaecyparis formosensis Matsum.) forest soils. The toposequence of transects was investigated for the humic layer from summit to footslope and lakeshore. The clay layer combined with a placic-like horizon in the subsoil may affect the distribution of soil P because both total P and organic P (P o) contents in all studied soils decreased with soil depth. In addition, P o content was negatively correlated with soil crystalline Fe oxide content, whereas inorganic P (P i) content was positively correlated with soil crystalline Fe oxide content and slightly increased with soil depth. Thus, P i may be mostly adsorbed by soil crystalline Fe oxides in the soils. Among all extractable P fractions, the NaOH-P o fraction appeared to be the major component, followed by NaHCO 3-P o ; the resin-P and HCl-P i fractions were lowest. In addition, we found no typical trend for P i and P o contents in soils with topographical change among the three sites. From the 31 P-NMR spectra, the dominant P o form in soils from all study sites was monoesters with similar spectra. The 31 P-NMR findings were basically consistent with those from chemical extraction. Soil formation processes may be the critical factor affecting the distribution of soil P. High precipitation and year-round high humidity may be important in the differentiation of the P species in this landscape.

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The productivity of forests is often considered to be limited by the availability of phosphorus (P). Knowledge of the role of organic and inorganic P in humid subtropical forest soils is lacking. In this study, we used chemical fractionation and 31P nuclear magnetic resonance (NMR) spectroscopy to characterize the form of P and its distribution in undisturbed perhumid Chamaecyparis forest soils. The toposequence of transects was investigated for the humic layer from summit to footslope and lakeshore. The clay layer combined with a placic-like horizon in the subsoil may affect the distribution of soil P because both total P and organic P (Po) contents in all studied soils decreased with soil depth. In addition, Po content was negatively correlated with soil crystalline Fe oxide content, whereas inorganic P (Pi) content was positively correlated with soil crystalline Fe oxide content and slightly increased with soil depth. Thus, Pi may be mostly adsorbed by soil crystalline Fe oxides in the soils. Among all extractable P fractions, the NaOH-Po fraction appeared to be the major component, followed by NaHCO3-Po; the resin-P and HCl-Pi fractions were lowest. In addition, we found no typical trend for Pi and Po contents in soils with topographical change among the three sites. From the 31P-NMR spectra, the dominant Po form in soils from all study sites was monoesters with similar spectra. The 31P-NMR findings were basically consistent with those from chemical extraction. Soil formation processes may be the critical factor affecting the distribution of soil P. High precipitation and year-round high humidity may be important in the differentiation of the P species in this landscape.

Motivation: Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in evolution. Shared orthologs between bacterial genomes have been used to measure their genome evolution. Here, organization of circular genomes is analyzed via distributions of shared orthologs between genomes. However, these distributions are often asymmetric and bimodal; to date, there is no joint distribution to model such data. This motivated us to develop a family of bivariate distributions with generalized von Mises marginals (BGVM) and its statistical inference.Results: A new measure based on circular grade correlation and the fraction of shared orthologs is proposed for association between circular genomes, and a visualization tool developed to depict genome structure similarity. The proposed procedures are applied to eight pairs of prokaryotes separated from domain down to species, and 13 mycoplasma bacteria that are mammalian pathogens belonging to the same genus. We close with remarks on further applications to many features of genomic organization, e.g. shared transcription factor binding sites, between any pair of circular genomes. Thus, the proposed procedures may be applied to identifying conserved chromosome backbones, among others, for genome construction in synthetic biology.Availability: All codes of the BGVM procedures and 1000+ prokaryotic genomes are available at http://www.stat.sinica.edu.tw/∼gshieh/bgvm.htm.Contact: gshieh@stat.sinica.edu.twSupplementary information: Supplementary data are available at Bioinformatics online.