The draft genome sequence of Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis, reveals genes associated with virulence and symbiosis.

Four percent of female Nasonia vitripennis carry the son-killer bacterium Arsenophonus nasoniae, a microbe with notably different biology from other inherited parasites and symbionts. In this paper, we examine a draft genome sequence of the bacterium for open reading frames (ORFs), structures and pathways involved in interactions with its insect host. The genome data suggest that A. nasoniae carries multiple type III secretion systems, and an array of toxin and virulence genes found in Photorhabdus, Yersinia and other gammaproteobacteria. Of particular note are ORFs similar to those known to affect host innate immune functioning in other bacteria, and four ORFs related to pro-apoptotic exotoxins. The genome sequences for both A. nasoniae and its Nasonia host are useful tools for examining functional genomic interactions of microbial survival in hostile immune environments, and mechanisms of passage through gut epithelia, in a whole organism context.

Characteristics of the genome of Arsenophonus nasoniae, son-killer bacterium of the wasp Nasonia.

We report the properties of a draft genome sequence of the bacterium Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis. The genome sequence data from this study are the first for a male-killing bacterium, and represent a microorganism that is unusual compared with other sequenced symbionts, in having routine vertical and horizontal transmission, two alternating hosts, and being culturable on cell-free media. The resulting sequence totals c. 3.5 Mbp and is annotated to contain 3332 predicted open reading frames (ORFs). Therefore, Arsenophonus represents a relatively large genome for an insect symbiont. The annotated ORF set suggests that the microbe is capable of a broad array of metabolic functions, well beyond those found for reproductive parasite genomes sequenced to date and more akin to horizontally transmitted and secondary symbionts. We also find evidence of genetic transfer from Wolbachia symbionts, and phage exchange with other gammaproteobacterial symbionts. These findings reflect the complex biology of a bacterium that is able to live, invade and survive multiple host environments while resisting immune responses.

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.

AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.

Ecological genomics in Daphnia: stress responses and environmental sex determination.

Ecological genomics is the study of adaptation of natural populations to their environment, and therefore seeks to link organism and population level processes through an understanding of genome organization and function. The planktonic microcrustacean Daphnia, which has long been an important system for ecology, is now being used as a genomic model as well. Here we review recent progress in selected areas of Daphnia genomics research. Production of parthenogenetic male offspring occurs through environmental cues, which clearly involves endocrine regulation and has also been studied as a toxicological response to juvenoid hormone analog insecticides. Recent progress has uncovered a putative juvenoid cis-response element, which together with microarray analysis will stimulate further research into nuclear hormone receptors and their associated transcriptional regulatory networks. Ecotoxicological studies indicate that mRNA profiling is a sensitive and specific research tool with promising applications in environmental monitoring and for uncovering conserved cellular processes. Rapid progress is expected to continue in these and other areas, as genomic tools for Daphnia become widely available to investigators.

A hot water supply as the source of Legionella pneumophila in incubators of a neonatology unit.

The humidification trays of five of seven incubators in a neonatology unit of a hospital were found to be colonized with Legionella pneumophila, serogroup 1. Bacteriological analysis of the water in the humidification trays showed very large numbers of heterotrophic bacteria, one of which also contained Pseudomonas aeruginosa. Two hot water systems supply the neonatology unit, either of which is used to add water to the humidification trays; one system (A) is maintained at about 60 degrees C, while the other system (B) is maintained at 45 degrees C. The latter was also found to be colonized with L. pneumophila, Sg1. Monoclonal antibody (Mab) subgrouping of the isolates, indicated that system B was the source of colonization of the humidification trays of the incubators.

Microbiological water quality in a large in-building, water recycling facility.

The Thames Water recycling plant at the Millennium Dome, London, reclaimed three sources of water: greywater from the washbasins, rainwater from the Dome roof and groundwater from a borehole on site. These were pre-treated separately, and the mixed stream filtered using ultrafiltration and reverse osmosis membranes. Monitoring for indicator microorganisms was undertaken throughout the plant and in the reclaimed water distribution system, as well as ad-hoc monitoring for the presence of pathogens in the raw waters. Treatment to the level of ultrafiltration was more than adequate to produce a water quality meeting existing worldwide reclaimed water guidelines for toilet flushing. Owing to the excellent quality of the water leaving the plant, no significant microbiological growth was observed in the reclaimed water distribution system during the year. The raw greywater exhibited a higher faecal bacterial load than the rainwater and groundwater, as predicted from more human contact (i.e. hand washing). Environmental strains of Legionella were observed in the three raw greywater samples analysed for pathogens, as was Cryptosporidium, Giardia and faecal enterococci. The rainwater had relatively high levels of faecal bacteria, probably of avian origin. Giardia was detected in one rainwater sample confirming the potential for this water source to contain pathogens.

Functional characterization of four metallothionein genes in Daphnia pulex exposed to environmental stressors.

We characterized the metallothionein genes (Mt1, Mt2, Mt3, and Mt4) in Daphnia pulex on both molecular and ecotoxicological level. We therefore conducted a bioinformatical analysis of the gene location and predicted protein sequence, and screened the upstream flanking region for regulatory elements. The number of these elements and their positions relative to the start codon varied strongly among the four genes and even among two gene duplicates (Mt1A and Mt1B), suggesting different roles of the four proteins in the organisms' response to stress. We subsequently conducted a chronic 16-day exposure of D. pulex to different environmental stressors (at sublethal levels causing approximately 50% reduction in reproduction). Based on prior knowledge, we exposed them to the metals Cd, Cu, and Ni, the moulting hormone hydroxyecdysone (20E), and the oxidative stressors cyanobacteria (Microcystis aeruginosa), and paraquat (Pq). We then compared mRNA expression levels of the four Mt genes under these stress conditions with control conditions in "The Chosen One" clone (TCO), for which the full genome was sequenced and annotated. All together, the mRNA expression results under the different stress regimes indicate that different Mt genes may play different and various roles in the response of D. pulex to stress and that some (but not all) of the differences among the four genes could be related to the pattern of regulatory elements in their upstream flanking region.

Presence of Legionella in London's water supplies.

Legionella occurs frequently (52 to 54%) in domestic water and cooling water inside commercial, industrial and health care buildings, and these types of water systems are now regarded as a normal habitat for Legionella. The factors that predispose a particular water system to colonization by these organisms are ill-defined, although it is fairly certain that biological and physicochemical environmental factors play an important role in allowing Legionella to multiply in the circulating water. It has been postulated that the organism may gain access to water systems inside buildings by one of three routes: contact with air through open points such as uncovered storage tanks or vents, ingress of soil or surface water during construction or repair, or intermittent seeding with organisms present in low numbers in the public water supply. Three studies in the USA have found Legionella in 0.4 to 8.8% of drinking-water samples, but these were not representative of the public supply network as a whole. The aim of this study was to determine, over a period of 1 year, the frequency of Legionella in London's drinking water--from the treatment plant through to the consumer's tap. To date, Legionella has not been isolated from raw river water entering London's treatment works or from treated water entering the distribution network. Sixty-two monitoring taps in buildings located in 21 supply areas have been sampled twice for Legionella; only 2 (2.4%) have proved positive during the autumn and winter of 1985/86. The strain found was L. pneumophila serotype 1, subgroup Olda, and the numbers ranged from 10(2) to 10(4)/l. Although the survey is incomplete, it is already clear that the public water supplies in London are not a source of strains of Legionella associated with disease.

The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure.

The small-subunit (SSU) ribosomal RNA (rRNA) gene of the Branchiopod crustacean, Daphnia pulex, was isolated from a phage library and subcloned into the plasmid pBluescript. Determination of the complete nucleotide sequence of this gene revealed it to be 2293 nt in length with a G + C content of 53.7%. This is the longest SSU rRNA gene yet reported from a crustacean. The predicted secondary structure of the rRNA is quite typical for eukaryotes except for length expansion in four regions that are known to be highly variable: V2, V4, V7, and V9. Increases in V4 and V7 were most notable. RT-PCR analysis of these two variable regions showed that they are present in the mature rRNA molecule. Potential secondary structures for these regions are proposed based on energetic criteria. Sequence simplicity analysis of V4 and V7 did not reveal the occurrence of clustered simple sequence motifs. This suggests that replication slippage may not be an important mechanism generating the length expansion in these regions as has been proposed for unusually long regions in insect SSU rRNA genes. On the other hand, there was a pronounced bias in nucleotide composition in the variable regions (G + C = 56.6% in V4 and 60% in V7) which is typical of long SSU rRNA genes in insects. Comparison of the lengths of regions V2, V4, V7, and V9 among diverse arthropods revealed that substantial increases in V4 and V7 tend to co-occur. This suggests the possibility of a functional relationship between these variable regions.

Distribution and persistence of Legionella in water systems.

The Legionellaceae are common aquatic organisms able to colonize man-made water systems. Inadequately maintained or seldom used systems provide ideal amplification sites, where the organisms grow and can be disseminated in aerosols. Legionellaceae can utilize, for growth, compounds leached from construction materials and the products of other organisms.

Microbiological evaluation of drinking water construction materials--comparison of two test procedures.

Materials used in contact with drinking water can impair water quality by supporting the growth of aquatic microorganisms. In order to prevent this problem several different test procedures have been developed but to date no comparative study of the performance of these methods has been published. During collaborative studies between the regional laboratories of the Thames Water Authority, London, and the Institute of Hygiene, University Bonn, duplicate samples of 11 PVC materials were exchanged and evaluated by the standard methods used in the United Kingdom (UK) and the Federal Republic of Germany (FRG). There was a good agreement between the results as assessed by the published criteria. When a stricter criterion for interpreting the results of the UK method was applied to the findings, a complete agreement between the methods was observed.

The systematics of North American Daphnia (Crustacea: Anomopoda): a molecular phylogenetic approach.

Despite extensive studies on the ecology and evolution of the freshwater microcrustacean Daphnia, there is little understanding of the evolutionary history of the genus. Past attempts at reconstructing phylogenetic relationships among Daphnia species have been highly controversial, mainly because of the poor taxonomy of the genus. However, following a revised taxonomy of the daphniid fauna of North America, we conducted a comprehensive appraisal of systematic relationships within the genus through the analysis of sequence diversity in 503 b.p. of the 12S rRNA gene of the mtDNA. The large sequence divergence among its 34 North American members indicates that the genus Daphnia originated during the Mesozoic, even though many lineages exhibit extreme morphological stasis. Results from both cladistic and phenetic analyses indicate the presence of three subgenera comprised of 15 species complexes. Only four of these lineages have shown active speciation over the past 3 Ma, suggesting that cladogenesis in the genus has been constrained. Our study also reveals that interspecific hybridization occurs between taxa which show very large sequence divergence (up to 14%), suggesting that reproductive isolation within the genus evolves slowly.

Treatment of water for aquatic bacterial growth studies.

The composition of a water is inextricably linked to its nutrient status and hence influences the behaviour of bacteria in artificial water systems. It has not yet been possible to devise a defined liquid medium representative of the complex composition of a treated water. Instead sterilized natural or distilled waters are used to study the growth or survival of aquatic bacteria in the laboratory. This has led to conflicting data and opposing opinions when the same water has proved toxic in some laboratory studies and growth-supporting in others. These differences may be explained by the variations in chemical compositions which occur when water is collected, transported and treated or stored in the laboratory. This study describes a simple, membrane filtration method of preparing a fresh sample of water collected from the environment or a building water system such that it is both sterile and chemically unaltered. The availability of such water may enhance understanding of the behaviour of bacteria in the aquatic environment.

Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation.

Although members of the crustacean genus Daphnia have been the target of much research, there is little understanding of the group's evolutionary history. We addressed this gap by inferring a phylogeny for one of the major species groups (longispina) using nucleotide sequence variation of a 525-bp segment of the mitochondrial 12S rDNA and allozyme variation at 21 loci. We identified the major lineages and their relationships, assessed the phylogenetic utility of the few morphological characters in the group, and examined Daphnia phylogeography. Nuclear and mtDNA phylogenies were generally concordant in recognizing the same four species complexes. An exception was the position of Daphnia galeata mendotae. The allozyme tree paired this species with the Daphnia rosea lineage, whereas the mtDNA trees grouped D. g. mendotae with Daphnia galeata galeata. This discordance was consistent with the reticulate evolution of nuclear genes supporting the hypothesis that D. g. mendotae represents a case of homoploid hybrid speciation. Striking morphological stasis in the longispina group was evidenced by its very limited morphological divergence over an estimated 100 MY, and by the unusual transitional saturation of the conservative 12S rRNA gene within a species group. Phylogenetic inference also provided evidence that similarities in cephalic crest shape likely resulted from convergent or parallel evolution among species. Endemism at the continental level was indicated for previously cosmopolitan species, but the estimated times of these divisions were inconsistent with vicariance events suggesting recent dispersal among continents. A significant role for divergent selection in new habitats during speciation was suggested by the neighboringly sympatric distributions of four sister species pairs over broad geographic areas.

Evolution of enterohemorrhagic Escherichia coli hemolysin plasmids and the locus for enterocyte effacement in shiga toxin-producing E. coli.

This study assessed the diversity of the enterohemorrhagic Escherichia coli (EHEC) hemolysin gene (ehxA) in a variety of Shiga toxin-producing E. coli (STEC) serotypes and the relationship between ehxA types and virulence markers on the locus for enterocyte effacement (LEE). Restriction fragment length polymorphism of the ehxA gene and flanking sequences and of the E. coli attaching and effacing (eae) gene was determined for 79 EHEC hemolysin-positive STEC isolates of 37 serotypes. Two main groups of EHEC hemolysin sequences and associated plasmids, which corresponded to the eae-positive and the eae-negative isolates, were delineated. Comparisons of the ehxA gene sequences of representative isolates of each group showed that this gene and the rest of the EHEC hemolysin operon are highly conserved. Digestion of an ehxA PCR product with the restriction endonuclease TaqI showed a unique restriction pattern for eae-negative isolates and another one for isolates of serotypes O157:H7 and O157:NM. A conserved fragment of 5.6 kb with four potential open reading frames was identified on the EHEC hemolysin plasmid of eae-positive STEC. Phylogenetic analysis of a subset of 27 STEC isolates, one enteropathogenic E. coli isolate, and a K-12 reference isolate showed that eae-positive STEC isolates all belong to a single evolutionary lineage and that the EHEC hemolysin plasmid and the ehxA gene evolved within this lineage without recent horizontal transfer. However, the eae gene and the LEE appear to have been transferred horizontally within this STEC lineage on several occasions. The reasons for the lack of transfer or maintenance of the LEE in other STEC lineages are not clear and require further study.

Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes.

Organisms producing resting stages provide unique opportunities for reconstructing the genetic history of natural populations. Diapausing seeds and eggs often are preserved in large numbers, representing entire populations captured in an evolutionary inert state for decades and even centuries. Starting from a natural resting egg bank of the waterflea Daphnia, we compare the evolutionary rates of change in an adaptive quantitative trait with those in selectively neutral DNA markers, thus effectively testing whether the observed genetic changes in the quantitative trait are driven by natural selection. The population studied experienced variable and well documented levels of fish predation over the past 30 years and shows correlated genetic changes in phototactic behavior, a predator-avoidance trait that is related to diel vertical migration. The changes mainly involve an increased plasticity response upon exposure to predator kairomone, the direction of the changes being in agreement with the hypothesis of adaptive evolution. Genetic differentiation through time was an order of magnitude higher for the studied behavioral trait than for neutral markers (DNA microsatellites), providing strong evidence that natural selection was the driving force behind the observed, rapid, evolutionary changes.

Water fittings as sources of Legionella pneumophila in a hospital plumbing system.

An extensive study of the plumbing systems in Kingston Hospital was made over the three years following the 1980 outbreak of legionnaires' disease. The introduction of chlorination and raising the water temperature controlled the outbreak but failed to decontaminate water outlets in the wards. Legionella pneumophila was isolated from rubber washers in shower fittings, and laboratory experiments demonstrated the ability of L pneumophila to grow in water in contact with these rubber components. All the components in the hospital's fittings were replaced with an approved type, and since then L pneumophila has not been isolated from water or components.

An outbreak of waterborne cryptosporidiosis in Swindon and Oxfordshire.

An outbreak of cryptosporidiosis resulted in 516 cases in Wiltshire and Oxfordshire. The outbreak caused widespread interest and led to an official inquiry. The majority of cases were in children; 8% of cases were admitted to hospital and the median duration of illness was 3 weeks. The geographical distribution of cases matched the distribution of water supplies from three treatment works and cryptosporidium oocysts were found at these works and in the treated water. Attack rates in electoral wards supplied by the three treatment works were significantly higher than in other wards. The cause of the outbreak appeared to be the failure of normal treatment to remove oocysts. Measures at the treatment works reduced the number of oocysts detected in treated water, after which the outbreak came to an end. The conclusion of the investigations was that cryptosporidiosis is a risk of conventionally treated public water supplies.