The contribution of species richness and composition to bacterial services.

Bacterial communities provide important services. They break down pollutants, municipal waste and ingested food, and they are the primary means by which organic matter is recycled to plants and other autotrophs. However, the processes that determine the rate at which these services are supplied are only starting to be identified. Biodiversity influences the way in which ecosystems function, but the form of the relationship between bacterial biodiversity and functioning remains poorly understood. Here we describe a manipulative experiment that measured how biodiversity affects the functioning of communities containing up to 72 bacterial species constructed from a collection of naturally occurring culturable bacteria. The experimental design allowed us to manipulate large numbers of bacterial species selected at random from those that were culturable. We demonstrate that there is a decelerating relationship between community respiration and increasing bacterial diversity. We also show that both synergistic interactions among bacterial species and the composition of the bacterial community are important in determining the level of ecosystem functioning.

Determining the effects of a spatially heterogeneous selection pressure on bacterial population structure at the sub-millimetre scale.

A key interest of microbial ecology is to understand the role of environmental heterogeneity in shaping bacterial diversity and fitness. However, quantifying relevant selection pressures and their effects is challenging due to the number of parameters that must be considered and the multiple scales over which they act. In the current study, a model system was employed to investigate the effects of a spatially heterogeneous mercuric ion (Hg(2+)) selection pressure on a population comprising Hg-sensitive and Hg-resistant pseudomonads. The Hg-sensitive bacteria were Pseudomonas fluorescens SBW25::rfp and Hg-resistant bacteria were P. fluorescens SBW25 carrying a gfp-labelled, Hg resistance plasmid. In the absence of Hg, the plasmid confers a considerable fitness cost on the host, with µ(max) for plasmid-carrying cells relative to plasmid-free cells of only 0.66. Two image analysis techniques were developed to investigate the structure that developed in biofilms about foci of Hg (cellulose fibres imbued with HgCl(2)). Both techniques indicated selection for the resistant phenotype occurred only in small areas of approximately 178-353 µm (manually defined contour region analysis) or 275-350 µm (daime analysis) from foci. Hg also elicited toxic effects that reduced the growth of both Hg-sensitive and Hg-resistant bacteria up to 250 µm from foci. Selection for the Hg resistance phenotype was therefore highly localised when Hg was spatially heterogeneous. As such, for this model system, we define here the spatial scale over which selection operates. The ability to quantify changes in the strength of selection for particular phenotypes over sub-millimetre scales is useful for understanding the scale over which environmental variables affect bacterial populations.

Heterogeneous selection in a spatially structured environment affects fitness tradeoffs of plasmid carriage in pseudomonads.

Environmental conditions under which fitness tradeoffs of plasmid carriage are balanced to facilitate plasmid persistence remain elusive. Periodic selection for plasmid-encoded traits due to the spatial and temporal variation typical in most natural environments (such as soil particles, plant leaf and root surfaces, gut linings, and the skin) may play a role. However, quantification of selection pressures and their effects is difficult at a scale relevant to the bacterium in situ. The present work describes a novel experimental system for such fine-scale quantification, with conditions designed to mimic the mosaic of spatially variable selection pressures present in natural surface environments. The effects of uniform and spatially heterogeneous mercuric chloride (HgCl(2)) on the dynamics of a model community of plasmid-carrying, mercury-resistant (Hg(r)) and plasmid-free, mercury-sensitive (Hg(s)) pseudomonads were compared. Hg resulted in an increase in the surface area occupied by, and therefore an increase in the fitness of, Hg(r) bacteria relative to Hg(s) bacteria. Uniform and heterogeneous Hg distributions were demonstrated to result in different community structures by epifluorescence microscopy, with heterogeneous Hg producing spatially variable selection landscapes. The effects of heterogeneous Hg were only apparent at scales of a few hundred micrometers, emphasizing the importance of using appropriate analysis methods to detect effects of environmental heterogeneity on community dynamics. Heterogeneous Hg resulted in negative frequency-dependent selection for Hg(r) cells, suggesting that sporadic selection may facilitate the discontinuous distribution of plasmids through host populations in complex, structured environments.

Progress towards understanding the fate of plasmids in bacterial communities.

Plasmid-mediated horizontal gene transfer influences bacterial community structure and evolution. However, an understanding of the forces which dictate the fate of plasmids in bacterial populations remains elusive. This is in part due to the enormous diversity of plasmids, in terms of size, structure, transmission, evolutionary history and accessory phenotypes, coupled with the lack of a standard theoretical framework within which to investigate them. This review discusses how ecological factors, such as spatial structure and temporal fluctuations, shape both the population dynamics and the physical features of plasmids. Novel data indicate that larger plasmids are more likely to be harboured by hosts in complex environments. Plasmid size may therefore be determined by environmentally mediated fitness trade-offs. As the correlation between replicon size and complexity of environment is similar for plasmids and chromosomes, plasmids could be used as tractable tools to investigate the influence of ecological factors on chromosomes. Parallels are drawn between plasmids and bacterial facultative symbionts, including the evolution of some members of both groups to a more obligate relationship with their host. The similarity between the influences of ecological factors on plasmids and bacterial symbionts suggests that it may be appropriate to study plasmids within a classical ecological framework.

Life in earth: the impact of GM plants on soil ecology?

The impact of changes incurred by agricultural biotechnology has led to concern regarding soil ecosystems and, rightly or wrongly, this has focused on the introduction of genetically modified (GM) crops. Soils are key resources, with essential roles in supporting ecosystems and maintaining environmental quality and productivity. The complexity of soils presents difficulties to their inclusion in the risk assessment process conducted for all GM plants. However, a combined approach, informed by both soil ecology and soil quality perspectives, that considers the impacts of GM crops in the context of conventional agricultural practices can provide a regulatory framework to ensure the protection of soils without being overly restrictive.

Distribution of repC plasmid-replication sequences among plasmids and isolates of Rhizobium leguminosarum bv. viciae from field populations.

The distribution of four classes of related plasmid replication genes (repC) within three field populations of Rhizobium leguminosarum in France, Germany and the UK was investigated using RFLP, PCR-RFLP and plasmid profile analysis. The results suggest that the four repC classes are compatible: when two or more different repC sequences are present in a strain they are usually associated with different plasmids. Furthermore, classical incompatibility studies in which a Tn5-labelled plasmid with a group IV repC sequence was transferred into field isolates by conjugation demonstrated that group IV sequences are incompatible with each other, but compatible with the other repC groups. This supports the idea that the different repC groups represent different incompatibility groups. The same field isolates were also screened for chromosomal (plac12) and symbiotic gene (nodD-F region) variation. Comparison of these and the plasmid data suggest that plasmid transfer does occur within field populations of R. leguminosarum but that certain plasmid-chromosome combinations are favoured.

Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet.

The plasmid pQBR103 was found within Pseudomonas populations colonizing the leaf and root surfaces of sugar beet plants growing at Wytham, Oxfordshire, UK. At 425 kb it is the largest self-transmissible plasmid yet sequenced from the phytosphere. It is known to enhance the competitive fitness of its host, and parts of the plasmid are known to be actively transcribed in the plant environment. Analysis of the complete sequence of this plasmid predicts a coding sequence (CDS)-rich genome containing 478 CDSs and an exceptional degree of genetic novelty; 80% of predicted coding sequences cannot be ascribed a function and 60% are orphans. Of those to which function could be assigned, 40% bore greatest similarity to sequences from Pseudomonas spp, and the majority of the remainder showed similarity to other gamma-proteobacterial genera and plasmids. pQBR103 has identifiable regions presumed responsible for replication and partitioning, but despite being tra+ lacks the full complement of any previously described conjugal transfer functions. The DNA sequence provided few insights into the functional significance of plant-induced transcriptional regions, but suggests that 14% of CDSs may be expressed (11 CDSs with functional annotation and 54 without), further highlighting the ecological importance of these novel CDSs. Comparative analysis indicates that pQBR103 shares significant regions of sequence with other plasmids isolated from sugar beet plants grown at the same geographic location. These plasmid sequences indicate there is more novelty in the mobile DNA pool accessible to phytosphere pseudomonas than is currently appreciated or understood.

Two dnaB genes are associated with the origin of replication of pQBR55, an exogenously isolated plasmid from the rhizosphere of sugar beet.

Plasmid pQBR55 ( approximately 149 kb) represents one of five (Groups I-V) genetically distinct transfer proficient, mercury resistance plasmid groups that have been observed in the phytosphere pseudomonad community at a single geographic location in Oxford, UK. A 4.9-kb HindIII fragment was cloned from pQBR55 (a Group III plasmid) that facilitates autonomous replication of a narrow host range cloning vector, pKIL29, in the non-permissive host Pseudomonas putida UWC1. Sequencing revealed that the fragment contains a unique tandem array of dnaB genes (one partial and one complete), a homologue of the traA gene of plasmid RP4 and several potential open reading frames with little homology to any known sequences. The fragment also contains: a short region of direct and indirect repeats, two sequences that resemble the consensus Escherichia coli DnaA box motif, an A+T rich region and evidence of a GC-skew inversion. All features associated with origins of replication. Two specific oligonucleotide primer pairs, one targeted at the tandem dnaB genes and the other at the dnaB-traA arrangement were used for PCR analysis of other plasmids isolated from the same field site. PCR generated amplification products were only amplified from Group III plasmids (defined by RFLP typing) but not from plasmids belonging to Group I, II, IV or V. The nucleotide sequences of the amplified fragments were identical to those of pQBR55, even though the other Group III plasmids had distinct RFLP patterns. The results of a more general PCR screen, using primers to amplify a 389-bp fragment of all described pseudomonad dnaB genes, suggests that closely related dnaB sequences are only associated with Group III plasmids.

Identification and analysis of rhizobial plasmid origins of transfer.

Twelve Rhizobium leguminosarum isolates from France, Germany and the UK, each carrying between four and seven plasmids, were screened by PCR using primers designed to amplify partial traA and traC genes and the intergenic spacer (igs) between them, which is expected to contain oriT (the nick site for conjugal transfer). Five strains, 1062, RES-2, RES-6, RES-7 and RES-9, generated oriT-containing PCR fragments. Sequencing identified three types that are related to but different from other rhizobial plasmid oriT sequences in the database. Sequence comparisons revealed conserved motifs in the igs, including a 14-bp putative nic site, a stem-loop and a tra box. The RES-2, RES-6 and RES-9 PCR products were used as probes in Southern hybridisation studies to screen the 12 strains for related sequences. Eleven strains contain at least one homologous sequence, but of the 64 plasmids present among the 12 strains only 17 hybridised to the oriT probes. Four sequence variants of the repC plasmid replication initiation gene have previously been described in these strains, but there is no correlation between repC and oriT sequence distributions, and there is evidence for recombination to generate different repC-oriT combinations. Three plasmids, pYK32, pYK36 and pYK39, containing the oriT amplified from RES-2, RES-6 and RES-9, respectively, were constructed for functional analysis of the oriT sequence variation. Each plasmid was transformed into R. leguminosarum strains 1062, RES-2 and RES-9 to generate nine donor-plasmid combinations, and their mobilisation frequencies into Escherichia coli and Agrobacterium tumefaciens measured following biparental matings. All three plasmid constructs were mobilised at a similar frequency (10(-7) to 10(-8) per recipient) by each donor strain, suggesting that there is no discrimination by the transfer proteins between the different oriT sequences.

Enzymological and physiological consequences of restructuring the lipoyl domain content of the pyruvate dehydrogenase complex of Escherichia coli.

The core-forming lipoate acetyltransferase (E2p) subunits of the pyruvate dehydrogenase (PDH) complex of Escherichia coli contain three tandemly repeated lipoyl domains although one lipoyl domain is apparently sufficient for full catalytic activity in vitro. Plasmids containing IPTG-inducible aceEF-IpdA operons which express multilip-PDH complexes bearing one N-terminal lipoyl domain and up to seven unlipoylated (mutant) domains per E2p chain, were constructed. Each plasmid restored the nutritional lesion of a strain lacking the PDH complex and expressed a sedimentable PDH complex, although the catalytic activities declined significantly as the number of unlipoylated domains increased above four per E2p chain. It was concluded that the extra domains protrude from the 24-meric E2p core without affecting assembly of the E1p and E3 subunits, and that the lipoyl cofactor bound to the outermost domain can participate successfully at each of the three types of active site in the assembled complex. Physiological studies with two series of isogenic strains expressing multilip-PDH complexes from modified chromosomal pdh operons (pdhR-aceEF-IpdA) showed that three lipoyl domains per E2p chain is optimal and that only the outermost domain need be lipoylated for optimal activity. It is concluded that the reason for retaining three lipoyl domains is to extend the reach of the outermost lipoyl cofactor rather than to provide extra cofactors for catalysis.

Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands.

Transferable antibiotic resistance in Haemophilus influenzae was first detected in the early 1970s. After this, resistance spread rapidly worldwide and was shown to be transferred by a large 40- to 60-kb conjugative element. Bioinformatics analysis of the complete sequence of a typical H. influenzae conjugative resistance element, ICEHin1056, revealed the shared evolutionary origin of this element. ICEHin1056 has homology to 20 contiguous sequences in the National Center for Biotechnology Information database. Systematic comparison of these homologous sequences resulted in identification of a conserved syntenic genomic island consisting of up to 33 core genes in 16 beta- and gamma-Proteobacteria. These diverse genomic islands shared a common evolutionary origin, insert into tRNA genes, and have diverged widely, with G+C contents ranging from 40 to 70% and amino acid homologies as low as 20 to 25% for shared core genes. These core genes are likely to account for the conjugative transfer of the genomic islands and may even encode autonomous replication. Accessory gene clusters were nestled among the core genes and encode the following diverse major attributes: antibiotic, metal, and antiseptic resistance; degradation of chemicals; type IV secretion systems; two-component signaling systems; Vi antigen capsule synthesis; toxin production; and a wide range of metabolic functions. These related genomic islands include the following well-characterized structures: SPI-7, found in Salmonella enterica serovar Typhi; PAP1 or pKLC102, found in Pseudomonas aeruginosa; and the clc element, found in Pseudomonas sp. strain B13. This is the first report of a diverse family of related syntenic genomic islands with a deep evolutionary origin, and our findings challenge the view that genomic islands consist only of independently evolving modules.