Commensalism in an agroecosystem: hydraulic redistribution by deep-rooted legumes improves survival of a droughted shallow-rooted legume companion

We investigated commensalism of water use among annual shallow-rooted and perennial deep-rooted pasture legumes by examining the effect of hydraulic lift by Cullen pallidum (N.T.Burb.) J.W.Grimes and Medicago sativa on growth, survival and nutrient uptake of Trifolium subterraneum L. A vertically split-root design allowed separate control of soil water in top and bottom soil. Thirty-five days after watering ceased in the top tube, but soil remained at field capacity in the bottom tube, an increase in shallow soil water content by hydraulic lift was 5.6 and 5.9 g kg−1 soil overnight for C. pallidum and M. sativa, respectively. Trifolium subterraneum in this treatment maintained higher leaf water potentials (with M. sativa) or exhibited a slower decline (with C. pallidum) than without companion perennial plants; and shoot biomass of T. subterraneum was 56% (with C. pallidum) and 67% (with M. sativa) of that when both top and bottom tubes were at field capacity. Uptake of rubidium (a potassium analog) and phosphorus by T. subterraneum was not facilitated by hydraulic lift. Interestingly, phosphorus content was threefold greater, and shoot biomass 1.5–3.3-fold greater when T. subterraneum was interplanted with C. pallidum compared with M. sativa, although dry weight of C. pallidum was much greater than that of M. sativa. This study showed that interplanting with deep-rooted perennial legumes has benefited the survival of T. subterraneum.

An Ecological and Evolutionary Framework for Commensalism in Anthropogenic Environments

Acknowledgements We would like to thank Jean-Denis Vigne, members of the Searle lab, and SNEEB at Cornell University for a stimulating environment and many early discussions and comments. We would also like to thank Maeve McMahon for comments on the manuscript.

Molecular analysis of asymptomatic bacteriuria escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition

Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder.

Surface Proteins of Lactobacillus crispatus: Adhesive Properties and Cell Wall Anchoring

Bacterial surface-associated proteins are important in communication with the environment and bacteria-host interactions. In this thesis work, surface molecules of Lactobacillus crispatus important in host interaction were studied. The L. crispatus strains of the study were known from previous studies to be efficient in adhesion to intestinal tract and ECM. L. crispatus JCM 5810 possess an adhesive surface layer (S-layer) protein, whose functions and domain structure was characterized. We cloned two S-layer protein genes (cbsA; collagen-binding S-layer protein A and silent cbsB) and identified the protein region in CbsA important for adhesion to host tissues, for polymerization into a periodic layer as well as for attachment to the bacterial cell surface. The analysis was done by extensive mutation analysis and by testing His6-tagged fusion proteins from recombinant Escherichia coli as well as by expressing truncated CbsA peptides on the surface of Lactobacillus casei. The N-terminal region (31-274) of CbsA showed efficient and specific binding to collagens, laminin and extracellular matrix on tissue sections of chicken intestine. The N-terminal region also contained the information for formation of periodic S-layer polymer. This region is bordered at both ends by a conserved short region rich in valines, whose substitution to leucines drastically affected the periodic polymer structure. The mutated CbsA proteins that failed to form a periodic polymer, did not bind collagens, which indicates that the polymerized structure of CbsA is needed for collagen-binding ability. The C-terminal region, which is highly identical in S-layer proteins of L. crispatus, Lactobacillus acidophilus and Lactobacillus helveticus, was shown to anchor the protein to the bacterial cell wall. The C-terminal CbsA peptide specifically bound to bacterial teichoic acid and lipoteichoic acids. In conclusion, the N-terminal domain of the S-layer protein of L. crispatus is important for polymerization and adhesion to host tissues, whereas the C-terminal domain anchors the protein to bacterial cell-wall teichoic acids. Lactobacilli are fermentative organisms that effectively lower the surrounding pH. While this study was in progress, plasminogen-binding proteins enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were identified in the extracellular proteome of L. crispatus ST1. In this work, the cell-wall association of enolase and GAPDH were shown to rely on pH-reversible binding to the cell-wall lipoteichoic acids. Enolase from L. crispatus was functionally compared with enolase from L. johnsonii as well as from pathogenic streptococci (Streptococcus pneumoniae, Streptococcus pyogenes) and Staphylococcus aureus. His6-enolases from commensal lactobacilli bound human plasminogen and enhanced its activation by human plasminogen activators similarly to, or even better than, the enolases from pathogens. Similarly, the His6-enolases from lactobacilli exhibited adhesive characteristics previously assigned to pathogens. The results call for more detailed analyses of the role of the host plasminogen system in bacterial pathogenesis and commensalism as well of the biological role and potential health risk of the extracellular proteome in lactobacilli.

Cryptic species and Miocene diversification of Palaearctic naked-toed geckos (Squamata: Gekkonidae) in the Indian dry zone

We sampled Palaearctic naked-toed geckos from across their range in India and used two mitochondrial and two nuclear genes to reconstruct relationships within a global phylogeny. Published sequences of Peninsular Indian Hemidactylus allow us to contrast these two groups in dating analyses - providing insights into the history of the Indian dry zone. Palaearctic naked-toed geckos first moved onto the Indian Plate in the Oligocene, with higher-level diversification probably linked to collision of the Indian and Eurasian plates, and subsequent dispersal into-India and diversification with increasing Miocene aridity. An independent gekkonid radiation with species in the dry zone, Hemidactylus diversified during the same period in Peninsular India. Our results demonstrate that dry zone taxa across India may date back to at least the Miocene, with a potential historical climatic barrier between the Indus and Peninsular Indian Divisions. `Cyrtopodion' aravallense is revealed to be a complex with seven genetically and environmentally divergent lineages that began diversifying in the late Miocene, congruent with increased aridity in north-western India. This discovery of cryptic diversity in the Indian dry zone represents the first terrestrial vertebrate radiation from north-western central India and highlights how little we understand of the regions' biodiversity, emphasizing the need for systematic geographic sampling and multiline evidence to reveal true patterns of diversity. The ancestor of `Cyrtopodion' aravallense came into the nascent Indian dry zone in the Miocene and has since diversified, potentially in the absence of any sympatric scansorial rupicolous geckos. Cyrtopodion scabrum represents a unique case of commensalism and shows phylogeographic structure in its presumed native range. The taxonomic implications of our study include a number of undescribed species, recognition of `Cyrtopodion' as a distinct lineage and the non-monophyly of Altiphylax.

High-throughput identification of chemical inhibitors of E. coli Group 2 capsule biogenesis as anti-virulence agents.

Rising antibiotic resistance among Escherichia coli, the leading cause of urinary tract infections (UTIs), has placed a new focus on molecular pathogenesis studies, aiming to identify new therapeutic targets. Anti-virulence agents are attractive as chemotherapeutics to attenuate an organism during disease but not necessarily during benign commensalism, thus decreasing the stress on beneficial microbial communities and lessening the emergence of resistance. We and others have demonstrated that the K antigen capsule of E. coli is a preeminent virulence determinant during UTI and more invasive diseases. Components of assembly and export are highly conserved among the major K antigen capsular types associated with UTI-causing E. coli and are distinct from the capsule biogenesis machinery of many commensal E. coli, making these attractive therapeutic targets. We conducted a screen for anti-capsular small molecules and identified an agent designated "C7" that blocks the production of K1 and K5 capsules, unrelated polysaccharide types among the Group 2-3 capsules. Herein lies proof-of-concept that this screen may be implemented with larger chemical libraries to identify second-generation small-molecule inhibitors of capsule biogenesis. These inhibitors will lead to a better understanding of capsule biogenesis and may represent a new class of therapeutics.

Precious transition metals: the importance of Zn2+, Mn2+ and Cu2+ in the human pathogen Enterococcus faecalis

Dissertation presented to obtain the Ph.D degree in Biology

Biotic interactions recorded in shells of recent rhynchonelliform brachiopods from San Juan Island, USA

Biotic interactions between brachiopods and spionid polychaete worms, collected around San Juan Islands (USA), were documented using observations from live-collected individuals and traces of bioerosion found in dead brachiopod shells. Specimens of Terebratalia tranversa (Sowerby), Terebratulina unguicula (Carpenter), Laqueus californianus (Koch), and Hemithiris psittacea (Gmelin) were collected from rocky and muddy substrates, from sites ranging from 14.7-93.3 m in depth. Out of 1,131 specimens, 91 shells showed traces of bioerosion represented by horizontal tubes. Tubes are U-shaped, straight or slightly curved, sometimes branched, with both tube openings communicating externally. on internal surfaces of infested shells, blisters are observed. All brachiopod species yielded tubes, except for H. psittacea. Tubes are significantly more frequent on live specimens, and occur preferentially on larger, ventral valves. This pattern suggests selectivity by the infester rather than a taphonomic bias. Given the mode of life of studied brachiopods (epifaunal, sessile, attached to the substrate, lying on dorsal valve), ventral valves of living specimens should offer the most advantageous location for suspension-feeding infesters. Frequent infestation of brachiopods by parasitic spionids is ecologically and commercially noteworthy because farmed molluscs are also commonly infested by parasitic polychaetes. In addition, brachiopod shells are among the most common marine macroscopic fossils found in the Phanerozoic fossil record. From a paleontological perspective, spionid-infested brachiopod shells may be a prime target for studying parasite-host interactions over evolutionary time scales.

A new Fenestrulina (Bryozoa, Cheilostomata) commensal with tube-dwelling anemones (Cnidaria, Ceriantharia) in the tropical southwestern Atlantic

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

CLEANER SHRIMP (CARIDEA: PALAEMONIDAE) ASSOCIATED WITH SCYPHOZOAN JELLYFISH

Shrimp are found in association with many hosts (sponges, anthozoans, mollusks, echinoids, ascidians and fish). Shrimp are rarely observed in association with jellyfish. The interaction between the cleaner shrimp Periclimenes paivai and jellyfish is poorly known, with only one published report for Brazilian waters. We add new information about this association, based on field and laboratory observations. Shrimp were collected from three locations on the coast Of Sao Paulo State (Cananeia, Santos and Sao Sebastiao) and from two species of scyphozoan rnedusae: Chrysaora lactea and Lychnorhiza lucerna. We classify the association as facultative commensalism, since the shrimp gain protection and probably feed on mucus produced by the jelly fish. The maximum carapace length of the shrimp collected was 9.2 min. Medusa bel I diameter ranged between about 10 and 19 cm for C. lactea and between 4.5 and 25 cm for L. lucerna. We also provide a list of records of Periclimenes in association with different scyphornedUsae, and additional information on the size and coloration of P. paivai.

Effective carrying capacity and analytical solution of a particular case of the Richards-like two-species population dynamics model

We consider a generalized two-species population dynamic model and analytically solve it for the amensalism and commensalism ecological interactions. These two-species models can be simplified to a one-species model with a time dependent extrinsic growth factor. With a one-species model with an effective carrying capacity one is able to retrieve the steady state solutions of the previous one-species model. The equivalence obtained between the effective carrying capacity and the extrinsic growth factor is complete only for a particular case, the Gompertz model. Here we unveil important aspects of sigmoid growth curves, which are relevant to growth processes and population dynamics. (C) 2011 Elsevier B.V. All rights reserved.

A new Fenestrulina (Bryozoa, Cheilostomata) commensal with tube-dwelling anemones (Cnidaria, Ceriantharia) in the tropical southwestern Atlantic

A new species of cheilostome bryozoan, Fenestrulina commensalis n. sp., was collected in December 2008 by scuba at 5–10 meters depth at Guaibura Beach, Guarapari, Espírito Santo state, southeastern Brazil. The specimen was found associated with tubes of the cerianthid Pachycerianthus sp., representing the first commensal association between a bryozoan and a tube-dwelling anemone. Fenestrulina commensalis n. sp. is the third species of the genus found in Brazilian waters; it is distinguished from other Atlantic species of Fenestrulina by its small angular orificial condyles, a single oral spine and basal anchoring rhizoids arising from abfrontal pore chambers. Morphological adaptations to encrust the tubes of cerianthids include anchoring rootlets and weakly contiguous zooids. These morphological features allow the colony the flexibility to grow around the tube and feed relatively undisturbed by silt and detritus, being raised well above the softsediment substratum in which the tube-anemone grows.