Contact and voter processes on the infinite percolation cluster as models of host-symbiont interactions

We introduce spatially explicit stochastic processes to model multispecies host-symbiont interactions. The host environment is static, modeled by the infinite percolation cluster of site percolation. Symbionts evolve on the infinite cluster through contact or voter type interactions, where each host may be infected by a colony of symbionts. In the presence of a single symbiont species, the condition for invasion as a function of the density of the habitat of hosts and the maximal size of the colonies is investigated in details. In the presence of multiple symbiont species, it is proved that the community of symbionts clusters in two dimensions whereas symbiont species may coexist in higher dimensions.Comment: Published in at http://dx.doi.org/10.1214/10-AAP734 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Symbiont diversity is not involved in depth acclimation in the Mediterranean sea whip Eunicella singularis

In symbiotic cnidarians, acclimation to depth and lower irradiance can involve physiological changes in the photosynthetic dinoflagellate endosymbiont, such as increased chlorophyll content, or qualitative modifications in the symbiont population in favour of better adapted strains. It has been argued that a lack of capacity to acquire new symbionts could limit the bathymetric distribution of the host species, or compromise its long-term survival in a changing environment. But is that always true? To address this question, we investigated the symbiont genetic diversity in Eunicella singularis, a Mediterranean sea whip species with a wide bathymetric distribution (10 to 50 m depth), which has recently suffered from mass mortalities after periods of abnormally high sea temperatures. We measured symbiont population densities and chlorophyll content in natural populations, and followed the response of the holobionts after reciprocal transplantations to deep and shallow depths. A total of 161 colonies were sampled at 2 depths (10 and 30 m) at 5 sites in the northwestern Mediterranean. All colonies harboured a single ribosomal Symbiodinium clade (A'), but a relatively high within-clade genetic diversity was found among and within colonies. This diversity was not structured by depth, even though the deeper colonies contained significantly lower population densities of symbionts and less chlorophyll. We did, however, reveal host-symbiont specificity among E. singularis and other Mediterranean cnidarian species. Transplantation experiments revealed a limit of plasticity for symbiont population density and chlorophyll content, which in turn questions the importance of the trophic role of Symbiodinium in E. singularis

Comparison of 16S rRNA gene sequences of genus Methanobrevibacter

BACKGROUND: The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter. RESULTS: The phylogenetic analysis of the genus based on 786 bp aligned region from fifty-four representative sequences of the 120 available sequences for the genus revealed seven multi-member groups namely, Ruminantium, Smithii, Woesei, Curvatus, Arboriphilicus, Filiformis, and the Termite gut symbionts along with three separate lineages represented by Mbr. wolinii, Mbr. acididurans, and termite gut flagellate symbiont LHD12. The cophenetic correlation coefficient, a test for the ultrametric properties of the 16S rRNA gene sequences used for the tree was found to be 0.913 indicating the high degree of goodness of fit of the tree topology. A significant relationship was found between the 16S rRNA sequence similarity (S) and the extent of DNA hybridization (D) for the genus with the correlation coefficient (r) for logD and logS, and for [ln(-lnD) and ln(-lnS)] being 0.73 and 0.796 respectively. Our analysis revealed that for this genus, when S = 0.984, D would be <70% at least 99% of the times, and with 70% D as the species "cutoff", any 16S rRNA gene sequence showing <98% sequence similarity can be considered as a separate species. In addition, we deduced group specific signature positions that have remained conserved in evolution of the genus. CONCLUSIONS: A very significant relationship between D and S was found to exist for the genus Methanobrevibacter, implying that it is possible to predict D from S with a known precision for the genus. We propose to include the termite gut flagellate symbiont LHD12, the methanogenic endosymbionts of the ciliate Nyctotherus ovalis, and rat feces isolate RT reported earlier, as separate species of the genus Methanobrevibacter

Genetic Diversity and Potential Function of Microbial Symbionts Associated with Newly Discovered Species of Osedax Polychaete Worms

We investigated the genetic diversity of symbiotic bacteria associated with two newly discovered species of Osedax from Monterey Canyon, CA, at 1,017-m (Osedax Monterey Bay sp. 3 "rosy" [Osedax sp. MB3]) and 381-m (Osedax Monterey Bay sp. 4 "yellow collar") depths. Quantitative PCR and clone libraries of 16S rRNA gene sequences identified differences in the compositions and abundances of bacterial phylotypes associated with the newly discovered host species and permitted comparisons between adult Osedax frankpressi and juveniles that had recently colonized whalebones implanted at 2,891 m. The newly discovered Osedax species hosted Oceanospirillales symbionts that are related to Gammaproteobacteria associated with the previously described O. frankpressi and Osedax rubiplumus (S. K. Goffredi, V. J. Orphan, G. W. Rouse, L. Jahnke, T. Embaye, K. Turk, R. Lee, and R. C. Vrijenhoek, Environ. Microbiol. 7:1369-1378, 2005). In addition, Osedax sp. MB3 hosts a diverse and abundant population of additional bacteria dominated by Epsilonproteobacteria. Ultrastructural analysis of symbiont-bearing root tissues verified the enhanced microbial diversity of Osedax sp. MB3. Root tissues from the newly described host species and O. frankpressi all exhibited collagenolytic enzyme activity, which covaried positively with the abundance of symbiont DNA and negatively with mean adult size of the host species. Members of this unusual genus of bone-eating worms may form variable associations with symbiotic bacteria that allow for the observed differences in colonization and success in whale fall environments throughout the world's oceans

Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host.

Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system

Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2

Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans(1,2). Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host(3-6). We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)(7,8) and has a genomic repertoire similar to that of rickettsial parasites(9,10), but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations(11-13). This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter

The potential of Symbiont Ba cteria in Melo melo Gastropod found in Pekalongan Waters as a source of MDR antibacterial active compound

The increasing resistance of many pathogenic microorganisms against antibiotics compounds creates an alarming issue in medical world. This concern has created research opportunities in new antibiotics compounds as alternative options. The gastropod Melo melo is a species whose main diet consists of other smaller gastropods. However, Melo-melo does not have any self-defense mechanism save for its thin shell. To protect itself from various pathogenic bacteria existing in its food, Melo melo produces secondary metabolites, which are suspected to contain bioactive compounds with antibacterial properties. This fact puts Melo melo as a marine biota with potential as a source of new antibacterial compounds. This research aims to discover the potency of symbiont bacteria in the gastropod Melo melo with capabilities in producing Multi-drug resistant (MDR) antibacterial compounds. Samples of Melo melo are collected from the vicinity of Pekalongan waters, Central Java, Indonesia. This research begins with the isolation of symbiont bacteria, screening of symbiont bacteria with potency in MDR antibacterial activities, antibacterial test, and isolation of MDR clinical pathogenic bacteria. These protocols are then followed by antibacterial sensitivity test, and identification of bacterial species active against MDR by biochemical test and molecular analysis. Molecular analyses are carried out sequentially by DNA extraction, DNA amplification by PCR, and DNA sequencing. Results of 16S rDNA are analyzed using Genetix program and then followed by sequence analysis of the 16S rDNA. In this research, 11 bacteria in Melo melo are isolated and there are 4 isolates which show antibacterial activities against MDR bacteria from Pseudomonas sp. and Enterobacter sp species. Molecular analysis of the most active isolates identifies that isolate PM 26 matches in characteristics with Brevibacterium celere strain KMM 3637 with 89% homology match. On the other hand, biochemical test shows that isolate PM 26 is identical with Bacillus sp. This research concludes that symbiont bacteria found in Melo melo possess antibacterial activities against bacteria of MDR strain

EXPLORATION OF BACTERIA Symbionts Mangrove Waste FOR THE PRODUCTION OF DECOMPOSTER

Mangrove waste comprises of naturally decomposed dead mangrove leaves, twigs, and branches. This research aims to determine the types of bacterial symbionts in mangrove waste with potency as anti-bacterial agents. These anti-bacterial agents will subsequently be used in the production of compost with bio-activators. The research process involves isolation of symbiont bacteria, identification for symbiont bacteria with potency as anti-bacterial agent, DNA extraction using High Pure PCR Temperature Preparation Kit (Roche), DNA amplification by PCR 16s rDNA, and DNA Sequencing. Resulting amplified 16S rDNA are analyzed and then sequenced using Genetix program. Symbionts with identified anti-bacterial properties are used in bio-activator production. Samples of Sargassum seaweed are treated separately with resulting bio-activator product from the research and other bio-activator products for nutritional content comparison. Four types of symbiont bacteria are identified as potential anti-bacterial agents, namely Pseudomonas sp., Flavobacterium sp., Acinetobacter sp., Bacillus subtilis. It is further found that bio-activator products from mangrove waste have better quality compared to those found in the market and non-bio activator added liquid organic fertilizers. Therefore, bio-activators from mangrove waste is a potential alternative as natural bio-activator product