Collaborative Research: Functional and Genomic Analysis of Polysymbiosis in the Wood-boring Bivalve Lyrodus pedicellatus

Each day massive quantities of wood and woody plant materials enter the oceans, providing resources upon which a large variety of marine organisms depend. However, the biological communities supported by marine wood are only poorly understood. Globally, the most important consumers of marine wood are wood-boring bivalves of the family Teredinidae (shipworms, primarily found above 150 m) and Pholadidae (subfamily Xylophagainae, primarily found in the deep sea, 150-8000 m). These clams depend on intracellular endosymbiotic bacteria (endocytobionts) to help them consume a substrate (lignocellulose) that cannot be utilized by most other animals. Two functions have been proposed for symbionts of wood-boring bivalves; 1) production of enzymes to facilitate lignocellulose digestion (xylotrophy) and 2) nitrogen fixation (diazotrophy) to supplement the host.s nitrogen-deficient diet. The purpose of the proposed research is to explore the physiological ecology of symbiotic xylotrophy in shipworms using molecular, biochemical and microbiological techniques. Three questions are foremost in this investigation; 1) What genetic variation occurs in symbiont populations within and between host species? 2) What is the quantitative contribution of symbionts to lignocellulose digestion and nitrogen fixation? and 3) What physical and biochemical mechanisms are involved in transfer of nutrients and enzymes between host and symbiont compartments

An Investigation of the Evolution of Autotrophic Endosymbioses in Bivalves By Comparative Molecular Phylogenetic Analysis of Host and Symbiont rRNA Sequences

Symbiotic associations between animals and bacteria are extremely diverse and commonplace in nature. In fact, it is difficult to find examples of animal species whose existence is not profoundly influenced by symbiotic associations with bacteria. For example, mitochondria (the structures within human cells that generate the energy for metabolic processes) are thought to have arisen from ancient bacteria that long ago formed a symbiotic association with the ancestor of all living animals. The support provided for this project will allow investigation of a type of symbiosis commonly found in clams and worms from deep-sea hydrothermal vents (marine hot springs) that can be used as a model system for studying the questions of how bacterial symbioses become established and what role they may play in the creation of new animal and bacterial species. This will be accomplished by comparing the primary DNA sequence (genetic code) of genes which are found in both symbionts and hosts. Computer analysis will be used to generate family trees demonstrating the relationships among symbionts and hosts. Comparison of the branching patterns of host and symbiont trees should reveal the point(s) in the lineages these hosts and symbionts first became associated and what impact their association has had on the diversification of the partner species. This understanding will lay the historical and conceptual foundation upon which future studies of the physiology and ecology of animal bacterial associations will be built. Symbiotic associations ranging from enteric bacteria in the human gut to nitrogen fixing bacteria associated with plant roots or luminous light organs in deep-sea fish provide a broad range of benefits to their hosts. Consequently, symbioses between bacteria and animals are critically important to our ecosystems, agriculture and health. This study will provide an experimental model system to address major questions about how bacterial/host symbioses came to exist and what role they have played in the history of life on earth

Composition and Function of a Novel Consortial Endosymbiosis in the Shipworm Lyrodus pedicellatus

Enormous quantities of wood and other woody plant materials(including leaves, bark, shoots, stems and nuts) are produced annually inthe environment. In fact, cellulose, the major component of woodymaterials, is thought to be the most abundant biological material on earth.This remarkably strong and enduring molecule is a polymer of glucose(sugar) linked by a type of chemical bond that makes it indigestible tomost living organisms. Therefore, this rich source of food energy isavailable to only a few animals (e.g., termites and ruminants) that candigest cellulose with the aid of microbes living in their guts.Surprisingly, some marine animals can also digest wood. The mostimportant group is the wood-boring clams, commonly known as shipworms. Unlike termites and ruminants, these animals lack microorganisms in their gut.Instead they harbor enormous numbers of symbiotic bacteria inside the cellsof their gills. These bacteria fall into at least four closely relatedfamilies based on DNA analyses. The PIs have proposed that these bacteriaproduce cellulolytic enzymes that are transported from the gills to thegut. The purpose of this investigation is to explore the diversity anddistribution of symbiont types in the shipworm gills, to determine if eachsymbiont type contributes different cellulolytic enzymes, and to discoverhow the host uses these bacterial products to exploit cellulose as a foodsource. These investigations should result in the discovery of newcellulolytic enzymes that may have industrial applications in such areas aspaper and textile processing and fuel (ethanol) production via biomassconversion of agricultural wastes. These efforts will also help the PIs tounderstand the physiology of symbiotic bacterial infections that arebeneficial rather than harmful to their hosts

Evolution of Endosymbiosis in (xylotrophic) Wood-Eating Bivalves

A grant has been awarded to Dr. Daniel L. Distel of the University of Maine to investigate the evolution of wood-boring clams. Though not well known to the general public, wood-boring clams are destructive species that may be considered the marine equivalent of termites. They include many diverse species that cause more than a billion dollars in damage to wooden structures, boats, and fishing gear annually in marine environments worldwide. The most destructive of these are the shipworms ; worm-like clams that burrow into and eat wood. These voracious wood eaters can destroy a twelve-inch diameter pier piling in less than one year\u27s time. Though they look like worms, molecular evidence suggests that they are closely related to the common steamer clam , a staple of New England cuisine. The purpose of this investigation is to use molecular data from several genes to reveal the evolutionary relationships of wood boring clams to other more common bivalves and to use these data to better understand how their destructive habits have evolved, including the role of associated bacteria.Although wood can be treated with broad-spectrum chemical biocides to control wood-borer damage, use of the most effective treatments has recently been restricted or banned in many states and nations due to environmental concerns. New environmentally sound control methods are critically needed, particularly in low-income coastal communities where wood is the only affordable marine construction material. Such control measures must be targeted specifically to wood-boring species to minimize ecological impact. Evolutionary studies will tell us how these nuisance species developed the ability to destroy wood and what makes them different from other more desirable and economically important marine species. This knowledge will be essential for developing control methods that are safe and highly specific to these destructive organisms

Collaborative Research: Toward Environmental Genomics: Can We Estimate Bacterial Diversity in the Ocean?

Environmental genomics, wherein the total genomic diversity of a natural community may be sampled and analyzed in an ecological context, remains an elusive goal. This is due, at least in part, to (I) a lack of reliable estimates of total community diversity and (II) a lack of information regarding the exact phylogenetic, genomic and ecological units measured by commonly used diversity estimators. Although ribosomal RNA approaches have provided the first steps towards diversity estimation, and are widely used as a proxy for unique bacterial types in natural populations, the genomic unit a ribotype measures remains largely unexplored. It is generally believed that ribotype is a poor indicator of ecotype because its slow molecular clock does not track many other genomic changes that are significant with respect to physiological functions and ecological roles. Further, there are reasons to believe microbes in typical natural environments encounter forces much different from those that shape genome evolution among the cultivated opportunists and pathogens that predominate in genomic studies. This project is using an approach that will allow the systematic sampling of environmental genomes by capturing large gene fragments anchored to ribosomal genes (the current standard biomarker for diversity estimation) as well as methods by which this approach can be extended to reassembling larger genome regions of uncultivated bacteria. The goals of this investigation are: 1) to estimate total ribotype diversity in a coastal marine environment taking into account new developments in understanding of PCR artifacts and new statistical approaches toward estimating sampling coverage, 2) to explore the relationship of ribotype diversity to genome diversity by sampling sequences contiguous to rRNA genes in abundant ribotypes, 3) to explore the mechanisms that may contribute to shaping genomes in natural communities, and 4) to continue development of methods to automate and extend the reach of genomic research in natural communities. This research will provide (I) boundaries for bacterial diversity estimates in the environment and (II) insights into how processes that are important in shaping the structure and dynamics of microbial communities may also be influential in shaping the evolution of microbial genomes

Expected Numbers of Proper Premises and Concept Intents

We compute the expected numbers of both formal concepts and proper premises in a formal context that is chosen uniformly at random among all formal contexts of given dimensions

Axiomatization of General Concept Inclusions from Finite Interpretations

Description logic knowledge bases can be used to represent knowledge about a particular domain in a formal and unambiguous manner. Their practical relevance has been shown in many research areas, especially in biology and the semantic web. However, the tasks of constructing knowledge bases itself, often performed by human experts, is difficult, time-consuming and expensive. In particular the synthesis of terminological knowledge is a challenge every expert has to face. Because human experts cannot be omitted completely from the construction of knowledge bases, it would therefore be desirable to at least get some support from machines during this process. To this end, we shall investigate in this work an approach which shall allow us to extract terminological knowledge in the form of general concept inclusions from factual data, where the data is given in the form of vertex and edge labeled graphs. As such graphs appear naturally within the scope of the Semantic Web in the form of sets of RDF triples, the presented approach opens up the possibility to extract terminological knowledge from the Linked Open Data Cloud. We shall also present first experimental results showing that our approach has the potential to be useful for practical applications

Teredinibacter turnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic c-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia: Teredinidae)

Author Posting. © Society for General Mircobiology, 2002. This article is posted here by permission of Society for General Mircobiology for personal use, not for redistribution. The definitive version was published in International Journal of Systematic Bacteriology 52 (2002): 2261-2269, doi:10.1099/ijs.0.02184-0.A cellulolytic, dinitrogen-fixing bacterium isolated from the gill tissue of a wood-boring mollusc (shipworm) Lyrodus pedicellatus of the bivalve family Teredinidae and 58 additional strains with similar properties, isolated from gills of 24 bivalve species representing 9 of 14 genera of Teredinidae, are described. The cells are Gram-negative, rigid, rods (0<4–0<6x3–6 lm) that bear a single polar flagellum. All isolates are capable of chemoheterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Xylan, pectin, carboxymethylcellulose, cellobiose and a variety of sugars and organic acids also support growth. Growth requires addition of combined nitrogen when cultures are vigorously aerated, but all isolates fix dinitrogen under microaerobic conditions. The pH, temperature and salinity optima for growth were determined for six isolates and are approximately 8<5, 30–35 °C and 0<3 M NaCl respectively. The isolates are marine. In addition to NaCl, growth requires elevated concentrations of Ca2M and Mg2M that reflect the chemistry of seawater. The DNA GMC content ranged from 49 to 51 mol%. Four isolates were identical with respect to small-subunit rRNA sequence over 891 positions compared and fall within a unique clade in the c-subclass of the Proteobacteria. Based on morphological, physiological and phylogenetic characteristics and specific symbiotic association with teredinid bivalves, a new genus and species, Teredinibacter turnerae gen. nov., sp. nov., is proposed. The type strain is T7902T (vATCC 39867TvDSM 15152T).This work was supported by grants from the National Science Foundation no. NSF DEB-9420051 and IBN- 9982982, the Maine Science and Technology Foundation's Center for Innovation in Biotechnology, and the University of Maine's Faculty Research program

<i>Teredinibacter waterburyi</i> sp. nov., a marine, cellulolytic endosymbiotic bacterium isolated from the gills of the wood-boring mollusc <i>Bankia setacea</i> (Bivalvia: Teredinidae) and emended description of the genus <i>Teredinibacter</i>

A cellulolytic, aerobic, gammaproteobacterium, designated strain Bs02T, was isolated from the gills of a marine wood-boring mollusc, Bankia setacea (Bivalvia: Teredinidae). The cells are Gram-stain-negative, slightly curved motile rods (2-5×0.4-0.6 µm) that bear a single polar flagellum and are capable of heterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Cellulose, carboxymethylcellulose, xylan, cellobiose and a variety of sugars also support growth. Strain Bs02T requires combined nitrogen for growth. Temperature, pH and salinity optima (range) for growth were 20 °C (range, 10-30 °C), 8.0 (pH 6.5-8.5) and 0.5 M NaCl (range, 0.0-0.8 M), respectively when grown on 0.5 % (w/v) galactose. Strain Bs02T does not require magnesium and calcium ion concentrations reflecting the proportions found in seawater. The genome size is approximately 4.03 Mbp and the DNA G+C content of the genome is 47.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences, and on conserved protein-coding sequences, show that strain Bs02T forms a well-supported clade with Teredinibacter turnerae. Average nucleotide identity and percentage of conserved proteins differentiate strain Bs02T from Teredinibacter turnerae at threshold values exceeding those proposed to distinguish bacterial species but not genera. These results indicate that strain Bs02T represents a novel species in the previously monotypic genus Teredinibacter for which the name Teredinibacter waterburyi sp. nov. is proposed. The strain has been deposited under accession numbers ATCC TSD-120T and KCTC 62963T