Wiliam R. Mayberry

Bio: Wiliam R. Mayberry is an academic researcher from East Tennessee State University James H. Quillen College of Medicine. The author has contributed to research in topics: Mimosine & Synergistes jonesii. The author has an hindex of 1, co-authored 1 publications receiving 196 citations.

Novel division level bacterial diversity in a Yellowstone hot spring.

Abstract: A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609–1613, 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved or Bacteria-specific rDNA primers and cloned. Unique rDNA types among >300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (≥98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing δ-Proteobacteria. The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial diversity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of division level bacterial phylogenetic diversity is collated and summarized.

The rumen bacteria

Abstract: This chapter will deal mainly with the characteristics of bacteria from the rumen that have been successfully cultivated in the laboratory. For some ecosystems, particularly those dominated by slow-growing or specialized microorganisms, it has become clear that only a very small fraction (often <1%) of the total microbial diversity has been recovered by cultural methods (Amann et al., 1995) and that descriptions of the ecosystem based on the available isolated strains can be highly misleading. These discrepancies are apparent both from comparison of direct microscopic and culturable counts, and from direct analyses of ribosomal RNA sequence diversity. In the rumen, organisms surviving in significant numbers must have growth rates sufficient to counteract the constant dilution due to turnover of rumen contents, and there are indications that the discrepancies may be less extreme. Leedle et al (1982) found that the culturable count fluctuated with time after feeding between 14% and 74% of the direct microscopic count in the rumens of animals fed on two different diets. Since the viability of several rumen species is known to change upon starvation, the lower figure could partly reflect changes in the viability of known, culturable species. Thus it is to be hoped that the major obstacles to cultivation of the most numerous rumen bacteria have been overcome by the development of sufficiently rigorous anaerobic methods and of suitable isolation media. It remains likely, however, that some functionally important groups (e.g. obligate syntrophs) may not have been recovered; Mclnerney et al (1981) used co-culture with Desulfovibrio in the presence of sulphate to isolate a fatty acid-oxidizing bacterium similar to Syntrophomonas wolfei from bovine rumen contents.

Rumen microbial ecosystem

Abstract: The inhabitants of the rumen microbial eco-system, a complex consortium of different microbial groups living in symbiotic relationship with the host, act synergistically for the bioconversion of lignocellulosic feeds intovolatile fatty acids which serve as a source of energy for the animals. The constraints, imposed by the host and the feed consumed by the animal, under which these microbes have to function, have been discussed. The eco-system is specialized and buffered in a narrow range of pH, which helps the animal to maintain a very well stabilized eco-system which is not disturbed by the incoming microbial contaminants into the fermentation sac (rumen) through feed and water intake. The microbial ecosystem is well studied for the rumen of domesticated animals like cattle, sheep and goat, but it is poorly studied in buffalo and wild ruminants. The necessity to use molecular biology techniques for identification and characterization of rumen microbes has been emphasized in this review.

Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics

Abstract: The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as developing world. Rumen fermentation is unique in that efficient plant cell wall degradation relies on the cooperation between microorganisms that produce fibrolytic enzymes and the host animal that provides an anaerobic fermentation chamber. Increasing the efficiency with which the rumen microbiota degrades fiber has been the subject of extensive research for at least the last 100 years. Fiber digestion in the rumen is not optimal, as is supported by the fact that fiber recovered from feces is fermentable. This view is confirmed by the knowledge that mechanical and chemical pretreatments improve fiber degradation, as well as more recent research, which has demonstrated increased fiber digestion by rumen microorganisms when plant lignin composition is modified by genetic manipulation. Rumen microbiologists have sought to improve fiber digestion by genetic and ecological manipulation of rumen fermentation. This has been difficult and a number of constraints have limited progress, including: (a) a lack of reliable transformation systems for major fibrolytic rumen bacteria, (b) a poor understanding of ecological factors that govern persistence of fibrolytic bacteria and fungi in the rumen, (c) a poor understanding of which glycolyl hydrolases need to be manipulated, and (d) a lack of knowledge of the functional genomic framework within which fiber degradation operates. In this review the major fibrolytic organisms are briefly discussed. A more extensive discussion of the enzymes involved in fiber degradation is included. We also discuss the use of plant genetic manipulation, application of free-living lignolytic fungi and the use of exogenous enzymes. Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen.