Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

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Diet rapidly and reproducibly alters the human gut microbiome

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

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Human gut microbiome viewed across age and geography

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.

/pdf/microbial-cellulose-utilization-fundamentals-and-4yec12qx1c.pdf

Microbial cellulose utilization: fundamentals and biotechnology.

The complete nucleotide sequence of a cryptic plasmid designated pBAW301, from the Gram-positive ruminal bacterium Ruminococcus flavefaciens R13e2, has been determined. This plasmid is 1768 bp in size and has an overall G+C content of 43.5%. Computer analysis of the sequence data revealed an open reading frame, ORF1 (256 amino acids), which is similar to the Rep protein of the Bacillus borstelensis plasmid pHT926. ORF1 is preceded by Shine-Dalgarno and Escherichia coli-10 and -35 like sequences. Nine smaller open reading frames showed no significant homologies to known protein sequences. Analysis of replication intermediates and the nucleotide sequence indicate that the plasmid does not replicate by a rolling-circle mode of replication similar to other plasmids from Gram-positive bacteria. Moreover, sequences typical of theta replication origins were not found in the nucleotide sequence of pBAW301. These data suggest that this plasmid either replicates by an as yet undescribed mechanism, or represents a new class of theta replicating plasmids.

Complete nucleotide sequence of a cryptic plasmid, pbaw301, from the ruminai anaerobe Ruminococcus flavefaciens R13e2

Reindeer in northern Norway experience large seasonal variations in access and quality of food. Pastures are often blocked by ice and snow during winter and reindeer are consequently exposed to periods of starvation. Supplementary feeding has become increasingly common during winter in the traditional reindeer husbandry in Norway. Transitional feeding may cause digestive problems that could be reduced by use of probiotics. This paper presents novel bacterial isolates from reindeer rumen contents, as characterized in a search for a probiotic for reindeer.

http://www.jafs.com.pl/pdf-73772-10553?filename=Novel rumen bacterial.pdf

Novel rumen bacterial isolates from reindeer (Rangifer tarandus tarandus)

The present disclosure provides methods for the conversion of hemicellulose into fermentable sugars using enzymes isolated from Prevotella bryantii. Hemicellulose-degrading enzymes include an endoxylanase, a β-xylosidase, a bifunctional β-xylosidase and β-glucosidase, a bifunctional arabinofuranosidase and β-xylosidase, a glucuronidase, and an acetyl xylan esterase. The enzymes can be used to release sugars present in hemicellulose for subsequent fermentation to produce value-added products such as ethanol.

Hemicellulose-degrading enzymes

The large-scale use of grains for bioenergy (ethanol) production is undesirable because it detracts from human and animal food supplies. Efficient fermentation of plant cell walls will facilitate the shift to “second generation,” cellulose-based bioenergy feedstocks, such as perennial grasses. Rumen microorganisms, which constitute a highly efficient system for cellulose fermentation, may point the way to economically feasible bioethanol production. The goal of this work is to characterize the diversity of fiberadherent rumen bacteria on three potential bioenergy feedstocks: corn stover, switchgrass (Panicum virgatum), and Miscanthus X giganteus. These feedstocks were incubated in live cows for 72 h, followed by DNA extraction (fibrous material and rumen fluid) and microbial community characterization by bacterial ARISA (automated ribosomal intergenic spacer analysis) and T-RFLP (terminal restriction fragment length polymorphism). In addition, subsamples of switchgrass were removed periodically over the course of a 72-h live incubation to investigate bacterial colonization dynamics. Fiber-adherent microbial biomass (indicated by total extractable DNA) increased rapidly over the first hour of incubation, and then slowly doubled over the course of the following 71 h. Final microbial biomass varied between  the feedstocks and between cows. The richness of bacterial phylotypes, assessed with ARISA, also varied by feedstock and cow, but the fiber-adherent communities were consistently more diverse than that of rumen fluid. The colonization of switch grass fibers occurred in several stages. Fiber associated bacteria increased from an initial 9 phylotypes to over 150 phylotypes after 2 h, but then richness and evenness dropped dramatically, fluctuating between 30 and 90 phylotypes for the duration. Both T-RFLP and ARISA indicated that fiber-associated communities were distinct from those of rumen fluid. Within each cow, different feedstocks accumulated different communities, but these differences tended to be smaller than  differences observed between cows. Thus, the colonization of plant fibers in the rumen is a dynamic process, and the composition of the fiber-associated microbiota depends both on the feedstock and on factors specific to each individual cow rumen.

Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumen

The mutually-beneficial interdependence of hydrogen-producing and hydrogen-utilizing bacteria was discovered by M. P. Bryant, M. J. Wolin and R. S. Wolfe at the University of Illinois in 1967. Base...

Interspecies Hydrogen Transfer and Its Effects on Global Transcript Abundance in Ruminococcus albus, a Predominant Fiber-Degrading Species in the Rumen

Roderick I. Mackie

Papers

Complete nucleotide sequence of a cryptic plasmid, pbaw301, from the ruminai anaerobe Ruminococcus flavefaciens R13e2

Novel rumen bacterial isolates from reindeer (Rangifer tarandus tarandus)

Hemicellulose-degrading enzymes

Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumen

Interspecies Hydrogen Transfer and Its Effects on Global Transcript Abundance in Ruminococcus albus, a Predominant Fiber-Degrading Species in the Rumen