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)

The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.

https://science.sciencemag.org/content/sci/307/5717/1915.full.pdf

Host-Bacterial Mutualism in the Human Intestine

Inhibition of anaerobic digestion process: A review

The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.

/pdf/metagenomic-analysis-of-the-human-distal-gut-microbiome-2y54zda7ut.pdf

Metagenomic Analysis of the Human Distal Gut Microbiome

Anaerobic degradation of recalcitrant compounds.

Anaerobic degradation of sodium dodecyl sulfate (SDS) by denitrifying bacteria

This study reports the ability of one hyperthermophilic and two thermophilic microorganisms to grow anaerobically by the reduction of chlorate and perchlorate. Physiological, genomic and proteome analyses suggest that the Crenarchaeon Aeropyrum pernix reduces perchlorate with a periplasmic enzyme related to nitrate reductases, but that it lacks a functional chlorite-disproportionating enzyme (Cld) to complete the pathway. Aeropyrum pernix, previously described as a strictly aerobic microorganism, seems to rely on the chemical reactivity of reduced sulfur compounds with chlorite, a mechanism previously reported for perchlorate-reducing Archaeoglobus fulgidus. The chemical oxidation of thiosulfate (in excessive amounts present in the medium) and the reduction of chlorite result in the release of sulfate and chloride, which are the products of a biotic-abiotic perchlorate reduction pathway in Ae. pernix. The apparent absence of Cld in two other perchlorate-reducing microorganisms, Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP, and their dependence on sulfide for perchlorate reduction is consistent with the observations made on Ar. fulgidus. Our findings suggest that microbial perchlorate reduction at high temperature differs notably from the physiology of perchlorate- and chlorate-reducing mesophiles and that it is characterized by the lack of a chlorite dismutase and is enabled by a combination of biotic and abiotic reactions.

/pdf/perchlorate-and-chlorate-reduction-by-the-crenarchaeon-2l501qn7qy.pdf

Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes

To demonstrate the contribution of atmospheric ammonium to soil acidification in acid forest soils, a field study with13N-ammonium as tracer was performed in an oak-birch forest soil. Monitoring and analysis of soil solutions from various depths on the13N-ammonium and15N-nitrate contents, showed that about 54% of the applied15N-ammonium was oxidized to nitrate in the forest floor. Over a period of one year about 20% of the15N remained as organic nitrogen in this layer. The percentage15N enrichment in ammonium and nitrate were in the same range in all the forest floor percolates, indicating that even in extremely acid forest soils (pH < 4) nitrate formation from ammonium can occur. Clearly, atmospheric ammonium can contribute to soil acidification even at low soil pH.

A field study on the fate of 15N-ammonium to demonstrate nitrification of atmospheric ammonium in an acid forest soil

Carboxydothermus hydrogenoformans is a thermophilic strictly anaerobic bacterium that catalyses the water gas shift reaction, the conversion of carbon monoxide with water to molecular hydrogen and carbon dioxide. The thermodynamically favorable growth temperature, compared to existing industrial catalytic processes, makes this organism an interesting alternative for production of cheap hydrogen gas suitable to fuel CO-sensitive fuel cells in a future hydrogen economy, provided sufficiently low levels of CO are reached. Here we study CO conversion and final CO levels in cultures of C. hydrogenoformans grown in batch cultures that were started with a 100% CO gas phase with and without removal of formed CO2. Final CO levels were 117 ppm without CO2 removal and below 2 ppm with CO2 removal. The Gibbs free energy change calculated with measured end concentrations and the detection of acetate suggest that C. hydrogenoformans shifted from a hydrogenogenic to an acetogenic metabolism.

/pdf/deep-conversion-of-carbon-monoxide-to-hydrogen-and-formation-3i7u5ms0mo.pdf

Alfons J. M. Stams

Papers

Anaerobic degradation of recalcitrant compounds.

Anaerobic degradation of sodium dodecyl sulfate (SDS) by denitrifying bacteria

Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes

A field study on the fate of 15N-ammonium to demonstrate nitrification of atmospheric ammonium in an acid forest soil

Deep Conversion of Carbon Monoxide to Hydrogen and Formation of Acetate by the Anaerobic Thermophile Carboxydothermus hydrogenoformans