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

Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

Because a natural entity “species” cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper, Int. J. Syst. Bacteriol. 37:463-464, 1987), in which a DNA reassociation value of about 70% plays a dominant role. With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology needs to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationships at the strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.

Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology

For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.

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The diversity and biogeography of soil bacterial communities

Evolution of Protein Molecules

SUMMARY Diversity analysis of functional marker genes provides physiological insights into microbial guilds that perform an ecologically relevant process. However, it is challenging to group functional gene sequences to valid taxonomic units, primarily because of differences in the evolutionary rates of individual genes and possible horizontal gene transfer events. We developed a python script package named DAFGA, which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. As a result, DAFGA provides gene-specific parameter sets for operational taxonomic unit clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME. AVAILABILITY AND IMPLEMENTATION DAFGA is freely available with a manual and test data from https://github.com/outbig/DAFGA.

DAFGA: diversity analysis of functional gene amplicons.

Managed grasslands cover 35% of the European agricultural landscape (184 Mio ha). Within the next century temperature and atmospheric CO2 increase will significantly affect this ecosystem type. In Hesse (Germany) 0.6 °C warming of air temperatures occurred already since 1960. At our grassland field site, we will treat ring plots (14.5 m2) with elevated CO2 (+20%), air temperature warming (+2 °C) and a combination of these two factors throughout the year, (at least) for three years. We use deep rRNA sequencing (Illumina RNAseq) to reveal bacterial phylogenetic community composition, analyze plant species diversity (Shannon and Ellenberg index) and then integrate treatment response across these traditional disciplines. Finally, measurements of N2O, CH4 and CO2 emissions measured by closed chambers approach and automated systems (LI-COR 8100), support the balance of emitted CO2 equivalents. GHG emissions emerge from both plants and microbes in the soil, and are associated with changes in the community composition of soil microbes. Furthermore, plant functional types can affect ecosystem net GHG emission. We expect that elevated CO2 will improve the plant water-use efficiency, and soil moisture differences will decrease, with consequences for diversity1. Elevated air temperatures will most likely stimulate transpiration and increase the VPD (water vapour deficit) causing rather a soil drying effect. Hence we expect that warming combined with elevated CO2 will be antagonistic. Besides the drying effect, the warming will have an impact on phenology and aboveground biomass production of the vegetation, consequently affecting GHG emissions. As elevated CO2 in the 15 year long running Giessen-FACE led to a doubling of N2O emissions2, a slight increase in CO2 emissions3 and a reduction in CH4 oxidation, turning the system from a GHG sink to a GHG source, we want to test if the combined air temperature warming will enforce those processes or if it will drive antagonistic processes.

Permanent Managed Grassland at Future Climate Change: Is There a Connection between GHG Emission and Composition of Plant and Microbial Communities?

In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. ABSTRACT A high NH4+ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH4+ levels. Relative to 1 mM NH4+, a high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH4+ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K+ “salt-in” strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2− and, upon decreasing O2 tension, N2O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH4+ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. IMPORTANCE In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. This is due to the competition of CH4 and NH3 for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH4+ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH4+ load.

Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition

Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils.

A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidizedmarine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite.Elemental sulfur was disproportionated to hydrogen sulﬁde and sulfate. Growth was observed exclusively inthe presence of a hydrogen sulﬁde scavenger, e.g., ferrihydrite. In the absence of a scavenger, sulﬁde and sulfateproduction were observed but no growth occurred. Strain SB164P1 grew also by disproportionation of thio-sulfate and sulﬁte. With thiosulfate, the growth efﬁciency was higher in ferrihydrite-supplemented media thanin media without ferrihydrite. Growth coupled to sulfate reduction was not observed. However, a slight sulﬁdeproduction occurred in cultures incubated with formate and sulfate. Strain SB164P1 is the ﬁrst bacteriumdescribed that grows chemolithoautotrophically exclusively by the disproportionation of inorganic sulfurcompounds. Comparative 16S rDNA sequencing analysis placed strain SB164P1 into the delta subclass of theclass

Werner Liesack

Papers

DAFGA: diversity analysis of functional gene amplicons.

Permanent Managed Grassland at Future Climate Change: Is There a Connection between GHG Emission and Composition of Plant and Microbial Communities?

Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition

Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils.

SedimentIsolated from Marine Surface