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

This paper considers the structure of freshwater phytoplankton assemblages and promotes a scheme of vegetation recognition', based upon the functional associations of species represented in the plankton. These groups are often polyphyletic, recognizing commonly shared adaptive features, rather than common phylogeny, to be the key ecological driver. Thirty-one such associations are outlined and the basic pattern of their distinctive ecologies is outlined. An invitation to other plankton scientists to assist in the development of this scheme is issued.

Towards a functional classification of the freshwater phytoplankton

The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.

Ecology of prokaryotic viruses

Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.

A Guide to the Natural History of Freshwater Lake Bacteria

The ecology of Cytophaga–Flavobacteria in aquatic environments

Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4–6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (� BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing

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Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition

Activity of extracellular acid phosphatases was measured at single-cell level in bacterioplankton groups defined by their morphology and size, in acidified mountain Lake Certovo, during the 2003 season, with a method based on use of the substrate ELF97 phosphate which provides fluorescent precipitates upon hydrolysis by phosphatases. The bacterial cell-associated precipitates were quantified by image analysis. A specific, conspicuous, apparently homogeneous morphotype of curved cells of approximately 5 microm average length, despite its low total biomass (average of 4%), contributed significantly (in average by 31%) to the total bacterioplankton phosphatase activity in Lake Certovo (ranging from 1.0 to 12.7 micromol l(-1) h(-1), using ELF97 phosphate as a substrate). Bacterial filaments (> 10 microm), although comprising in average 85% of bacterioplankton biomass, contributed to the total bacterioplankton activity only by 45%. Biomass-specific activity of extracellular (cell-surface) phosphatases of the main bacterioplankton morphotypes increased in the order filaments < cocci and rods < curved cells. The biomass-specific activity of bacterioplankton extracellular phosphatases (0-300 nmol microgC(-1) h(-1)) was generally highest in the spring and decreased gradually during summer. These changes could result from seasonal changes in the phosphorus status of the lake and from subsequent regulation of enzyme expression by bacteria.

Specific activity of cell-surface acid phosphatase in different bacterioplankton morphotypes in an acidified mountain lake.

On a solution of a generalized semi-coercive contact problem in thermo-elasticity

The fluorogenic substrate Enzyme-Labeled Fluorescence 97 (ELF-P) is hydrolyzed by the P-cleaving enzyme phosphatase, producing ELF 97 alcohol (ELFA), a fluorescent-insoluble product. This reaction is used for monitoring phosphatase activity at the single-cell level. Most frequently, ELF-P has been used to determine the P-limitation status of microphytoplankton, but rarely of heterotrophic bacteria. We incubated ELF-P on filters to monitor marine bacterial cultures and oligotrophic Mediterranean Sea samples. Results were compared to classical measurements of bulk alkaline phosphatase activity using the fluorogenic substrate 4-methylumbelliferyl phosphate (MUF-P). A high percentage of the cultured cells were labeled with ELFA (the ratio of ELFA spots to total DAPI counts in P-limited cultures ranged from 26 to 100%, depending on the strain). In contrast, this ratio never exceeded 0.01 % in Mediterranean samples, even when P was demonstrated to be a significant limiting factor. This protocol is useful for application on cruises and with cultures, but was not sufficiently sensitive to detect P-stressed bacterial cells in oligotrophic marine environments.

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Jirí Nedoma

Papers

Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition

Specific activity of cell-surface acid phosphatase in different bacterioplankton morphotypes in an acidified mountain lake.

On a solution of a generalized semi-coercive contact problem in thermo-elasticity

Alkaline phosphatase activity of marine bacteria studied with ELF 97 substrate: success and limits in the P-limited Mediterranean Sea

Effects of temperature on the phenology of germination of Isoetes echinospora