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Jirí Nedoma

Bio: Jirí Nedoma is an academic researcher from Academy of Sciences of the Czech Republic. The author has contributed to research in topics: Bacterivore & Phytoplankton. The author has an hindex of 14, co-authored 21 publications receiving 1382 citations.

Papers
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Journal ArticleDOI
TL;DR: Viral concentrations and frequencies of infected cells were highly significantly correlated with grazing rates, suggesting that protistan grazing may stimulate viral activity.
Abstract: Bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce ( 80% of the total bacteria by the end of the experiment. Once again, BCC changed strongly and a significant fraction of the large filaments was detected using a FISH probe targeted to members of the Flectobacillus lineage. Shifts of BCC were also reflected in DGGE patterns and in the increases in the relative importance of both beta proteobacteria and members of the Cytophaga-Flavobacterium cluster, which consistently formed different parts of the bacterial flocs. Viral concentrations and frequencies of infected cells were highly significantly correlated with grazing rates, suggesting that protistan grazing may stimulate viral activity.

360 citations

Journal ArticleDOI
TL;DR: Significant cultivation-dependent shifts of the bacterial community were observed toward (gamma)-Proteobacteria and members of the Cytophaga/Flavobacterium group, which demonstrated the rather poor agreement between cultivation-based approaches and oligonucleotide probing.
Abstract: In a two-stage continuous-flow system, we studied the impacts of different protozoan feeding modes on the morphology and taxonomic structure of mixed bacterial consortia, which were utilizing organic carbon released by a pure culture of a Rhodomonas sp. grown on inorganic medium in the first stage of the system. Two of three second stages operated in parallel were inoculated by a bacterivorous flagellate, Bodo saltans, and an algivorous ciliate, Urotricha furcata, respectively. The third vessel served as a control. In two experiments, where algal and bacterial populations grew at rates and densities typical for eutrophic waters, we compared community changes of bacteria, algae, and protozoa under quasi-steady-state conditions and during the transient stage after the protozoan inoculation. In situ hybridization with fluorescent oligonucleotide probes and cultivation-based approaches were used to tentatively analyze the bacterial community composition. Initially the cell size distribution and community structure of all cultivation vessels showed similar patterns, with a dominance of 1- to 2.5-(mu)m-long rods from the beta subdivision of the phylum Proteobacteria ((beta)-Proteobacteria). Inoculation with the ciliate increased bacterial growth in this substrate-controlled variant, seemingly via a recycling of nutrients and substrate released by grazing on algae, but without any detectable effect on the composition of bacterial assemblage. In contrast, an inoculation with the bacterivore, B. saltans, resulted in a decreased proportion of the (beta)-Proteobacteria. One part of the assemblage (<4% of total bacterial numbers), moreover, produced large grazing-resistant threadlike cells. As B. saltans ingested only cells of <3 (mu)m, this strategy yielded a refuge for (symbl)70% of total bacterial biomass from being grazed. Another consequence of the heavy predation in this variant was a shift to the numerical dominance of the (alpha)-Proteobacteria. The enhanced physiological status of the heavily grazed-upon segment of bacterial community resulted in a much higher proportion of CFU (mean, 88% of total bacterial counts) than with other variants, where CFU accounted for (symbl)30%. However, significant cultivation-dependent shifts of the bacterial community were observed toward (gamma)-Proteobacteria and members of the Cytophaga/Flavobacterium group, which demonstrated the rather poor agreement between cultivation-based approaches and oligonucleotide probing.

214 citations

Journal ArticleDOI
TL;DR: Investigating the role of protists, especially heterotrophic nanoflagellates (HNF), in microbial food webs during the summer phytoplankton bloom in the epilimnion and metalimnions of the eutrophic Rimov reservoir found no tight relationship between HNF and the concentration of bacteria and chlorophyll.
Abstract: An intensive 5 wk study was conducted to investigate the role of protists, especially heterotrophic nanoflagellates (HNF), in microbial food webs during the summer phytoplankton bloom in the epilimnion and metalimnion of the eutrophic Rimov reservoir (South Bohemia, Czech Republic). On average, protists consumed similar to 90% of bacterial production in both layers. The community composition of HNF and the relative importance of different HNF groups as picoplankton consumers were determined. Small HNF (<8 mu m), as chrysomonads, bodonids and choanoflagellates, usually accounted for <30% of total HNF biomass but numerically dominated the community in both layers. They consumed most of (similar to 70 to 85 %) the bacterioplankton as well as autotrophic picoplankton (APP, exclusively cyanobacteria) production in the reservoir, with the rest consumed by ciliates. Both ciliates and HNF had higher clearance rates on APP than on bacteria and their grazing was likely responsible for a sharp decrease in APP abundance (from 3-4 x 10(5) to <2 x 10(3) ml(-1)) and a very constant size structure of bacterioplankton in which short rods in the size class of 0.4 to 0.8 mu m constituted 55 to 80 % of the total bacterial biomass in both layers. The proportion of HNF to total picoplankton biomass in the epilimnion indicated that the picoplankton biomass was sufficiently high to support HNF growth for most of the study. Uptake of picoplankton by less numerous, but larger, HNF (kathablepharids, Goniomonas sp., and Streptomonas sp.) was negligible, while their biomass, especially in the metalimnion, exceeded that of small HNF and the total biomass of picoplankton. This suggested that food items other than picoplankton were consumed to meet their carbon requirements. Analyzing potential bottom-up and top-down factors controlling HNF numbers and biomass, we did not find a tight relationship between HNF and the concentration of bacteria and chlorophyll. Variability of HNF abundance and biomass in the epilimnion could largely be explained by cladocerans or by pooled abundances of all potential crustacean consumers of HNF. In the metalimnion, the mean cell volume of HNF was positively linked to chlorophyll but negatively to the abundance of Cyclopidae and to the pooled abundances of Ceriodaphnia quadrangula and Diaphanosoma brachyurum.

119 citations

Journal ArticleDOI
TL;DR: The main components of pelagic biomass were BAC, PHY and ZOOL+ZOOS, except for acidified lakes, where zooplankton was very low, and the percentage of extracellular production in the total primary production was considerable.
Abstract: A methodical approach for the assessment of pelagic biomass and the main carbon fluxes in remote and hardly accessible mountain lakes was elaborated and tested. Number and biomass of bacteria (BAC), autotrophic picoplankton (APP), heterotrophic nanoflagellates (HNF), ciliates (CIL), phytoplankton (PHY), zooplankton smaller than 40 μm (ZOOS) and zooplankton larger than 40 μm (ZOOL) were investigated regularly during two ice-free periods in 13 European mountain lakes (1st level approach – fixed samples elaborated in specialized laboratories). Carbon fluxes measured in 9 lakes included: primary production, exudation by PHY and BAC uptake of exudates, BAC production, elimination of BAC. These processes were measured in the field by specialized teams (2nd level approach). The ranges of values found in mountain lakes were evaluated and possible methodical and interpretative errors discussed. BAC were a significant component of pelagic biomass. The intercomparison between different partners showed differences in bacterial counts lower than 10%, whereas the mean cell volumes measured fluctuated by more than 40%. APP was never found in a significant quantity, except in one lake. HNF and CIL, though regularly found, were usually scarce and only occasionally significant in terms of biomass. The main components of pelagic biomass were BAC, PHY and ZOOL+ZOOS, except for acidified lakes, where zooplankton was very low. In oligotrophic mountain lakes, the percentage of extracellular production in the total primary production was considerable. Bacterial abundance and production often reached values quite comparable with the situation found in lowland mesotrophic lakes during winter.

109 citations

Journal ArticleDOI
TL;DR: It was found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of β-proteobacteria (targeted with the probe R-BT065), which showed the highest net growth rates and was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content.
Abstract: ´mov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 m), bacteria and heterotrophic nanoflagellates (<5 m), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of -proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class Actinobacteria, which profited from the enhanced protistan bacterivory.

108 citations


Cited by
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Journal ArticleDOI
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: 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

14,171 citations

Journal ArticleDOI
TL;DR: The structure of freshwater phytoplankton assemblages is considered and a scheme of vegetation recognition', based upon the functional associations of species represented in the plankton, is promoted.
Abstract: 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.

1,646 citations

Journal ArticleDOI
TL;DR: Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton, which can strongly influence microbial food web processes and biogeochemical cycles.
Abstract: 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.

1,547 citations

Journal ArticleDOI
TL;DR: A new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia is presented and a unifying vocabulary to discuss freshwater taxa is proposed, providing a coherent framework for future studies.
Abstract: 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.

1,230 citations

Journal ArticleDOI
TL;DR: This paper reviews recent studies that have applied molecular methods to examine uncultured Cytophaga–Flavobacteria in freshwaters and the oceans, with the ultimate goal of using this information to better understand the role of heterotrophic bacteria in carbon cycles and other biogeochemical processes.

1,182 citations