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At least 415 records · Page 23Linked to original sources
PubMed2006

Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group.

Phylogenetic screening of 3200 clones from a metagenomic library of Antarctic mesopelagic picoplankton allowed the identification of two bacterial 16S-rDNA-containing clones belonging to the Deltaproteobacteria, DeepAnt-1F12 and DeepAnt-32C6. These clones were very divergent, forming a monophyletic cluster with the environmental sequence GR-WP33-58 that branched at the base of the myxobacteria. Except for the possession of complete rrn operons without associated tRNA genes, DeepAnt-1F12 and DeepAnt-32C6 were very different in gene content and organization. Gene density was much higher in DeepAnt-32C6, whereas nearly one-third of DeepAnt-1F12 corresponded to intergenic regions. Many of the predicted genes encoded by these metagenomic clones were informational (i.e. involved in replication, transcription, translation and related processes). Despite this, a few putative cases of horizontal gene transfer were detected, including a transposase. DeepAnt-1F12 contained one putative gene encoding a long cysteine-rich protein, probably membrane-bound and Ca2+-binding, with only eukaryotic homologues. DeepAnt-32C6 carried some predicted genes involved in metabolic pathways that suggested this organism may be anaerobic and able to ferment and to degrade complex compounds extracellularly.

Antarctic Regions↗
PubMed2005

Target phase: an extra dimension for fish and plankton target identification.

The acoustic signal backscattered from a fish in water, Lbs(f), at a frequency, f, differs from the incident signal in both magnitude, /Lbs(f)/, and phase, arg[Lbs(f)], and it has been common practice for many years to use the backscatter magnitude from individual fish as an aid to species identification. However, very little use has been made of the phase of the backscattered signal relative to that of the incident acoustic pulse. If the gross phase changes due to propagation through water are compensated for, the residual phase signature is found to contain useful target-specific information. The phase signature can be characterized by estimating the rate at which the echo phase changes, relative to the transmitted pulse, during the echo from a fish. Clear groups are produced when single fish targets from in situ data are plotted in complex target space (target strength versus target rate of change of phase) and this is explored here by computing the acoustic backscatter, in complex target space, from a series of simple large and small model fish targets, both with and without gas-filled swimbladders, using a Monte Carlo technique. It is shown that all the features found in the in situ data can be explained in terms of the size and attitude of the fish. The modeling was carried out at the frequency of 38 kHz, which pertained to the in situ data, and the specific results only apply to this frequency. However, the complex target approach is generally applicable to fish target strength analysis independently of frequency.

Acoustics↗
PubMed2004

Abiotic forcing of plankton evolution in the Cenozoic.

We characterize the evolutionary radiation of planktic foraminifera by the test size distributions of entire assemblages in more than 500 Cenozoic marine sediment samples, including more than 1 million tests. Calibration of Holocene size patterns with environmental parameters and comparisons with Cenozoic paleoproxy data show a consistently positive correlation between test size and surface-water stratification intensity. We infer that the observed macroevolutionary increase in test size of planktic foraminifera through the Cenozoic was an adaptive response to intensifying surface-water stratification in low latitudes, which was driven by polar cooling.

Animals↗
PubMed2006

Coherent sign switching in multiyear trends of microbial plankton.

Since the 1990s, phytoplankton biomass on the continental shelf of Nova Scotia and in the Labrador Sea has undergone sustained changes in the spring and fall, which are accompanied by changes in bacterioplankton that are dampened in amplitude but coherent in the direction of change. A reversal of trend in biomass change, so-called sign switching, occurs both in time and in space. Thus, whenever (spring or fall) and wherever (Scotian Shelf or Labrador Sea) phytoplankton increase or decrease, so also does bacterioplankton. This tandem sign switch indicates coupling of the trophic levels at a multiyear time scale and contributes to an ecological fingerprint of systemwide forcing.

Atlantic Ocean↗
PubMed1970

Mercury compounds reduce photosynthesis by plankton.

Concentrations of organomercurial fungicides as low as 0.1 part per billion in water reduced photosynthesis and growth in laboratory cultures of one species of marine diatom and several natural phytoplankton communities from Florida lakes. The acute toxicity of mercury compounds to phytoplankton is dependent on the chemical nature of the mercury compound and on cell concentrations.

Antifungal Agents↗
PubMed1976

Gametogenesis in planktonic foraminifera.

Gametogenesis in Globigerinella aequilateralis and Globigerinoides sacculifer in culture is preceded by sinking of the organism and loss of its spines. Hundreds of thousands of flagellated gametes, about 5 micrometers in diameter, are produced within the parent shell and released within a period of 13 hours.

Male↗
PubMed2006

Roles for cell wall glycopeptidolipid in surface adherence and planktonic dispersal of Mycobacterium avium.

The opportunistic pathogen Mycobacterium avium is a significant inhabitant of biofilms in drinking water distribution systems. M. avium expresses on its cell surface serovar-specific glycopeptidolipids (ssGPLs). Studies have implicated the core GPL in biofilm formation by M. avium and by other Mycobacterium species. In order to test this hypothesis in a directed fashion, three model systems were used to examine biofilm formation by mutants of M. avium with transposon insertions into pstAB (also known as nrp and mps). pstAB encodes the nonribosomal peptide synthetase that catalyzes the synthesis of the core GPL. The mutants did not adhere to polyvinyl chloride plates; however, they adhered well to plastic and glass chamber slide surfaces, albeit with different morphologies from the parent strain. In a model that quantified surface adherence under recirculating water, wild-type and pstAB mutant cells accumulated on stainless steel surfaces in equal numbers. Unexpectedly, pstAB mutant cells were >10-fold less abundant in the recirculating-water phase than parent strain cells. These observations show that GPLs are directly or indirectly required for colonization of some, but by no means all, surfaces. Under some conditions, GPLs may play an entirely different role by facilitating the survival or dispersal of nonadherent M. avium cells in circulating water. Such a function could contribute to waterborne M. avium infection.

Bacterial Adhesion↗
PubMed1997

Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria.

Small-subunit (SSU) ribosomal DNA (rDNA) gene clusters are phylogenetically related sets of SSU rRNA genes, commonly encountered in genes amplified from natural populations. Genetic variability in gene clusters could result from artifacts (polymerase error or PCR chimera formation), microevolution (variation among rrn copies within strains), or macroevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand gene clusters this study assessed genetic diversity and distribution of a single environmental SSU rDNA gene cluster, the SAR11 cluster. SAR11 cluster genes, from an uncultured group of the alpha subclass of the class Proteobacteria, have been recovered from coastal and midoceanic waters of the North Atlantic and Pacific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA genes, from 80 and 250 m in the Sargasso Sea and from surface coastal waters of the Atlantic and Pacific, and analyzed them with previously published sequences. Two SAR11 genes were obviously PCR chimeras, but the biological (nonchimeric) origins of most subgroups within the cluster were confirmed by independent recovery from separate gene libraries. Using group-specific oligonucleotide probes, we analyzed depth profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly depth-specific distributions. We conclude that some of the genetic diversity within the SAR11 gene cluster represents macroevolutionary divergence correlated with niche specialization. Furthermore, we demonstrate the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations and show that a detailed knowledge of sequence variability may be needed to effectively design these probes.

Animals↗
PubMed1999

Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing.

We analyzed changes in bacterioplankton morphology and composition during enhanced protozoan grazing by image analysis and fluorescent in situ hybridization with group-specific rRNA-targeted oligonucleotide probes. Enclosure experiments were conducted in a small, fishless freshwater pond which was dominated by the cladoceran Daphnia magna. The removal of metazooplankton enhanced protozoan grazing pressure and triggered a microbial succession from fast-growing small bacteria to larger grazing-resistant morphotypes. These were mainly different types of filamentous bacteria which correlated in biomass with the population development of heterotrophic nanoflagellates (HNF). Small bacterial rods and cocci, which showed increased proportion after removal of Daphnia and doubling times of 6 to 11 h, belonged nearly exclusively to the beta subdivision of the class Proteobacteria and the Cytophaga-Flavobacterium cluster. The majority of this newly produced bacterial biomass was rapidly consumed by HNF. In contrast, the proportion of bacteria belonging to the gamma and alpha subdivisions of the Proteobacteria increased throughout the experiment. The alpha subdivision consisted mainly of rods that were 3 to 6 microm in length, which probably exceeded the size range of bacteria edible by protozoa. Initially, these organisms accounted for less than 1% of total bacteria, but after 72 h they became the predominant group of the bacterial assemblage. Other types of grazing-resistant, filamentous bacteria were also found within the beta subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster. We conclude that the predation regimen is a major structuring force for the bacterial community composition in this system. Protozoan grazing resulted in shifts of the morphological as well as the taxonomic composition of the bacterial assemblage. Grazing-resistant filamentous bacteria can develop within different phylogenetic groups of bacteria, and formerly underepresented taxa might become a dominant group when protozoan predation is the major selective pressure.

Animals↗
PubMed2002

Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton.

We describe a method for microscopic identification of DNA-synthesizing cells in bacterioplankton samples. After incubation with the halogenated thymidine analogue bromodeoxyuridine (BrdU), environmental bacteria were identified by fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-linked oligonucleotide probes. Tyramide signal amplification was used to preserve the FISH staining during the subsequent immunocytochemical detection of BrdU incorporation. DNA-synthesizing cells were visualized by means of an HRP-labeled antibody Fab fragment and a second tyramide signal amplification step. We applied our protocol to samples of prefiltered (pore size, 1.2 micro m) North Sea surface water collected during early autumn. After 4 h of incubation, BrdU incorporation was detected in 3% of all bacterial cells. Within 20 h the detectable DNA-synthesizing fraction increased to >14%. During this period, the cell numbers of members of the Roseobacter lineage remained constant, but the fraction of BrdU-incorporating Roseobacter sp. cells doubled, from 24 to 42%. In Alteromonas sp. high BrdU labeling rates after 4 to 8 h were followed by a 10-fold increase in abundance. Rapid BrdU incorporation was also observed in members of the SAR86 lineage. After 4 h of incubation, cells affiliated with this clade constituted 8% of the total bacteria but almost 50% of the visibly DNA-synthesizing bacterial fraction. Thus, this clade might be an important contributor to total bacterioplankton activity in coastal North Sea water during periods of low phytoplankton primary production. The small size and low ribosome content of SAR86 cells are probably not indications of inactivity or dormancy.

Animals↗
PubMed2002

Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations.

Temporal changes of the bacterioplankton from a meromictic lake (Lake Vilar, Banyoles, Spain) were analyzed with four culture-independent techniques: epifluorescence microscopy, PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, fluorescence in situ whole-cell hybridization and flow cytometry sorting. Microscopically, blooms of one cyanobacterium (Synechococcus sp.-like), one green sulfur bacterium (Chlorobium phaeobacteroides-like), and one purple sulfur bacterium (Thiocystis minor-like) were observed at different depths and times. DGGE retrieved these populations and, additionally, populations related to the Cytophaga-Flavobacterium-Bacteroides phylum as predominant community members. The analyses of partial 16S ribosomal DNA sequences from the DGGE fingerprints (550 bp analyzed) revealed higher genetic diversity than expected from microscopic observation for most of these groups. Thus, the sequences of two Synechococcus spp. (both had a similarity of 97% to Synechococcus sp. strain PCC6307 in 16S rRNA), two Thiocystis spp. (similarities to Thiocystis minor of 93 and 94%, respectively), and three Cytophaga spp. (similarities to Cytophaga fermentans of 88 and 89% and to Cytophaga sp. of 93%, respectively) were obtained. The two populations of Synechococcus exhibited different pigment compositions and temporal distributions and their 16S rRNA sequences were 97.3% similar. The two Thiocystis populations differed neither in pigment composition nor in morphology, but their 16S rRNA sequences were only 92.3% similar and they also showed different distributions over time. Finally, two of the Cytophaga spp. showed 96.2% similarity between the 16S rRNA sequences, but one of them was found to be mostly attached to particles and only in winter. Thus, the identity of the main populations changed over time, but the function of the microbial guilds was maintained. Our data showed that temporal shifts in the identity of the predominant population is a new explanation for the environmental 16S rRNA microdiversity retrieved from microbial assemblages and support the hypothesis that clusters of closely related 16S rRNA environmental sequences may actually represent numerous closely related, yet ecologically distinct, populations.

Animals↗
PubMed2005

Ecological differentiation within a cosmopolitan group of planktonic freshwater bacteria (SOL cluster, Saprospiraceae, Bacteroidetes).

Members of the monophyletic SOL cluster are large filamentous bacteria inhabiting the pelagic zone of many freshwater habitats. The abundances of SOL bacteria and compositions of SOL communities in samples from 115 freshwater ecosystems around the globe were determined by fluorescence in situ hybridization with cluster- and subcluster-specific oligonucleotide probes. The vast majority (73%) of sampled ecosystems harbored SOL bacteria, and all three previously described SOL subclusters (LD2, HAL, and GKS2-217) were detected. The morphometric and chemicophysical parameters and trophic statuses of ecosystems were related to the occurrence and subcluster-specific composition of SOL bacteria by multivariate statistical methods. SOL bacteria did not occur in acidic lakes (pH < 6), and their abundance was negatively related to high trophy and pH. The subcluster-specific variation in the compositions of SOL communities could be related to the pH, electrical conductivity, altitude, and trophic status of ecosystems. All three known SOL subclusters differed in respect to their tolerated ranges of pH and conductivity. Complete niche separation was observed between the vicarious subclusters GKS2-217 and LD2; the former occurred in soft-water lakes, whereas the latter was found in a broad range of hard-water habitats. The third subgroup (HAL) showed a wide environmental tolerance and was usually found sympatrically with the LD2 or GKS2-217 subcluster. Ecological differentiation of SOL bacteria at the subcluster level was most probably driven by differential adaptation to water chemistry. The distribution of the two vicarious taxa seems to be predominantly controlled by the geological backgrounds of the catchment areas of the habitats.

Animals↗
PubMed2005

Ecotypes of planktonic actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical, and tropical freshwater habitats.

Seven strains with identical 16S rRNA genes affiliated with the Luna2 cluster (Actinobacteria) were isolated from six freshwater habitats located in temperate (Austria and Australia), subtropical (People's Republic of China), and tropical (Uganda) climatic zones. The isolates had sequence differences at zero to five positions in a 2,310-nucleotide fragment of the ribosomal operon, including part of the intergenic spacer upstream of the 16S rRNA gene, the complete 16S rRNA gene, the complete 16S-23S internal transcribed spacer (ITS1), and a short part of the 23S rRNA gene. Most of the few sequence differences found were located in the internal transcribed spacer sequences. Two isolates obtained from habitats in Asia and Europe, as well as two isolates obtained from different habitats in the People's Republic of China, had identical sequences for the entire fragment sequenced. In spite of minimal sequence differences in the part of the ribosomal operon investigated, the strains exhibited significant differences in their temperature response curves (with one exception), as well as pronounced differences in their temperature optima (25.0 to 35.6 degrees C). The observed differences in temperature adaptation were generally in accordance with the thermal conditions in the habitats where the strains were isolated. Strains obtained from temperate zone habitats had the lowest temperature optima, strains from subtropical habitats had intermediate temperature optima, and a strain from a tropical habitat had the highest temperature optimum. Based on the observed temperature responses, we concluded that the strains investigated are well adapted to the thermal conditions in their home habitats. Consequently, these closely related strains represent different ecotypes adapted to different thermal niches.

Actinobacteria↗
PubMed2005

Spatial distribution and transcriptional activity of an uncultured clade of planktonic diazotrophic gamma-proteobacteria in the Arabian sea.

The spatial distribution of an uncultured clade of marine diazotrophic gamma-proteobacteria in the Arabian Sea was investigated by the development of a specific primer pair to amplify an internal fragment of nifH by PCR. These organisms were most readily detected in highly oligotrophic surface waters but could also be found in deeper waters below the nutricline. nifH transcripts originating from this clade were detected in oligotrophic surface waters and, in addition, in the deeper and the more productive near-coastal waters. The nifH sequences most closely related to the unidentified marine bacterial group are from environmental clones amplified from the Atlantic and Pacific Oceans. These findings suggest that these gamma-proteobacteria are widespread and likely to be an important component of the heterotrophic diazotrophic microbial community of the tropical and subtropical oceans.

Animals↗
PubMed2006

Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria.

Six environmental fosmid clones from Antarctic coastal water bacterioplankton were completely sequenced. The genome fragments harbored small-subunit rRNA genes that were between 85 and 91% similar to those of their nearest cultivated relatives. The six fragments span four phyla, including the Gemmatimonadetes, Proteobacteria (alpha and gamma), Bacteroidetes, and high-G+C gram-positive bacteria. Gene-finding and annotation analyses identified 244 total open reading frames. Amino acid comparisons of 123 and 113 Antarctic bacterial amino acid sequences to mesophilic homologs from G+C-specific and SwissProt/UniProt databases, respectively, revealed widespread adaptation to the cold. The most significant changes in these Antarctic bacterial protein sequences included a reduction in salt-bridge-forming residues such as arginine, glutamic acid, and aspartic acid, reduced proline contents, and a reduction in stabilizing hydrophobic clusters. Stretches of disordered amino acids were significantly longer in the Antarctic sequences than in the mesophilic sequences. These characteristics were not specific to any one phylum, COG role category, or G+C content and imply that underlying genotypic and biochemical adaptations to the cold are inherent to life in the permanently subzero Antarctic waters.

Acclimatization↗
PubMed2006

Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-Like bacterium.

Bacteria belonging to the Roseobacter clade of the alpha-Proteobacteria occupy a wide range of environmental niches and are numerically abundant in coastal waters. Here we reveal that Roseobacter-like bacteria may play a previously unrecognized role in the oxidation and cycling of manganese (Mn) in coastal waters. A diverse array of Mn(II)-oxidizing Roseobacter-like species were isolated from Elkhorn Slough, a coastal estuary adjacent to Monterey Bay in California. One isolate (designated AzwK-3b), in particular, rapidly oxidizes Mn(II) to insoluble Mn(III, IV) oxides. Interestingly, AzwK-3b is 100% identical (at the 16S rRNA gene level) to a previously described Pfiesteria-associated Roseobacter-like bacterium, which is not able to oxidize Mn(II). The rates of manganese(II) oxidation by live cultures and cell-free filtrates are substantially higher when the preparations are incubated in the presence of light. The rates of oxidation by washed cell extracts, however, are light independent. Thus, AzwK-3b invokes two Mn(II) oxidation mechanisms when it is incubated in the presence of light, in contrast to the predominantly direct enzymatic oxidation in the dark. In the presence of light, production of photochemically active metabolites is coupled with initial direct enzymatic Mn(II) oxidation, resulting in higher Mn(II) oxidation rates. Thus, Roseobacter-like bacteria may not only play a previously unrecognized role in Mn(II) oxidation and cycling in coastal surface waters but also induce a novel photooxidation pathway that provides an alternative means of Mn(II) oxidation in the photic zone.

Animals↗