Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria.

ABSTRACT: The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Římov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Římov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.

SUBMITTER: Fecskeova LK

PROVIDER: S-EPMC6904477 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake.

Project description:Aerobic anoxygenic photoheterotrophic (AAP) bacteria represent a functional group of prokaryotic organisms that harvests light energy using bacteriochlorophyll-containing photosynthetic reaction centers. They represent an active and rapidly growing component of freshwater bacterioplankton, with the highest numbers observed usually in summer. Species diversity of freshwater AAP bacteria has been studied before in lakes, but its seasonal dynamics remain unknown. In this report, we analysed temporal changes in the composition of the phototrophic community in an oligo-mesotrophic freshwater lake using amplicon sequencing of the pufM marker gene. The AAP community was dominated by phototrophic Gammaproteobacteria and Alphaproteobacteria, with smaller contribution of phototrophic Chloroflexota and Gemmatimonadota. Phototrophic Eremiobacteriota or members of Myxococcota were not detected. Interestingly, some AAP taxa, such as Limnohabitans, Rhodoferax, Rhodobacterales or Rhizobiales, were permanently present over the sampling period, while others, such as Sphingomonadales, Rhodospirillales or Caulobacterales appeared only transiently. The environmental factors that best explain the seasonal changes in AAP community were temperature, concentrations of oxygen and dissolved organic matter.

| S-EPMC10103773 | biostudies-literature

Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient.

Project description:Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient).

| S-EPMC5320280 | biostudies-literature

Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production.

Project description:Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.

| S-EPMC4918449 | biostudies-literature

Anoxygenic phototrophic microbial communities

Project description:Compositon of anoxygenic phototrophic microbial community enrichments from marine and freshwater environments

| PRJNA327250 | ENA

Anoxygenic Phototrophic Bacterial Diversity

Project description:Anoxygenic Phototrophic Bacterial Diversity in different habitats of India

| PRJEB22780 | ENA

Anoxygenic Phototrophic Bacterial Diversity

Project description:Anoxygenic Phototrophic Bacterial Diversity in different habitats of India

| PRJEB22783 | ENA

Anoxygenic Phototrophic Bacterial diversity

Project description:Anoxygenic Phototrophic Bacterial diversity in different habitats of India

| PRJEB22785 | ENA

Anoxygenic Phototrophic Bacterial Diversity

Project description:Anoxygenic Phototrophic Bacterial Diversity in different habitats of India

| PRJEB22787 | ENA

Anoxygenic Phototrophic Bacterial Diversity

Project description:Anoxygenic Phototrophic Bacterial Diversity in different habitats of India

| PRJEB22790 | ENA

Diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric CO₂.

Project description:Aerobic anoxygenic phototrophic bacteria (AAnPB) are recognized as an important group driving the global carbon cycling. However, the diversity of AAnPB in terrestrial environment remains largely unknown as well as their responses to the elevated atmospheric CO2. By using culture-independent techniques, the diversity of AAnPB in paddy soil and the changes in response to the rising atmospheric CO₂ were investigated within China FACE (Free-air CO₂ enrichment) platform. There was a phylogenetically diverse AAnPB community with large population size residing in paddy soil. The community structure of AAnPB in bulk and rhizospheric soils stayed almost identical, while the population size was higher in rhizospheric [2.0–2.5 x 10⁸ copy number of pufM genes g-1 dry weight soil (d.w.s.)] than that in bulk (0.7–0.8 x 10⁸ g-1 d.w.s.) soils. Elevated atmospheric CO2 appeared to significantly stimulate AAnPB abundance (up to 1.4–1.5 x 10⁸ g-1 d.w.s.) and result in a higher AAnPB percentage in total bacterial community (from 0.5% up to 1.5%) in bulk soil, whereas no significant effect was observed in rhizospheric soil. Our results would extend the functional ecotypes of AAnPB and indicate that environmental changes associated with the rising atmospheric CO₂ might affect AAnPB community in paddy soil.

| S-EPMC3815797 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data