Proteobacteria - Science topic

Interactions between fungi and bacteria are often complex and can be symbiotic.

People still considering Pseudomonas under the phylum Proteobacteria. Which one phylum is correct taxonomically ?

I am conducting a phylogenetic analysis on LuxR solo of alpha, beta and gammaproteobacteria. I am building three separate trees for each. What would serve as the best outgroup in all three trees?

I want to construct a phylogenetic tree on bacterial isolates (16srna) of groups- Firmicutes and proteobacteria containing both gram negative and gram positive strains. I need to construct a tree for these species with some outgroup. Please suggest me which bacterial genus would serve best as outgroup for the above mentioned bacterial groups or how to find it.

Hi,

My team was trying to profile bacterial phylum composition in food sample using qPCR. We used 16s universal primers and primers specific for certain phylum such as Firmicutes and Proteobacteria. By using this approach we expected to be able to calculate how much the ratio of a certain phylum compared to the total number of bacteria. We used E. coli as standard for amplification with universal primers and other pure culture for the other phylum-specific primers (e.g. Lactobacillus for firmicutes). When the result came out, we found that in some samples, the copy number using phylum specific primer was higher than amplification of the same sample with universal primer. Logically this should not be possible since that implies we have more firmicutes for example than the total number of bacteria in that sample. What would be the explanation behind this? Is qPCR technically feasible for the analysis that we were planning to do?

Can Proteobacteria and Burkholderiales being Gram-negative (thin cell wall) be easily destroyed by antimicrobial producing Gram-positive genera for instance Actinobacteria and Salinospora in soil?

The anoxygenic Type II reaction center in purple bacteria has 4 bacteriochlorophyll pigments, 2 bacteriopheophytin pigments, while the reaction center in green non-sulfur bacteria has 3 bacteriochlorophyll and 3 bacteriopheophytin pigments. The third one is located at the position of the monomeric bacteriochlorophyll on the M branch (Bchl_M).

In purple bacteria, the Bchl_M is in contact with a carotenoid, which has a protective role. Could the "third bacteriopheophytin" (Φ_M) have a similar role? I feel like it could not, but I'm not sure... perhaps in a different way.

Apparently, in a mutant of the purple bacteria where a bacteriopheophytin is located at the position of Bchl_M charge separation can occur on the M branch. Some experiments by Yakovlev et al., 2009 (Biochemistry Moscow) using femtosecond studies, determined that extremely fast charge separation to Φ_M occurred reversibly, but then the normal charge separation on the L branch would be the stable charge separation route with full yield.

Do you know what is the mechanistic significance of this adaptation in the green non-sulfur bacteria? Or alternatively, do you have any speculations as to what the role of Φ_M could be?

I observed different microbial abundance in soil right from Phylum, Class, Order and Genus. E.g. If Proteobacteria is the most abundant PHYLUM, it is expected that Gram negative genera would be colonising more, but how come in the abundance of Proteobacteria , Gram positive genera have more OTU's. What would be the possible reasoning

In one of the recent metagenomic study performed by me, I found the above observation.

Looking for expert advice on this

Online, i found primers that are specific for just one or two sub groups.

I'm looking for Pseudomonas meridiana type strain MTCC 4993. I could not get any response from the indian collection (MTCC). Maybe somebody here is working with this strain and knows how to get it.

I am trying to construct an experiment in which we will inoculate 2 bacteria and 2 yeasts on to a specific media and examine the competitive outcome of this community. In order to make this a fair game, we need equal CFU's from each of the 4 contestants. While we are quantifying yeasts and proteobacteria by serial dilution, it is difficult to quantify the actinomycetes in broth since they precipitate and clump. How can I get to a comparable CFU/ml for all 4 species (1 proteo, 1 actino, 2 yeasts)?

What are the bacteria present in drilling mud or fracking water used in hydraulic fracturing? Is it possible to culture bacteria present in drilling in our lab? What would be the best way to culture bacteria like γ- proteobacteria, α- proteobacteria, δ- proteobacteria, Clostridia, Thermotogae, Synergistes, Spirochetes, Bacterodetes and Archaea in lab?

The external NO2- concentration is 1-2 micromolar. I don't know what the periplasmic concentration would be, possibly higher. The timescale I am interested in is 1-24 hours. The bacteria I am looking at are beta proteobacteria, specifically ammonia oxidizers.

The external pH is about neutral, so almost all the NO2- is in the anionic form (not HNO2). I gather that NO2- is probably small enough to pass through porins, but I do not know if the outer cell membrane would be a critical barrier or not over the timescale or concentrations I am interested in.

Does anyone know how I might figure this out? Thanks!

I have confusion as Moulin et al, 2001 described Nodules induced on M. atropurpureum by strain STM678 (Burkholderia) were ineffective in terms of nitrogen fixation. or  now it is proved that β-rhizobia can make effective nodule in term of nitrogen fixation.

Reference

Moulin, L., Munive, A., Dreyfus, B., Boivin-Masson, C. (2001) Nodulation of legumes by members of the β-subclass of proteobacteria. Nature 411, 948.

i want to isolate pesticide resistant methanotrophs.

I have carried out study of insect gut diversity using 16srRNA. We got almost sequences of approximately  50 strains and  found out in which seven group of distinct genera formed and gut communities dominated by <10 bacterial species in three phyla:  Actinobacteria=2.17%. , Proteobacteria= 73.91%, Firmicutes=23.91%. BLASTn identity for most of the strain are 95-100%.   We are looking for diversity, polymorphism, strain difference, phylogenetic analysis with this information . In this aspect what software I can go with to submit this work as valid study. Your suggestions regarding this are highly appreciated.

I've been using LB to study tolerance to copper, cobalt, silver and zinc, but it seem to interact somehow with these heavy metals. 

Should I use a minimal medium instead?

Thanks you all.

Are there any specific primers for Actinobacteria and proteobacteria with a size of under than 250 bp?

Other than in brain heart infusion (BHI), in which other medium can Neisseria gonorrhoeae grow? I am afraid that I do not have BHI right now.

I would like to know if anyone can share a Campylobacter rectus strain? Because we have some problems to buy it al atcc and LMG.

Thanks!

Proteobacteria is broadly divided in different groups–alpha,beta, gamma, delta, epsilon, and zeta. Evolution shows that beta and gamma are paralogous and considered unique as compared to other members. Moreover, focusing precisely on the cell division machinary, again both these groups (beta and gamma) have unique proteins that lack any reportable homologs in other groups. So what makes beta and or gammaproteobacteria unique? Is this related to adaptive evolution as they are relatively "younger" than others. Or is there any other specific reason for this, as cell division is a fundamental process and should be highly conserved. What could be the reason for inclusion of unique or species specific members.? 

Optimization of violacein from chromobacterium violaceum

Are they still regarded as different strains of a single pathogen or different species of Xanthomonas?

Can anyone confirm that C. jejuni does in fact has only one VS1 gene per cell? We have noticed varying results in our lab and since VS1 gene function is not known, it is difficult to interpret what we are seeing.

Could anyone give me the description of a solid medium preparation for cultivation of Acidithiobacillus ferroxidans?

Because I would like to phagocyte the S. typhi.

Hi All,

I want to work on the possibility of infecting a Burkholderia with its phage to enhance its mineral weatherability. What phage do you suggest I use?

Hi guys, I am pretty sure that some strains have similar 16S rRNA sequences but have distinct metabolic repertoires. But I couldn't find any paper discussing about that. If you have a copy of this kind of paper, please send it to me. Thanks :)

I ask this question because I find in my research the diversity derived from functional gene array (GeoChip) is much more greater at phylum level than the 16S rRNA pyrosequencing illustrated (33 phyla vs. 11 phyla). It can be argued that functional gene probes couldn't suggest the exact phylogenetic assignment due to HGT across different species. But Geochip totally outrages 16S rRNA pyrosequencing, though the top 8 abundant phyla are quite similar.

Based on 16S rRNA analysis, betaproteobacteria is the predominant group. Could betaproteobacteria carries lots of genes derived from other phyla?

I have been observing that when monsoon moisture moves over certain tropical forests located in SE Asia or India, rain clouds with very long streaks form.  Has anyone studied if this is caused by Pseudomonas bacteria that live on particular species of tropical trees, and if so which tree species produce the most rain clouds?  Attached is a satellite image from August 2014 showing these particular clouds forming over the forests along the SW coast of India.

I am working with bacterial leaf blight of rice caused by Xanthomonas oryae.  Already I have isolated the pathogen and confirmed by using molecular techniques, in order to prove the koch postulate I am in need of this rice variety ,can anyone help me with this, when I asked in few rice research stations they gave a negative answer like this is no longer in use .

Only biochemical methods please.

I work on symbiotic-nitrogen fixing Burkholderia (so there is no problem to isolate Burkholderia sp. from nodules). This time I would like to isolate bacteria of Burkholderia genus from rice rhizosphere and from seeds, where the bacterial diversity can be very high. I wondered if there exists a selective culture medium to get rid of the gram-positives bacteria, or even to specifically select Burkholderia, in order to avoid identification of all bacterial isolates.

Soil micro-organisms have different ways to interact with uranium in uranium contaminated soils. Proteobacteria have been reported to carry out the reduction of hexavalent uranium to tetravalent uranium under anaerobic conditions. Can anybody tell me what could be the potential role of proteobacteria in uranium contaminated aerobic soils?