Questions related to Microbial Diversity
What kind of soil is rich with microorganisms and impact of introducing new microorganisms to soil microbial diversity?
I recently received metagenomic 16S rRNA gene sequence data from a company, which includes both raw reads, and clean data with barcodes removed. My goal is to analyze these sequences and obtain information on the taxonomic diversity and abundance of the species present in the sample.
Since I use a Windows system and cannot utilize Mac or Linux, I would greatly appreciate guidance on how to proceed with this analysis. Are there any web server-based applications available that can assist with this task?
Furthermore, if there are any researchers or experts interested in this project, I would be grateful to explore potential collaborations. Please feel free to reach out to me if you are interested or have any recommendations.
Thank you in advance for your assistance.
Why is microbial diversity important in the ecosystem and relationship between soil microbial diversity and ecosystem function?
What is the role of microbes in maintaining temperature and microbial diversity changing with climate change?
How does microbial diversity help the environment and potential impacts of climate change on microbial communities?
My undergraduate thesis partner and I will be identifying and characterizing the microbial diversity in 3 sample sites from an urban river. We were thinking of using Sanger sequencing since we would just like to identify what is in the river, but NGS yields a lot of data to really characterize the bacteria present. Our main issue with NGS however would be cost. We are planning to apply for subsidies but our budget is around PHP 20,000 or USD 360. If we will be sending 3 samples, which institution has the most affordable NGS sequencing service? What are possible alternatives to NGS that are more cost-friendly to undergraduate students?
I am studying microbial diversity and wants to know which culture media should I use to get a better understanding of microbial diversity
Actually I am writing a review on Microbial diversity of a medicinal plant and want my article to be published in Reviews in Microbiology of Natures. I have gone through previously published articles and also guide to author section of the journal but still have few confusions regarding the formatting of article. I want to ask that should we have to give the details of frequently used words into separate boxes/sections? as I have seen it is provided into separate boxes in previously published articles. Please try to help me regarding this.
Dear researchers, I am conducting an experiment with five treatments, out of which four treatments are used as a rotation, while the 5th one is used as a control (bare plot).
How can I take a soil sample from these plots for soil microbial diversity analysis? In rotation plots, rhizosphere samples can be taken but in the bare fallow plots, which method do I use to take samples. If I take rhizosphere samples in vegetable plots, then fallow plot soil would be considered as bulk soil. How can I compare the bulk soil with rhizosphere soil?
I appreciate any help you can provide.
I am interested in doing microbial diversity analysis associated with a plant. I was looking for PNA clamps suppliers who can provide me mitochondrial PNA and plastid PNAs. Let me know if anyone has used it in their experiments or if someone can provide me as a courtesy.
Thanks in advance.
Hi, can anyone recommend any papers exploring the relationship between microbial biomass and microbial diversity? Some papers I have looked at just say there’s a moderately positive correlation in their introductions but it’s not the focus of the study or the studies cited.
I also would love if anyone could share papers expounding on the Fungal:Bacteria and G+:G- bacterial ratios and their link to ecosystem functioning/soil health. I have tried searching for studies that go deeper into why these ratios are the objects of many experiments‘ focii, but I still feel I am missing some gaps in their connection with soil health (and soil biodiversity/biomass).Thanks!
extensive exploitation of soil by following un-scientific practices of agriculture and introducing new Micro-Organisms (Beneficial Microorganisms for Agriculture ) to local soil microbial diversity. Are we altering the ecosystem of such microbial diversity of the respective soil?
I want to determine the effect of paddy farming on microbial biodiversity without using molecular methods since they are expensive and I don't have access to it.
Can anyone point to any studies (other than the one below) that suggest a loss of microbial diversity in a given habitat exacerbates the spread of ARGs, or that increasing microbial diversity (e.g. via inoculation) reduces ARGs?
And/or if you have any general thoughts on this, please leave comments.
I am comparing the gut microbial diversity of 2 groups of individuals. I found that the alpha diversity is significantly different but the beta diversity is not significantly different. Can I still assume that the groups are different in their microbial population?
The fact that fewer birds from each replicate will be used for sampling leaving more than half from each experiment unused is the problem, which in effect is related to cost.
DR. Kan asked for more datails about the study. (please see below).
Experimental Procedure Experiment 1.
Effects of dietary supplementation of a phytobiotic or synbiotic on the growth performance, immune status, and cecal microbiota of pasture-based broilers. A total of 180 one-day-old, male Cornish Cross broiler chicks will be purchased from a local commercial hatchery. All birds will be fed a corn-soy meal starter diet containing 23% CP. After two weeks, the birds will be blocked by weight and randomly allocated in triplicate (20 birds per replicate) to one of three dietary treatments. For six weeks, birds will be fed the control diet (CON), the control diet supplemented with thymol and carvadiol or the control diet supplemented with symbiotic. All birds will have free access to pasture from sunrise to sunset.
On 28 and 42 days of age, six birds from each treatment (two birds from each replicated pen) will be randomly selected, individually weighed and samples taken.
Effects of dietary supplementation of thymol or synbiotic on laying performance, egg quality, and cecal microbial diversity of pasture-based laying hens. A total of 90 Rhode Island Red hens at point-of-lay will be used in this study. The birds will be randomly allocated in triplicate (10 birds per replicate) to one of three dietary treatments. For 12 weeks, the birds will be fed control diet (CON), the control diet supplemented with thymol and carvadiol or the control diet supplemented with symbiotic. Birds will be placed on commercial layer diet (16% CP) with free access to pasture from sunrise to sunset.
On week 10, samples will be collected from one bird from each replicate.
Data will be analyzed using the GLIMMIX procedure of SAS. Each replicate will be considered the experimental unit and the model will include the fixed effect of treatment. Effects will be declared significant at P ≤ 0.05 and tendencies will be considered when 0.05 < P ≤ 0.10.
NOTE: In Expt. 1, 36 birds will be sampled out of a total of 180 (144 birds will not be used)
In Expt. 2, 9 birds will be sampled out of a total of 90 (81 birds will not be used)
Different taxonomic levels are used in mono-gastric animal feeding experiments which report changes in intestinal microbial diversity indexes and relative abundance caused by dietary treatments. For example, paper report changes in diversity indexes and relative abundance of fecal microbiol in phylum level, family level or genus level for studying effects of buytric acid (a feed additive) supplementation. And sometimes researchers relate the changes in intestinal microbial diversity indexes and relative abundance to the improvements in growth performance and incidence of diarrhea of experimental animals. Can someone experienced in this field explain the criteria for choosing the correct taxonomic level for comparing microbial diversity following dietary treatments? What factors should be considered? Thank you.
Hi you all,
I'm looking for a not very expensive journal to submit our work related to microbial diversity in a beverage drink using an amplicon perspective. Any suggestion is welcome because I am lost!
Thank you in advance
What are the suitable software to analyze the raw DNA sequences (16S rRNA data ) for microbial diversity analysis ?
i would like to analysis/identify the microbial diversity at the ripening of passion fruit, and want to anlysis about which fugus, bacteria or microbe are present and which species.s
so which analysi should recommend ? as 16s, 18s and ITS ?
which one is suitable ?
First, how to isolate DNA from effective microorganisms? is it the more to genomic DNA isolation or metagenomic DNA isolation protocol?
Second, is the Bacterial 16s rRNA Amplicon Sequencing with Illumina 250 PE/ 300 PE strategy, suitable to study their microbial diversity?
I have sampled the roots of specific crop along with soil from four different areas of Sindh Province of Pakistan. Can you suggest me the technique to determine the microbial diversity in these samples please?
I woultd like to study the microbial diversity of hypersaline water by PCR-DGEE followed by sequencing. Before this step I have sequenced the 16s rRNA gene of some isolated strains from this sample by using the following archaea specif pair of primers
A20F (TCC GGT TGA TCC TGC CG)
A1540R (GGA GGT GAT CCA GCC G)
Do I have to use this pair of primers in DGGE?
For the DGGE analysis of bacterial diversity I will use another pair of primers.
I am pursuing my PhD degree from vit university, india. I wish to apply for short term visiting fellowship (3-9 months) in different countries (except USA,UK, FRANCE, KOREA). My domain of research includes the study of microbial diversity in high background radiation area and their adaptive strategy. I passionately want to work in the field of radio ecology and bioremediation of radioactive waste which are similar to my research interest.
I look forward to any suggestion of research laboratory/ institutes/ universities related to my field of research.
Thank you all in advance.
I am in the process of a microbial diversity study of soil samples through 16S rRNA sequencing and overall microbiome analysis. Through this analysis, I have identified one single microbe that is of particular interest in the Chloroflexi phyla, and I would like to isolate this microbe from leftover soil samples and culture it for further study.
What would be the best method(s) to isolate the specific microbe from the overall soil sample, and then culture the microbe from there?
What are the classic papers about interaction effect of extreme drought and plant composition(diversity) in the grassland ?
Hello everyone! I'm looking for information about interaction effect of extreme drought and plant composition(diversity) in the steppe and I want to start reading the papers about this topic, especially its influence on the carbon exchange and soil microbial diversity.
I would like to study the metagenomic diversity of actinobacteria associated with the marine sponges. In this context, I would like to use actinospecific primers to capture the complete actinobacteria phylum rather than using universal primers. Especially, would like to explore the rare actinobacteria like Salinispora.
I am aware the actinospecific primers given by Stach et al. 2003 ( SC-Act-235aS20, SC-Act-878aA19) may be useful in my case. However, as the primer read length is 640 bp it can not be used for Illumina.
Illumina can deliver less than 400 bp.
Blackwood et al., 2005 has also proposed Phyla specific primers. He has reported that the Actinobacteria Phyla specific primer "Act1159R" captures most of the actinobacteria they tested. Can it be useful in my case? Whether the Reverse primer alone sufficient to explore the actinobacterial Phyla?
Kindly, some one can provide me the write primer that will be helpful for me.
Thanks in Advance.
To explore the soil microbial diversity, usually we analyse the alpha and beta-diversity of microbes. what is the significance of both indicators, what these indices explicit the true microbial picture? If only analysed alpha-diversity by 454-pyrosequencing, is that enough in data. If beta-diversity appear with no significant difference with treatments and control, can we exclude it from data ? If Only alpha-diversity has significant different between treatments, is that enough for data?
To explore the microbial diversity through High sequencing approach like 454- Pyrosequencing or Mi seq Illumina sequence, sometime the terms microbial community and microbial diversity may confuse, or look similar in meanings. Kindly precisely differentiate that...
I have around 30 samples of sequenced plant microbiomes from one location. I would like to find out if there is any correlation between how far the samples are away from each other and their overall similarity.
An idea is to create pairwise distance measurements between samples and plot them against similarity values.
1) Is it possible to get a similarity values (say between 0-1) for samples?
2) Does anyone know of a better/existing method for such comparisons?
Thanks a lot
I'm working on soil microbiology and I want to check the microbial diversity in the soil. so, I have 2 options,PE illumina or 454-Pyrosequencing. I want to ask that which technique is better to use and why is this so?
Ralstonia solanacearum, a harmful plant pathogen of warm climate zone, worldwide plant quarantine organism is often found in irrigation water at more cold areas (Turkey, Poland, Russia) without causing plant diseases in fields around the isolation site. It is long-surviving in soil bacterium in tropical area. I see the only possible explanation - association between Rs and some soil/fresh water algae (like done by Pseudomonas syringae).
So, can Rs go to North with its potential host under progress of the Global warming? Any other ideas?
If you want to do taxonomic profiling of your ngs data, mainly comprising the variable regions of 16S (v3-v4), which database you will prefer and why ?
I am working on microbial diversity and planing to send samples for Next Generation Sequencing (NGS); Which hypervariable region of 16S rRNA gene will appropriate to target most of bacterial taxa present in seawater.
Good evening respected teachers/scholar/researcher, I hope you are fine and doing well, I am Ph. D student in china, working on current project "Sustainable vegetable production in china" in College of Horticulture, Northwest A&F University, China. I analysed soil microbial diversity by Illumina MiSeq platform. i have data in figure form, some of them i couldn't understand How to interpret it well especially "Heat map analysis" ? my capabilities are very limited in soil bio diversity and microbial ecology. So i need assistance belong to bioinformatic or soil microbial ecology experts for my figure illustration? Details about these figures are in attached file. I really thankful if someone help me in this regard.
Does anybody know which is the best way of calculating alpha and beta diversity from molecular fingerprint techniques? I have done DGGE with environmental samples in order to determine the diversity of microalgae, I have the band patterns with the number of species in each sample, but I'm not sure how to calculate diversity, taking into account that I don't have abundance data, only number of species.
Year 2015 is being celebrated as International year of Soil.As we are all aware soil is foundation to agroecosystems and base for agricultural production.Soil is living system ,store house for carbon and microbial diversity, biochemical laboratory, filter, decontaminant. By providing ecosystem services, food security, climate resilience,supporting animal and human health,soils are serving the humanity.So,what can be done for safe ,secure and sustainable use of soil in future.
I am looking for microbial diversity pattern in soil samples from different altitudes through DGGE. I used FastDNA™ SPIN Kit for Soil DNA extraction but I am getting lot of brownish color in the final eluted DNA. Can anyone suggest me a method to get rid of this problem, as this is hampering further downstream process.
There are so many microbial diversity investigations using high-throughput sequencing on variety of natural environments, e.g. land soil, fresh and salt water, sediment etc. Some of them sampling their samples in a site, and then mixed them for one sample to do the next study. I want to know if this kind of sampling method are scientific and rigorous? And how to do a scientific and rigorous sampling when we do microbial diversity investigation in natural environments?
I would like to calculate diversity index from DGGE banding patterns.
Can the DGGE band strength/intensity actually be estimated visually as described by Gafan et al. (2005)?
Anyone knows any papers that make use of the same approach?
Gafan, G. P., Lucas, V. S., Roberts, G. J., Petrie, A., Wilson, M., & Spratt, D. A. (2005). Statistical analyses of complex denaturing gradient gel electrophoresis profiles. Journal of clinical microbiology, 43(8), 3971-3978.
Literature findings are contrasting and published cytograms are not convincing.
Are there any latest molecular tools beside DGGE, TRFLP and Illumina to assess microbial diversity of environmental samples with ease? If yes kindly suggest..otherwise which among three is better suited for the same?
I´m studying microbial community development in time (using 16S sequencing) and would like to tell what taxa are changing in time and in what way (significantly increase, decrease...). I have an OTU table, what analysis is advisable?
I am growing TG1 cells on 2XYT media without any antibiotic and getting two types of colonies, one is opaque and another one is transparent . i dont know which one is actually TG1. Can anyone help me ?
I have extracted genomic DNA from 4 single lesions derived from one rust isolate. By PCR amplifying elongation factor gene, I saw different band pattern on the gel. Can anybody let me know whether even spores derived from Single Spore Isolation are still genetically different?
I would like to know what is common practice in countries outside The Netherlands. Do you use a name like Dolichospermum for planktic Anabaena?
Is there a website,database or a manual where the CDMs are listed? I have been digging through various papers from 1960s, but may be there is an easier way. Thanks.
I want to study the molecular diversity and homogeneity of bla-CTX-M genes in E. coli isolates from different localities in relation to their phenotypic characteristics, such as antibiotic resistance to various drugs, based on some molecular techniques. As, I am not a molecular biologist, therefore, I need guidance in this context. Thank you very much.
I would like to study on spatial distribution of soil organic matter fractions [such as dissolved organic carbon (DOC), dissolved organic nitrogen (DON), particulate organic carbon (POC) and particulate organic nitrogen (PON)] and also microbial respiration, microbial biomass C and N in mono-species 20-year old plantations of alder (A. subcordata C. A. M.) and oak (Q. castaneifolia C. A. M.), planted at a spacing of 2×2 m, located in northern Iran. The stands were never fertilized. The study areas show very similar climatic conditions and management practices. The experimental plots were located at an altitude of 300 m above sea level. The area is on flat and uniform terrain with low slope (0–3%).
Unfortunately I didn’t find any reference about soil sampling design. I have two questions about this project:
Question 1: How many soil samples (the minimum) are enough for study on spatial distribution of soil organic matter fractions and microbial features for each of these stands?
Question 2: Which sampling design is the best for soil sampling?
May you please help me about these questions? Do you have any references about these to present?
What possibles outcomes or conclusion can be drawn from comparative taxonomic/functional diversity analysis of different hot springs on the basis of pH, Temperature and locations?
When I studied the microbial diversity, I wanted to choose a good method for the relationships between microbial diversity and environmental factors. So I found some relatives. I thought db-RDA and CAP are good methods for my study, but I don't know the difference between them. Can you give me some advices. Thanks!
I am working on exploration of hidden microbial diversity using shotgun sequencing approach.
I need to analyze my data using PAST.
I installed PAST in my PC drive, I read the manual also, but I'm still facing problem for transfer MG-RAST tsv. file from excel into PAST. Help me.
The effects of nitrogen addition, and more widely fertilizer, on soil microbial (bacteria, archaea and fungi) diversity and activity have been investigated, but the understanding of the effect of potassium alone (e.g. in the form of potassium sulphate) on soil microbial communities seems to be more limited. Are we expecting a negative/positive direct or indirect effect (or no effect?) on soil microorganisms, due for example to a change in soil pH or in plant growth (reduction in N uptake, decrease in roots exudate)?
Dual/multiple inoculation of rhizo-competent microbes is now almost a common practice, irrespective of crop and soil type. In the process , there has been growing concerns about exploiting the rhizosphere microbial diversity , in order to develop the crop specific microbial consortium . We have developed a microbial consortium for citrus . The developed microbial consortium consists of five microbes viz., Bacillus polymyxa, Pseudomonas flourescens, Trichoderma harzianum, Azotobacter chroococcum, and Bacillus mycoides , isolated from rhizosphere of citrus grown on smectite rich alkaline black clay soils . Their complementarity test , shelf life , response in nursary , and in field ( Under INM mode ) have comprehensively established the excellent performance of developed microbial consortium . I call upon my esteemed colleagues to express their opinion as how to further improve the efficacy of microbial consortium . We now intend to carry out further studies with respect to following:
# There has been some antagonistic effect of Pseudomonas on the population of Trichoderma during the complentarity test , what shall be our strategy to overcome such relation in the context of long shelf life of microbial consortium ?.
# What could be the probable options to use cheaper growing media to lessen the cost of the microbial consortium ?.
# Is it possible to improve the nutrient value of microbial consortium by supply some additional nutrients into the growing medium ? .
# How can we extend the shelf life of microbial consortium ?.
# Do we need to develop a different microbial consortium for citrus, if grown on a different soil type ?.
Microbial abundance of soil is normally considered synonymous to higher bio-availability of nutrients , and hence soils are biologically more responsive to any management input(s). The soil microbial diversity in a given soil is claimed to undergo transformation in response to metabolic requirement of any crop being grown on a specific soil. In this background , I call upon my esteemed colleagues to throw some valuable comments on the following issues:
# How does a stable microbial diversity in a given soil undergo reorientation in response to heavy metal accumulation/contamination/.
# Do we expect a definite change in structural and functional composition of microbial diversity in the light of contaminated soil vis-a-vis uncontaminated/normal soil ?.
# Which group of microbes is considered more sensitive ( Prevalence of one species over other ) to such disturbances in soil microbial environment?.
# What kind of implications of contaminants , do you anticipate in the context of bioavailability of nutrients in soil ?.
I want to quantify the microbial diversity in the rhizospheric soil of paddy field. kindly provide me the standard protocol with references.
EcoSim software can be used to calculate the checkboard score with species absence/presence pattern in order to evaluate species interaction. However, in a community, speices density is going to be an important factor that affects the interactions between species, especially in microbial systems. Is there any robust tool (null models) to handle microbial abundence data to indicate the direction and extent of the interacting process?
I am looking for good an most of all recent estimates of bacterial diversity in different ecosystems, i.e seawater, freshwater and soil.
The two numbers that are cited everywhere are 20 000 species per litter of seawater and 10 000 species per gram of soil. The first number comes from Sogin et al (2006) and is based on an extrapolation with the Chao1 index. They observed about 6000 OTUs clustered at the 3% level. The second number come from Gans et al (2006) who cites Torsvik et al from 1990!
Given the development of NGS sequencing, there must be better estimates around than these 9 to 25 years old paper.
Do you know of any?
Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D., Huse, S. M., Neal, P. R., et al. (2006). Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proceedings of the National Academy of Sciences of the United States of America, 103(32), 12115–12120.
Torsvik, Vigdis, Jostein Goksøyr, and FRIDA LISE Daae. "High diversity in DNA of soil bacteria." Applied and environmental microbiology 56.3 (1990): 782-787.
Gans, J., Wolinsky, M., & Dunbar, J. (2005). Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science, 309(5739), 1387–1390. http://doi.org/10.1126/science.1112665
Currently, the co-occurrence network were built base on correlation, regression, or other statistical methods. However, these results are ambiguous for understand the interactions. Is there some other method to identify the interactions in microbial network?
Normally for pure bacteria culture isolation people refer to do 16s RNA sequencing and they get phylogenetic tree, in my case i have mixed of microorganisma in a solution, I want to know the microbial diversity with phylogentic tree in my solution. For that what kind of DNA sequencing i have to refer.
I am studying microbial diversity from environmental samples. I am using v4 of 16S rRNA gene sequenced with Illumina MiSeq (paired-end). Quality control and statistics were done using Mothur package from which BIOM file was generated and imported in MEGAN5 for visualization. From my OTU file, Proteinclasticum is the most abundant, BUT when get bar plots from MEGAN5 I can not see them most abundant OTU? What could be wrong?. Thanks
I have Isolated and identified many enteric, bacillus and nonfermenters from Bovine manure during decomposition process on the basis of morphological and biochemical characteristics. Now I would like to go for clostridium, how it can be possible? and what protocols should be followed?
Thanks in advance!
I have isolated some bacteria and I want to identify them at stain level. I have determined their 16s RNA sequences and after BLAST they showed the similarities with many bacillus bacteria. The results are in attached picture. So what I need to do next to find the name of these bacteria at strain level?
I am currently analysing 16S amplicon data of microbial populations from environmental samples, and trying to apply network analysis to explore OTU-OTU and OTU-environmental properties relationships. At the moment I have successfully created OTU co-occurrance networks using the Cytoscape plugin CoNet, and I am now trying to move forward to the ecological interpretation of the networks. Since I wasn't able to find some good references regarding ecological interpretation of the networks shape, and interpretation and use of network properties, Can anybody suggests some review/articles/books or other resources type covering the use of network analysis in (microbial) population studies?