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Agricultural soil community analysis

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In this tutorial we will analyze bacterial 16S-based communities originating from soil samples of three different farming systems. The sequences were originally published by Hartmann and Widmer (2004).

Getting started

Download and align sequences

Download the sequences from NCBI GenBank by using the command DQ827724:DQ829627 [ACCN] or from DOK03.zip. We will first generate a multiple sequence alignment of the 1904 16S sequences by using mothur. You can download and unpack the greengenes or silva database to the mothur folder. Open the mothur terminal and align the sequences in DOK03.fasta against one of the reference databases, for example against greengenes, and use a filter to remove columns only represented by gaps:

mothur > align.seqs(candidate=DOK03.fasta, template=core_set_aligned.imputed.fasta)
mothur > filter.seqs(fasta=DOK03.kmer.needleman.nast.align)

We rename this file to DOK03.al.greengenes.fasta. Alternatively, you can use a database-independent alignment algorithm such as MAFFT. For this purpose, upload DOK03.fasta to the server and use the default parameters to run MAFFT. Copy the fasta formatted alignment into a text editor and rename the file to DOK03.al.mafft.fasta.

Create distance matrix

We will use the Phylip program DNAdist to generate a distance matrix. Before we can run our file, we have to convert the fasta to phylip formatted files. Use ReadSeq or equivalent tools to convert the aligned fasta files by using the format phylip4. We name the files DOK03.al.greengenes.phy and DOK03.al.mafft.phy. The DNAdist algorithm can be run online (e.g. trishul.sci.gu.edu.au, mobyle.pasteur.fr) or downloaded and used according to the following instructions:

  1. Download the Phylip package.
  2. Copy the executable dnadist.exe into the directory with your data files and execute the program.
  3. When prompted for the input file type the name of the phylip formatted alignment file (e.g. DOK03.al.greengenes.phy).
  4. Create new outfile (e.g. DOK03.al.greengenes.dist).
  5. Press D to select Jukes-Cantor as distance. Default can be used for all other parameters.
  6. Copy the file into the mothur folder.

OTU-based analyses

Single-sample analysis

Alignment accuracy

Now we can start analyzing our dataset with mothur and determine the number of operational taxonomic units (OTUs) in our communities. First, we will evaluate the two alignment algorithms. Do both strategies lead to a similar binning into OTUs? Load the distance matrix by using the read.dist command, cluster sequences into OTUs using the cluster command, and perform rarefaction analysis using the rarefaction.single command:

mothur > read.dist(phylip=DOK03.al.greengenes.dist, cutoff=0.05)
mothur > cluster()
mothur > rarefaction.single()

and/or

mothur > read.dist(phylip=DOK03.al.mafft.dist, cutoff=0.05)
mothur > cluster()
mothur > rarefaction()

This will create four files for each alignment, e.g. DOK03.al.greengenes.fn.list, DOK03.al.greengenes.fn.rabund, DOK03.al.greengenes.fn.sabund, and DOK03.al.greengenes.fn.rarefaction. Plot rarefaction curves of both alignments at OTU levels unique, 0.03 and 0.05 and you will see that both alignments perform very similarly in generating OTUs.

Rarefaction curves at OTU levels unique, 0.03 and 0.05 for both alignments, i.e. greengenes (G) and mafft (M).

Richness/diversity of samples

Now we are ready to analyze our communities in more detail. For this purpose, we will go ahead with one alignment, e.g. DOK03.al.greengenes.dist. Our dataset contains sequences from three agriculturally managed soils, i.e. unfertilized (NOFERT), conventionally managed (CONFYM), and bio-dynamically managed (BIODYN). To investigate differences between the three treatments, we need to parse the defined OTUs in file DOK03.al.greengenes.fn.list into the three groups by using the definition file DOK.groups and the read.otu command:

mothur > read.otu(list=DOK03.al.greengenes.fn.list, group=DOK.groups)

This command will generate the files DOK03.al.greengenes.fn.shared, DOK03.al.greengenes.fn.NOFERT.list, DOK03.al.greengenes.fn.CONFYM.list, and DOK03.al.greengenes.fn.BIODYN.list. Look at examples for a shared or list file. We are of course interested in how well our sampling effort covers the diversity of the bacterial communities as well as how diversity/richness of the communities compare between the three different treatments. For this purpose, we perform a rarefaction analysis on the parsed list files.

mothur > read.otu(list=DOK03.al.greengenes.fn.NOFERT.list)
mothur > rarefaction.single()

and

mothur > read.otu(list=DOK03.al.greengenes.fn.CONFYM.list)
mothur > rarefaction.single()

and

mothur > read.otu(list=DOK03.al.greengenes.fn.BIODYN.list)
mothur > rarefaction.single()
Rarefaction curves for samples NOFERT, CONFYM and BIODYN at OTU level 0.03. Lower and higher confidence intervals are indicated as dashed lines.

The three datasets show no difference in the rarefaction curves, indicating that they have very similar diversity. We will calculate and compare some commonly used richness and diversity estimators such as Chao1, ACE, Shannon, and Simpson:

mothur > read.otu(list=DOK03.al.greengenes.fn.NOFERT.list)
mothur > summary.single(calc=chao-ace-shannon-simpson)

and

mothur > read.otu(list=DOK03.al.greengenes.fn.CONFYM.list)
mothur > summary.single(calc=chao-ace-shannon-simpson)

and

mothur > read.otu(list=DOK03.al.greengenes.fn.BIODYN.list)
mothur > summary.single(calc=chao-ace-shannon-simpson)
Richness (Chao1, ACE) and diversity (Shannon, 1-Simpson) estimators of the datasets NOFERT, BIODYN, and CONFYM at an OTU definition level of 0.03. Lower and higher confidence intervals are indicated as error bars.

Generally, only small differences in richness and diversity were observed among the three communities. The Simpson diversity index indicated that the unfertilized sample NOFERT might have a lower diversity when compared to the other two treatments.

Multiple-sample analysis

Universal richness and diversity estimators revealed no differences between the three communities. However, communities with similar richness and/or diversity can have significantly different underlying community structures. Multiple-sample analyses allow us to evaluate differences in shared OTUs between the communities. Let us first look at the number of OTUs that are shared between pairs or all three samples:

mothur > read.otu(shared=DOK03.al.greengenes.fn.shared, label=unique-0.03-0.05)
mothur > summary.shared()

This will create two files called DOK03.al.greengenes.fn.shared.summary and DOK03.al.greengenes.fn.sharedmultiple.summary that give several calculators of shared richness (e.g. Shared Sobs, Shared Chao1, Shared ACE) and community similarity (e.g. Jaccard Similarity, Sorenson Similarity, Yue & Clayton Similarity). Richness and similarity indices indicate that the two systems receiving fertilizer (BIODYN, CONFYM) are more similar to each other than to the unfertilized system (NOFERT), whereas CONFYM is more similar to NOFERT than BIODYN to NOFERT.

Shared richness (Sobs, Chao1, ACE) and similarity (abundance-based Jaccard and Sorenson, Yue & Clayton) indices of datasets NOFERT, BIODYN, and CONFYM at an OTU definition level of 0.03.

Venn diagrams are particularly useful to display such data as long as the number of comparisons is not higher than three.

mothur > read.otu(shared=DOK03.al.greengenes.fn.shared, label=unique-0.03-0.05)
mothur > venn(label=0.03)
Venn diagram for shared richness (Sobs) among the datasets NOFERT, BIODYN, and CONFYM at OTU definition of 0.03.

Hypothesis-based analyses

Despite high similarity in OTU diversity between samples NOFERT, BIODYN, and CONFYM, we have found indication that the community structures of the samples might be different. The original study concluded that community structures from treatments receiving manure, i.e. BIODYN and CONFYM, are more similar to each other when compared to NOFERT. The results gained from the sequence libraries were in agreement with replicated community profiling data from a preceding study. I re-generated the cluster analysis used in the original study with the data gained by mothur in the shared file.

Cluster analysis of NOFERT, BIODYN, and CONFYM at an OTU definition level of 0.03.

We evaluate if these results can be confirmed by using hypothesis testing approaches such as the libshuff command.

mothur > read.dist(phylip=DOK03.al.greengenes.dist, group=DOK.groups)
mothur > libshuff()

After correction for multiple comparisons (e.g. 0.05/6 = 0.0083), we can conclude that community structures are probably significantly different between all three samples, although the test was not convincing for the comparison NOFERT-CONFYM.

Comparison          	dCXYScore	Significance
BIODYN-CONFYM       	0.00049472	0.0027
CONFYM-BIODYN       	0.00108234	<0.0001
BIODYN-NOFERT       	0.00186151	<0.0001
NOFERT-BIODYN       	0.00212569	<0.0001
CONFYM-NOFERT       	0.00102956	<0.0001
NOFERT-CONFYM       	0.00020876	0.0909

We can also test for significant differences using one of the tree-based method implemented in mothur, i.e. Parsimony analysis, Unweighted UniFrac, or Weighted UniFrac. First, we need to build a tree based on our sequence alignment, for example by the Phylip program neighbor. The neighbor algorithm can be run online (mobyle.pasteur.fr) or downloaded and used according to the following instructions:

  1. Download the Phylip package.
  2. Copy the executable neighbor.exe into the directory with your data files and execute the program.
  3. When prompted for the input file type the name of the DNA distance matrix created above, i.e. DOK03.al.greengenes.dist).
  4. Create new outfile (e.g. DOK03.al.greengenes.report).
  5. Run neighbor.exe using default settings.
  6. Create new treefile (e.g. DOK03.al.greengenes.tree).
  7. Copy the file into the mothur folder.

Now we are ready to run the parsimony test in mothur:

mothur > read.tree(tree=DOK03.al.greengenes.tree, group=DOK.groups)
mothur > parsimony()

or use unifrac.unweighted and Weighted UniFrac method:

mothur > read.tree(tree=DOK03.al.greengenes.tree, group=DOK.groups)
mothur > unifrac.unweighted()
mothur > unifrac.weighted()

This process might use a lot of time and memory to perform.