Ecological Archives E093-145-A2

Jessica A. Bryant, Frank J. Stewart, John M. Eppley, and Edward F. DeLong. 2012. Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology 93:1659–1673. http://dx.doi.org/10.1890/11-1204.1

Appendix B. Abundance and richness within broad taxonomic groups.

Table B1. Taxonomic richness (TR) within broad taxonomic groups at the Eastern Tropical South Pacific (ETSP) in 2009.*

Clade 35 m 50 m 70 m 110 m 200 m Change across
gradient†
Flavobacteria 15.99 11.77 4.78 3.1 2.13 13.86
Alphaproteobacteria 54.89 47.51 46.55 32.89 42.55 12.34
Cyanobacteria 9.55 12.68 1.26 0.34 0.37 9.18
Euryarchaeota 7.68 14.03 6.56 3.33 2.44 5.25
Other Eukaryote 5.81 7.64 1.87 0.79 0.69 5.12
Fungi 2.97 3.91 0.15 0.7 0.79 2.18
Betaproteobacteria 3.37 2.4 2 2.03 2.09 1.28
A Alveolata 1.4 1.6 0.44 0 0.2 1.2
Sphingobacteria 1.27 1.37 0.6 0.32 0.4 0.87
Gammaproteobacteria 26.28 19.18 22.21 29.76 25.58 0.7
Metazoa 1.03 0.96 1.06 0.93 0.59 0.44
Verrucomicrobia 1.02 0.62 1.64 0.32 0.73 0.29
Other Bacteroidetes 0.33 0 0.15 0.18 0.21 0.12
Other Proteobacteria 0.51 0.72 0.75 2.41 0.41 0.1
Crenarchaeota 1.74 1.77 4.23 1.05 1.83 -0.09
BD1-5 0.43 0.14 1.01 0 0.79 -0.36
Acidobacteria 0 0 0.15 0 0.39 -0.39
Actinobacteria 2.55 2.97 3.92 3.19 3.07 -0.52
Other Bacteria 0.81 1.27 1.84 1.84 1.99 -1.18
Chloroflexi 0.64 0.27 2.15 1.21 2.28 -1.63
Firmicutes 2.55 3.94 4.58 2.68 4.44 -1.89
Deferribacteres 7.17 6.32 13.82 11.48 10.99 -3.83
Planctomycetes 2 1.74 5.46 8.33 6.78 -4.78
Deltaproteobacteria 4.7 7.1 12.73 6.72 11.06 -6.37

*TR at all depths was normalized to the smallest BATS library using rarefaction.
†Differences in TR between 35 m samples and 200 m samples. Positive values indicate TR is higher at 35 m. Negative values indicate that TR is higher at 200 m.


Table B2. Abundance of broad taxonomic groups at the ETSP in 2009.*

Clade 35 m 50 m 70 m 110 m 200 m Change across
gradient†
Flavobacteria 19.09 13.36 5 3.3 2.88 16.21
Cyanobacteria 10.55 15.98 1.3 0.36 0.43 10.12
Euryarchaeota 10.65 25 8 3.38 2.51 8.14
Other Eukaryote 7.53 9.56 1.93 0.85 0.81 6.72
Fungi 3.61 5.09 0.15 0.82 0.8 2.81
Betaproteobacteria 6 3.86 3.1 5.35 3.85 2.15
Metazoa 2.27 3.25 2.57 1.56 0.8 1.47
Alveolata 1.49 1.72 0.41 0 0.17 1.32
Sphingobacteria 1.27 1.54 0.59 0.32 0.41 0.86
Verrucomicrobia 1.02 0.64 2.1 0.34 0.85 0.17
Other Bacteroidetes 0.35 0 0.16 0.16 0.21 0.14
Other Proteobacteria 0.5 0.74 0.72 2.81 0.4 0.1
Crenarchaeota 1.83 2 5.87 1.15 1.85 -0.02
Alphaproteobacteria 73.14 62.73 61.63 53.27 73.35 -0.21
BD1-5 0.48 0.15 1.21 0 0.76 -0.28
Acidobacteria 0 0 0.14 0 0.4 -0.4
Actinobacteria 2.79 3.03 5.29 3.91 3.84 -1.05
Other Bacteria 0.83 1.39 2.1 2.02 2.03 -1.2
Chloroflexi 0.65 0.31 2.21 1.33 2.25 -1.6
Firmicutes 10.83 11.94 17.89 15.4 17.59 -6.76
Planctomycetes 3.24 2.92 6.86 11.53 10.8 -7.56
Deferribacteres 9.15 7.5 20.98 17.91 17.68 -8.53
Deltaproteobacteria 6.2 11.38 28.65 11.94 17.39 -11.19
Gammaproteobacteria 33.54 22.92 28.14 69.32 44.94 -11.4

*Abundance at all depths was normalized to the smallest BATS library using rarefaction.
†Differences in abundance between 35 m samples and 200 m samples. Positive values indicate that abundances are higher at 35 m. Negative values indicate that abundances are higher at 200 m.


Table B3. Taxonomic richness (TR) within broad taxonomic groups at BATS.*

Clade 20 m 50 m 100 m 500 m Change across
gradient†
Alphaproteobacteria 75.38 64 62.93 45 30.38
Cyanobacteria 9.36 11.68 13.19 1 8.36
Flavobacteria 7.69 4.71 9.91 2 5.69
Gammaproteobacteria 27.03 26.94 22.21 23 4.03
Other Bacteria 1.43 0.35 0.38 0 1.43
Betaproteobacteria 3.12 1.58 2.36 2 1.12
Planctomycetes 2.09 1.27 1.38 1 1.09
Sphingobacteria 1.04 1.67 1.49 0 1.04
Fungi 1.05 1.09 1.44 1 0.05
Verrucomicrobia 2.67 2.28 0.77 3 -0.33
Actinobacteria 2.56 3.44 4.98 3 -0.44
Alveolata 0 0.36 0.37 1 -1
Other Eukaryote 1.3 0.33 3.45 3 -1.7
Metazoa 0 0.59 0 2 -2
Acidobacteria 0 0 0 4 -4
Firmicutes 1.71 3.48 2.73 6 -4.29
Deltaproteobacteria 2.12 3.14 4.26 7 -4.88
Crenarchaeota 0 0 0 7 -7
Euryarchaeota 0 3.23 1.07 8 -8
Deferribacteres 4.58 9.3 7.52 14 -9.42
Chloroflexi 0 1.01 0.35 14 -14

*TR at all depths was normalized to the smallest BATS library using rarefaction.
†Differences in TR between 20 m samples and 500 m samples. Positive values indicate TR is higher at 20 m. Negative values indicate that TR is higher at 500 m.


Table B4. Abundance of broad taxonomic groups at BATS.*

Clade 20 m 50 m 100 m 500 m Change across
gradient†
Alphaproteobacteria 105.01 83.26 88.66 58 47.01
Cyanobacteria 13.55 33.93 28.02 1 12.55
Flavobacteria 9.7 6.17 11.59 2 7.7
Gammaproteobacteria 38.02 35.63 25.99 33 5.02
Firmicutes 14.46 12.46 16.92 11 3.46
Other Bacteria 1.74 0.38 0.39 0 1.74
Betaproteobacteria 4.66 2.43 3.34 3 1.66
Planctomycetes 2.09 2.41 3.82 1 1.09
Sphingobacteria 1.03 2.06 1.53 0 1.03
Actinobacteria 3.1 4.18 6.02 3 0.1
Fungi 1.04 0.99 1.52 1 0.04
Verrucomicrobia 3.8 2.39 0.75 4 -0.2
Alveolata 0 0.33 0.36 1 -1
Other Eukaryote 1.38 0.35 3.79 3 -1.62
Metazoa 0 0.66 0 2 -2
Acidobacteria 0 0 0 4 -4
Crenarchaeota 0 0 0 7 -7
Deltaproteobacteria 2.16 3.78 4.54 15 -12.84
Euryarchaeota 0 3.41 1.12 15 -15
Deferribacteres 5.26 11.17 8.27 24 -18.74
Chloroflexi 0 1.02 0.37 19 -19

*Abundance at all depths was normalized to the smallest BATS library using rarefaction.
†Differences in abundance between 20 m samples and 500 m samples. Positive values indicate that abundances are higher at 20 m. Negative values indicate that abundances are higher at 500 m.


Table B5. Taxonomic richness (TR) within broad taxonomic groups at HOT.*

Clade 25 m 75 m 110 m 500 m Change across
gradient†
Gammaproteobacteria 35.6 29.39 15.13 19.2 16.41
Cyanobacteria 12.1 15.51 16.86 3.7 8.41
Flavobacteria 8.91 7.47 5.67 1.61 7.3
Alphaproteobacteria 49.22 47.55 51.59 44.84 4.38
Metazoa 2.37 0.42 2.62 0.96 1.41
Other Eukaryote 2.36 1.74 10.1 1.19 1.17
Sphingobacteria 1.45 1.64 0 0.46 0.99
Alveolata 1.18 0.25 2.58 0.47 0.71
Other Bacteroidetes 0.26 0.47 0 0 0.26
Fungi 0.93 0.93 4.41 0.9 0.04
BD1-5 0 0.29 0.26 0 0
Other Bacteria 1.93 0 0.55 2.01 -0.08
Planctomycetes 1.11 1.74 1.32 1.38 -0.27
Betaproteobacteria 0.9 1.38 1.09 1.45 -0.55
Verrucomicrobia 1.74 2.23 2.5 2.51 -0.78
Euryarchaeota 3.6 2.57 5.71 4.7 -1.1
Firmicutes 2.77 2.47 3.09 4.2 -1.43
Actinobacteria 4.98 4.3 5.22 6.62 -1.64
Acidobacteria 0 0 0 2.31 -2.31
Deferribacteres 5.94 7.4 7.82 12.09 -6.14
Chloroflexi 0 1.46 1.38 6.42 -6.42
Deltaproteobacteria 1.94 4.11 6.45 13.95 -12.01
Crenarchaeota 0 0 0 17.05 -17.05

*Abundance at all depths was normalized to the smallest BATS library using rarefaction.
†Differences in TR between 25 m samples and 500 m samples. Positive values indicate that TR is higher at 25 m. Negative values indicate that TR is higher at 500 m.


Table B6. Abundance of broad taxonomic groups at HOT.*

Clade 25 m 75 m 110 m 500 m Change across
gradient†
Cyanobacteria 43.94 56.08 35.89 4.62 39.32
Gammaproteobacteria 45 35.31 16.89 23.82 21.18
Flavobacteria 9.57 8.89 6.75 1.89 7.68
Alphaproteobacteria 59.49 57.41 62.94 57.39 2.1
Other Eukaryote 2.69 2.13 13.65 1.27 1.42
Alveolata 1.53 0.25 2.8 0.48 1.05
Sphingobacteria 1.52 2.05 0 0.5 1.02
Other Bacteria 2.98 0 0.55 2.09 0.89
Planctomycetes 2.01 2.33 1.37 1.53 0.48
Other Bacteroidetes 0.24 0.5 0 0 0.24
Fungi 0.98 1.03 5.47 0.97 0.01
BD1-5 0 0.23 0.3 0 0
Metazoa 2.98 0.5 15.28 3.04 -0.06
Verrucomicrobia 2.04 2.5 3.54 2.65 -0.61
Betaproteobacteria 2 1.78 1.74 3.24 -1.24
Euryarchaeota 4.13 2.79 6.52 6.09 -1.96
Firmicutes 11.48 12.64 8.71 13.53 -2.05
Acidobacteria 0 0 0 2.23 -2.23
Actinobacteria 5.74 5.2 7.32 8.23 -2.49
Chloroflexi 0 2.29 1.35 7.41 -7.41
Deferribacteres 6.69 8.86 8.84 17.74 -11.05
Deltaproteobacteria 1.99 4.24 7.1 22.07 -20.08
Crenarchaeota 0 0 0 26.2 -26.2

*Abundance at all depths was normalized to the smallest BATS library using rarefaction.
†Differences in abundance between 25 m samples and 500 m samples. Positive values indicate that abundances are higher at 25 m. Negative values indicate that abundances are higher at 500 m.

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