Diatoms GoA SEM 2020-22
Yoav Avrahami
09/07/2022
~~~
Data collection and preparation
An investigation of diatom succession and community composition in the Gulf of Aqaba/ Eilat over 2 seasons (2020-22). Data collected by routine sampling (bi-weekly to daily) of seawater from st. A, filtering several L on polycarbonate 0.8 um filter (in duplicates).
Filters were counted in transect method (100-300 screens) by scanning electron microscope (SEM). Counts of individual diatoms were translated to concentration (individuals mL-1).Total concentration
Concentration based on size-fraction of 2 catergories: larger or smaller than 50 um.
Designated dataset for community analysis was compiled, by averaging duplicates at each time point, and log-transforming concentration (after addition of +1 to avoid log 0).
semtot<-read.csv("SEM_total_avg_log.csv",header = TRUE, row.names = 1)
Heatmap showing log-concentration of each species
To quantify similarities in community composition
over the different time-points, Bray-Curtis method was applied. Below
the green light are time points with high similarity (>80%). The red
line shows which samples share low simillarity (<50%).
tot.bc.dist <- vegdist(semtot, method = "bray")
tot.bc.clust <- hclust(tot.bc.dist, method = "average")
To look for patterns across the entire time points, I applied cluster analysis to see how the communities are grouped without interference. For deciding number of clusters I applied the elbow method and NbClust, which provides 30 indices for determining the relevant number of clusters and proposes the best clustering scheme from the different results.
# elbowtot<-fviz_nbclust(semtot, kmeans, method = "wss") +
# geom_vline(xintercept = 3, linetype = 2)+
# labs(subtitle = "Elbow method")
# nb <- NbClust(semtot, distance = "euclidean", min.nc = 2,
# max.nc = 10, method = "kmeans")
nbclust evaluation
Following these tests, the data was divided to 3 clusters.
grp <- cutree(tot.bc.clust, 3)NMDS ordination was applied to better visualize the distances between samples.
NMDStot <- metaMDS(semtot, k = 2, trymax = 100, trace = F, autotransform = FALSE, distance="bray")According to the stress value (0.13), and visually inspecting a Shepard plot, the ordination distances represents fairly the observed distances.
# stresstot<-stressplot(NMDStot)
Environmental variables were added to the ordination, to test correlation with the corresponding community composition.
NMDS.envfit <- envfit(NMDStot, env, permutations = 999)
NMDS shows 3 clusters following the cluster selection methods. Grey lines show the main environmental parameters and how they are driving the differences between clusters. In general, one cluster includes summer-fall-early winter, second cluster shows winter and spring bloom, and the third cluster contains fewer samples, of the 2022 early April bloom event.
Inferring ordination analysis
To better characterize the 3 communities that emerged from the ordination data, further analysis was applied to describe each community individually, and also to detect differences between these communities.The first anlaysis is analysis of similarity (ANOSIM). ANOSIM statistic compares the mean of ranked dissimilarities between groups to the mean of ranked dissimilarities within groups. An R value close to “1.0” suggests dissimilarity between groups while an R value close to “0” suggests an even distribution of high and low ranks within and between groups (credit: GUSTA ME).
anosim_res<-anosim(semtot, grouping = site.scrs$clusters, permutations=1000, distance="bray")
anosim_res$statistic<-round(anosim_res$statistic,digits=3)
anosim_res$signif<-round(anosim_res$signif,digits=3)
Dissimilarity between groups is higher then dissimilarity within
groups, suggesting each cluster has a distinct diatoms community.
The next procedure is Similarity Percentages analysis (SIMPER), that
addresses the relative contribution of species ‘k’ to the Bray-Curtis
dissimilarity between two groups of samples (credit: QM18’).
simper_res1 = simper(semtot,group=site.scrs$clusters)##
## Contrast: 1_2
##
## average sd ratio ava avb cumsum p
## Thalassiosiraceae 0.16313 0.12205 1.33660 0.75470 0.10830 0.296 0.004 **
## C_Closterium 0.09416 0.07837 1.20160 0.53480 0.24080 0.467 0.003 **
## X50.Pennate.20 0.06002 0.04570 1.31330 0.32250 0.15340 0.576 0.040 *
## X20.Pennate 0.05041 0.03363 1.49890 0.45360 0.35270 0.667 0.040 *
## P_nitzschia_sp 0.03987 0.03056 1.30470 0.23320 0.08380 0.739 0.530
## Centric_ungrouped 0.02907 0.03753 0.77470 0.09860 0.10660 0.792 0.155
## C_hyalochaete 0.02348 0.02425 0.96820 0.10360 0.01390 0.835 0.677
## N_hasleae 0.01703 0.02127 0.80090 0.06120 0.00000 0.865 0.111
## Thalassionemataceae 0.01484 0.02951 0.50290 0.05490 0.00000 0.892 0.272
## Pennate.50 0.01421 0.01139 1.24810 0.05550 0.00200 0.918 0.048 *
## D_mediterraneus 0.01360 0.01204 1.12910 0.05680 0.01440 0.943 0.048 *
## Leptocylindrus_sp 0.00906 0.00928 0.97550 0.03680 0.00000 0.959 0.992
## Rhizosolenia 0.00586 0.01017 0.57580 0.02100 0.00000 0.970 0.543
## B_sp 0.00348 0.00411 0.84540 0.01360 0.00000 0.976 0.304
## L_delicatulum 0.00220 0.00670 0.32860 0.00550 0.00390 0.980 0.070 .
## L_annulata 0.00186 0.00314 0.59160 0.00730 0.00000 0.984 0.998
## C_hyalochaete.spore..single.cell. 0.00172 0.00471 0.36480 0.00750 0.00000 0.987 1.000
## N_indica 0.00135 0.00416 0.32330 0.00480 0.00000 0.989 0.291
## C_rostratus 0.00130 0.00213 0.61210 0.00420 0.00200 0.991 0.741
## H_sinensis 0.00119 0.00216 0.54850 0.00480 0.00000 0.994 1.000
## C_pseudodichaeta 0.00074 0.00106 0.69430 0.00270 0.00000 0.995 0.216
## C_peruvianus 0.00066 0.00142 0.46720 0.00250 0.00000 0.996 0.457
## C_hyalochaete.spore..in.chain. 0.00061 0.00350 0.17310 0.00260 0.00000 0.997 1.000
## S_grevillei 0.00054 0.00110 0.49170 0.00220 0.00000 0.998 0.996
## Chaetoceros_unassigned 0.00027 0.00093 0.28830 0.00100 0.00000 0.999 0.253
## Thalassiosiraceae_aggregate_5_cells 0.00027 0.00094 0.28440 0.00120 0.00000 0.999 1.000
## C_weissflogii 0.00018 0.00080 0.21880 0.00060 0.00000 0.999 0.116
## C_dadayi..tetrastichon 0.00009 0.00032 0.28960 0.00030 0.00000 1.000 0.189
## C_phaeoceros 0.00009 0.00038 0.23300 0.00040 0.00000 1.000 0.128
## D_pumila 0.00008 0.00038 0.22010 0.00030 0.00000 1.000 0.137
## Actinocyclus_sp 0.00004 0.00025 0.16280 0.00010 0.00000 1.000 0.056 .
## A_cleveanus 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.908
## Thalassiosiraceae_w_.webs 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.999
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Contrast: 1_3
##
## average sd ratio ava avb cumsum p
## P_nitzschia_sp 0.08836 0.01964 4.49800 0.23320 1.56010 0.134 0.001 ***
## Thalassiosiraceae 0.07839 0.04644 1.68800 0.75470 1.89080 0.253 1.000
## C_hyalochaete 0.07094 0.01362 5.21000 0.10360 1.18070 0.360 0.001 ***
## Leptocylindrus_sp 0.07058 0.03633 1.94300 0.03680 1.18980 0.468 0.001 ***
## C_hyalochaete.spore..single.cell. 0.07029 0.01931 3.64100 0.00750 1.04010 0.574 0.001 ***
## X50.Pennate.20 0.04411 0.01858 2.37400 0.32250 0.98430 0.641 0.306
## Thalassiosiraceae_w_.webs 0.03187 0.01984 1.60600 0.00000 0.53610 0.690 0.001 ***
## Centric_ungrouped 0.03132 0.01404 2.23000 0.09860 0.53410 0.737 0.166
## Thalassiosiraceae_aggregate_5_cells 0.02122 0.01866 1.13700 0.00120 0.37000 0.769 0.001 ***
## H_sinensis 0.01988 0.01221 1.62900 0.00480 0.31130 0.799 0.001 ***
## C_Closterium 0.01869 0.01171 1.59600 0.53480 0.59240 0.828 1.000
## C_hyalochaete.spore..in.chain. 0.01692 0.01434 1.18000 0.00260 0.23490 0.853 0.002 **
## X20.Pennate 0.01515 0.01001 1.51300 0.45360 0.61480 0.876 1.000
## Pennate.50 0.01512 0.00581 2.60200 0.05550 0.29610 0.899 0.013 *
## L_annulata 0.01394 0.00458 3.04400 0.00730 0.22490 0.920 0.001 ***
## Rhizosolenia 0.01375 0.00977 1.40700 0.02100 0.25410 0.941 0.017 *
## S_grevillei 0.01320 0.01223 1.08000 0.00220 0.23680 0.961 0.001 ***
## Thalassionemataceae 0.00554 0.00673 0.82300 0.05490 0.04900 0.970 1.000
## C_rostratus 0.00505 0.00256 1.97300 0.00420 0.08400 0.977 0.002 **
## N_hasleae 0.00427 0.00510 0.83800 0.06120 0.00000 0.984 1.000
## B_sp 0.00410 0.00375 1.09300 0.01360 0.06800 0.990 0.179
## D_mediterraneus 0.00360 0.00261 1.38000 0.05680 0.05120 0.996 1.000
## A_cleveanus 0.00135 0.00235 0.57500 0.00000 0.02620 0.998 0.003 **
## C_peruvianus 0.00055 0.00076 0.72400 0.00250 0.00650 0.998 0.633
## L_delicatulum 0.00037 0.00196 0.19000 0.00550 0.00000 0.999 0.958
## N_indica 0.00034 0.00107 0.31500 0.00480 0.00000 0.999 0.998
## C_pseudodichaeta 0.00019 0.00028 0.66900 0.00270 0.00000 1.000 1.000
## Chaetoceros_unassigned 0.00007 0.00024 0.28500 0.00100 0.00000 1.000 0.992
## C_weissflogii 0.00004 0.00019 0.22200 0.00060 0.00000 1.000 0.961
## C_phaeoceros 0.00002 0.00011 0.22200 0.00040 0.00000 1.000 0.978
## C_dadayi..tetrastichon 0.00002 0.00008 0.28400 0.00030 0.00000 1.000 0.989
## D_pumila 0.00002 0.00010 0.20800 0.00030 0.00000 1.000 0.941
## Actinocyclus_sp 0.00001 0.00005 0.16000 0.00010 0.00000 1.000 0.933
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Contrast: 2_3
##
## average sd ratio ava avb cumsum p
## Thalassiosiraceae 0.13827 0.02870 4.81800 0.10830 1.89080 0.166 0.246
## P_nitzschia_sp 0.11149 0.01440 7.74300 0.08380 1.56010 0.299 0.001 ***
## C_hyalochaete 0.08751 0.01255 6.97500 0.01390 1.18070 0.404 0.001 ***
## Leptocylindrus_sp 0.08202 0.04114 1.99400 0.00000 1.18980 0.503 0.001 ***
## C_hyalochaete.spore..single.cell. 0.08083 0.02443 3.30900 0.00000 1.04010 0.600 0.001 ***
## X50.Pennate.20 0.06216 0.02048 3.03600 0.15340 0.98430 0.674 0.065 .
## Thalassiosiraceae_w_.webs 0.03561 0.02286 1.55700 0.00000 0.53610 0.717 0.001 ***
## Centric_ungrouped 0.03251 0.01780 1.82700 0.10660 0.53410 0.756 0.274
## C_Closterium 0.02718 0.00770 3.53200 0.24080 0.59240 0.788 0.966
## Thalassiosiraceae_aggregate_5_cells 0.02371 0.02146 1.10500 0.00000 0.37000 0.817 0.003 **
## H_sinensis 0.02286 0.01434 1.59400 0.00000 0.31130 0.844 0.001 ***
## Pennate.50 0.02119 0.00479 4.42700 0.00200 0.29610 0.870 0.002 **
## X20.Pennate 0.02064 0.01131 1.82400 0.35270 0.61480 0.894 0.825
## C_hyalochaete.spore..in.chain. 0.01962 0.01785 1.09900 0.00000 0.23490 0.918 0.003 **
## Rhizosolenia 0.01669 0.01074 1.55400 0.00000 0.25410 0.938 0.021 *
## L_annulata 0.01631 0.00498 3.27500 0.00000 0.22490 0.957 0.001 ***
## S_grevillei 0.01483 0.01386 1.07000 0.00000 0.23680 0.975 0.003 **
## C_rostratus 0.00584 0.00287 2.03700 0.00200 0.08400 0.982 0.002 **
## Thalassionemataceae 0.00456 0.00560 0.81500 0.00000 0.04900 0.988 0.712
## B_sp 0.00438 0.00510 0.85800 0.00000 0.06800 0.993 0.225
## D_mediterraneus 0.00365 0.00354 1.03100 0.01440 0.05120 0.997 0.983
## A_cleveanus 0.00148 0.00269 0.55300 0.00000 0.02620 0.999 0.073 .
## C_peruvianus 0.00053 0.00096 0.55300 0.00000 0.00650 1.000 0.581
## L_delicatulum 0.00031 0.00048 0.64900 0.00390 0.00000 1.000 0.560
## C_dadayi..tetrastichon 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.399
## C_pseudodichaeta 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.979
## C_phaeoceros 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.290
## Chaetoceros_unassigned 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.513
## Actinocyclus_sp 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.153
## D_pumila 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.291
## C_weissflogii 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.292
## N_hasleae 0.00000 0.00000 NaN 0.00000 0.00000 1.000 1.000
## N_indica 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.679
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999
Repeating the analysis after application of cutoff for rare species
To exclude the effect of rare species on community analysis, I re-analyzed the dataset after applying 2 types of cutoff for rare species (keeping only species that pass both criteria):
- 10% Occurrence frequency: Species that are present in more than 10% of all sampling points
- 1% Relative abundance: Species that contribute 1%
(or more) to the total relative abundance in at least one sampling
point.
Below are results of similar analysis (for data after cutoff). It includes NMDS, ANOSIM, and SIMPER (results show representative comparisons between several clusters).
##
## Contrast: 1_2
##
## average sd ratio ava avb cumsum p
## Thalassiosiraceae 0.18570 0.07465 2.48750 0.06860 1.07140 0.366 0.001 ***
## C_Closterium 0.09090 0.05477 1.65970 0.83230 0.39750 0.545 0.001 ***
## X50.Pennate.20 0.03926 0.03282 1.19630 0.34930 0.31010 0.622 0.791
## X20.Pennate 0.03739 0.02961 1.26270 0.33990 0.50600 0.696 0.053 .
## P_nitzschia_sp 0.03241 0.02716 1.19300 0.19690 0.25000 0.760 1.000
## Thalassionemataceae 0.02261 0.02795 0.80910 0.12460 0.02280 0.804 0.003 **
## Centric_ungrouped 0.02025 0.03563 0.56810 0.02460 0.13270 0.844 0.830
## C_hyalochaete 0.01946 0.01825 1.06630 0.06270 0.12250 0.882 1.000
## N_hasleae 0.01313 0.01482 0.88590 0.03620 0.07280 0.908 0.277
## D_mediterraneus 0.01093 0.00904 1.20910 0.03650 0.06620 0.930 0.048 *
## Pennate.50 0.00927 0.00755 1.22740 0.05840 0.05410 0.948 0.955
## Rhizosolenia 0.00807 0.00897 0.89980 0.04530 0.00990 0.964 0.268
## Leptocylindrus_sp 0.00779 0.00696 1.11950 0.03690 0.03670 0.979 0.999
## N_indica 0.00279 0.00431 0.64740 0.01520 0.00000 0.985 0.001 ***
## L_delicatulum 0.00278 0.00815 0.34090 0.01610 0.00060 0.990 0.172
## C_hyalochaete.spore..single.cell. 0.00199 0.00436 0.45720 0.00000 0.01100 0.994 1.000
## H_sinensis 0.00129 0.00176 0.73000 0.00240 0.00590 0.997 1.000
## C_hyalochaete.spore..in.chain. 0.00070 0.00333 0.21130 0.00000 0.00380 0.998 0.996
## S_grevillei 0.00061 0.00096 0.64070 0.00070 0.00280 0.999 0.998
## Thalassiosiraceae_aggregate_5_cells 0.00031 0.00089 0.35110 0.00000 0.00170 1.000 0.999
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Contrast: 1_3
##
## average sd ratio ava avb cumsum p
## C_Closterium 0.18516 0.06138 3.01670 0.83230 0.24080 0.359 0.001 ***
## X50.Pennate.20 0.07501 0.05420 1.38400 0.34930 0.15340 0.504 0.003 **
## X20.Pennate 0.04557 0.03491 1.30510 0.33990 0.35270 0.592 0.100 .
## P_nitzschia_sp 0.03858 0.02823 1.36650 0.19690 0.08380 0.667 0.631
## Thalassionemataceae 0.03380 0.04645 0.72780 0.12460 0.00000 0.732 0.036 *
## Thalassiosiraceae 0.02780 0.02335 1.19040 0.06860 0.10830 0.786 1.000
## Centric_ungrouped 0.02342 0.02687 0.87150 0.02460 0.10660 0.832 0.425
## Pennate.50 0.01630 0.01365 1.19420 0.05840 0.00200 0.863 0.021 *
## C_hyalochaete 0.01509 0.01069 1.41170 0.06270 0.01390 0.892 0.961
## Rhizosolenia 0.01314 0.01512 0.86920 0.04530 0.00000 0.918 0.085 .
## N_hasleae 0.01160 0.01287 0.90140 0.03620 0.00000 0.940 0.500
## Leptocylindrus_sp 0.01052 0.01286 0.81800 0.03690 0.00000 0.961 0.757
## D_mediterraneus 0.01022 0.00887 1.15200 0.03650 0.01440 0.980 0.384
## L_delicatulum 0.00480 0.01166 0.41180 0.01610 0.00390 0.990 0.066 .
## N_indica 0.00430 0.00664 0.64780 0.01520 0.00000 0.998 0.071 .
## H_sinensis 0.00080 0.00134 0.59480 0.00240 0.00000 1.000 0.966
## S_grevillei 0.00023 0.00077 0.29590 0.00070 0.00000 1.000 0.979
## C_hyalochaete.spore..single.cell. 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.996
## C_hyalochaete.spore..in.chain. 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.882
## Thalassiosiraceae_aggregate_5_cells 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.958
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Contrast: 1_4
##
## average sd ratio ava avb cumsum p
## Thalassiosiraceae 0.13685 0.02189 6.25200 0.06860 1.89080 0.188 0.145
## P_nitzschia_sp 0.10024 0.01745 5.74400 0.19690 1.56010 0.326 0.001 ***
## C_hyalochaete 0.08161 0.01231 6.62900 0.06270 1.18070 0.438 0.001 ***
## Leptocylindrus_sp 0.07888 0.04083 1.93200 0.03690 1.18980 0.546 0.001 ***
## C_hyalochaete.spore..single.cell. 0.07815 0.01980 3.94700 0.00000 1.04010 0.654 0.001 ***
## X50.Pennate.20 0.04562 0.02025 2.25300 0.34930 0.98430 0.716 0.365
## Centric_ungrouped 0.03778 0.01432 2.63800 0.02460 0.53410 0.768 0.159
## Thalassiosiraceae_aggregate_5_cells 0.02400 0.02125 1.12900 0.00000 0.37000 0.801 0.001 ***
## H_sinensis 0.02224 0.01348 1.65000 0.00240 0.31130 0.832 0.001 ***
## X20.Pennate 0.01999 0.01050 1.90300 0.33990 0.61480 0.859 0.964
## C_Closterium 0.01933 0.01248 1.54800 0.83230 0.59240 0.886 0.999
## C_hyalochaete.spore..in.chain. 0.01860 0.01540 1.20800 0.00000 0.23490 0.911 0.001 ***
## Pennate.50 0.01675 0.00703 2.38200 0.05840 0.29610 0.934 0.006 **
## S_grevillei 0.01492 0.01383 1.07900 0.00070 0.23680 0.955 0.001 ***
## Rhizosolenia 0.01423 0.01109 1.28300 0.04530 0.25410 0.974 0.022 *
## Thalassionemataceae 0.00999 0.01033 0.96800 0.12460 0.04900 0.988 0.651
## D_mediterraneus 0.00355 0.00283 1.25800 0.03650 0.05120 0.993 1.000
## N_hasleae 0.00277 0.00276 1.00600 0.03620 0.00000 0.997 1.000
## L_delicatulum 0.00116 0.00358 0.32300 0.01610 0.00000 0.998 0.360
## N_indica 0.00113 0.00179 0.63300 0.01520 0.00000 1.000 0.516
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Contrast: 2_3
##
## average sd ratio ava avb cumsum p
## Thalassiosiraceae 0.22765 0.09531 2.38850 1.07140 0.10830 0.405 0.001 ***
## X50.Pennate.20 0.05387 0.04040 1.33350 0.31010 0.15340 0.501 0.116
## C_Closterium 0.05334 0.04322 1.23420 0.39750 0.24080 0.596 0.718
## X20.Pennate 0.05330 0.03330 1.60030 0.50600 0.35270 0.691 0.023 *
## P_nitzschia_sp 0.04101 0.03215 1.27570 0.25000 0.08380 0.764 0.546
## Centric_ungrouped 0.03194 0.04151 0.76950 0.13270 0.10660 0.821 0.166
## C_hyalochaete 0.02778 0.02804 0.99070 0.12250 0.01390 0.870 0.507
## N_hasleae 0.01975 0.02398 0.82370 0.07280 0.00000 0.905 0.065 .
## D_mediterraneus 0.01533 0.01313 1.16780 0.06620 0.01440 0.933 0.019 *
## Pennate.50 0.01349 0.01042 1.29520 0.05410 0.00200 0.957 0.108
## Leptocylindrus_sp 0.00853 0.00728 1.17140 0.03670 0.00000 0.972 0.972
## Thalassionemataceae 0.00633 0.00927 0.68270 0.02280 0.00000 0.983 0.926
## Rhizosolenia 0.00259 0.00393 0.65870 0.00990 0.00000 0.988 0.997
## C_hyalochaete.spore..single.cell. 0.00252 0.00555 0.45430 0.01100 0.00000 0.992 0.990
## H_sinensis 0.00138 0.00247 0.56020 0.00590 0.00000 0.995 0.975
## L_delicatulum 0.00105 0.00143 0.73100 0.00060 0.00390 0.997 0.633
## C_hyalochaete.spore..in.chain. 0.00089 0.00426 0.21020 0.00380 0.00000 0.998 0.922
## S_grevillei 0.00070 0.00122 0.57140 0.00280 0.00000 0.999 0.947
## Thalassiosiraceae_aggregate_5_cells 0.00039 0.00112 0.34980 0.00170 0.00000 1.000 0.956
## N_indica 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.998
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Contrast: 2_4
##
## average sd ratio ava avb cumsum p
## P_nitzschia_sp 0.09122 0.02199 4.14800 0.25000 1.56010 0.151 0.001 ***
## Leptocylindrus_sp 0.07472 0.03881 1.92500 0.03670 1.18980 0.275 0.001 ***
## C_hyalochaete.spore..single.cell. 0.07283 0.01852 3.93200 0.01100 1.04010 0.396 0.001 ***
## C_hyalochaete 0.07273 0.01496 4.86300 0.12250 1.18070 0.517 0.001 ***
## Thalassiosiraceae 0.05850 0.03593 1.62800 1.07140 1.89080 0.614 1.000
## X50.Pennate.20 0.04764 0.01980 2.40600 0.31010 0.98430 0.693 0.210
## Centric_ungrouped 0.03129 0.01472 2.12600 0.13270 0.53410 0.745 0.175
## Thalassiosiraceae_aggregate_5_cells 0.02268 0.02017 1.12400 0.00170 0.37000 0.783 0.001 ***
## H_sinensis 0.02076 0.01274 1.63000 0.00590 0.31130 0.817 0.001 ***
## C_Closterium 0.01999 0.01209 1.65400 0.39750 0.59240 0.850 1.000
## C_hyalochaete.spore..in.chain. 0.01733 0.01411 1.22800 0.00380 0.23490 0.879 0.002 **
## Pennate.50 0.01601 0.00630 2.54000 0.05410 0.29610 0.906 0.009 **
## Rhizosolenia 0.01512 0.01060 1.42700 0.00990 0.25410 0.931 0.011 *
## X20.Pennate 0.01446 0.01041 1.38900 0.50600 0.61480 0.955 1.000
## S_grevillei 0.01404 0.01321 1.06300 0.00280 0.23680 0.978 0.001 ***
## N_hasleae 0.00533 0.00602 0.88500 0.07280 0.00000 0.987 0.996
## D_mediterraneus 0.00394 0.00272 1.44700 0.06620 0.05120 0.994 1.000
## Thalassionemataceae 0.00390 0.00358 1.09100 0.02280 0.04900 1.000 0.997
## L_delicatulum 0.00004 0.00016 0.26000 0.00060 0.00000 1.000 1.000
## N_indica 0.00000 0.00000 NaN 0.00000 0.00000 1.000 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Contrast: 3_4
##
## average sd ratio ava avb cumsum p
## Thalassiosiraceae 0.14714 0.02653 5.54700 0.10830 1.89080 0.178 0.169
## P_nitzschia_sp 0.11911 0.01412 8.43800 0.08380 1.56010 0.323 0.001 ***
## C_hyalochaete 0.09353 0.01276 7.33100 0.01390 1.18070 0.436 0.001 ***
## Leptocylindrus_sp 0.08885 0.04494 1.97700 0.00000 1.18980 0.544 0.001 ***
## C_hyalochaete.spore..single.cell. 0.08599 0.02370 3.62900 0.00000 1.04010 0.649 0.001 ***
## X50.Pennate.20 0.06647 0.02180 3.04900 0.15340 0.98430 0.729 0.039 *
## Centric_ungrouped 0.03482 0.01894 1.83800 0.10660 0.53410 0.772 0.263
## C_Closterium 0.02890 0.00731 3.95300 0.24080 0.59240 0.807 0.965
## Thalassiosiraceae_aggregate_5_cells 0.02599 0.02373 1.09500 0.00000 0.37000 0.838 0.004 **
## H_sinensis 0.02454 0.01529 1.60400 0.00000 0.31130 0.868 0.001 ***
## Pennate.50 0.02282 0.00580 3.93100 0.00200 0.29610 0.896 0.003 **
## X20.Pennate 0.02216 0.01243 1.78300 0.35270 0.61480 0.922 0.796
## C_hyalochaete.spore..in.chain. 0.02060 0.01801 1.14400 0.00000 0.23490 0.948 0.001 ***
## Rhizosolenia 0.01811 0.01194 1.51700 0.00000 0.25410 0.970 0.014 *
## S_grevillei 0.01620 0.01527 1.06100 0.00000 0.23680 0.989 0.004 **
## Thalassionemataceae 0.00475 0.00571 0.83300 0.00000 0.04900 0.995 0.703
## D_mediterraneus 0.00387 0.00374 1.03300 0.01440 0.05120 1.000 0.988
## L_delicatulum 0.00033 0.00050 0.65500 0.00390 0.00000 1.000 0.525
## N_hasleae 0.00000 0.00000 NaN 0.00000 0.00000 1.000 1.000
## N_indica 0.00000 0.00000 NaN 0.00000 0.00000 1.000 0.658
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999