Culture-independent study of bacterial communities in tropical river sediment

Figures & data

Table 1. Physicochemical properties of sediments of the Chao Phraya and the Tha Chin rivers in Thailand.

Sample	Sand	Silt	Clay	pH			EC^a	Total C	OC^b	IC^c	Active P	Active S
	(%)			Field	(H2O)	NaF	(ms/cm)	(%)			(mg kg^−1)
CP1	7.7	37	55	7.26	6.5	9.2	1.14	2.02	1.97	0.047	823	1343
CP2	0.9	47	52	7.40	5.5	9.1	0.13	2.20	2.16	0.045	1144	166
CP3	7.2	38	55	6.67	5.8	8.5	2.48	2.49	2.45	0.039	1298	666
CP4	20	34	46	6.70	6.3	9.6	0.53	2.86	2.79	0.074	965	333
CP5	21	52	27	6.83	6.5	10.2	1927	4.59	4.40	0.191	1278	2431
CP6	19	37	44	7.06	7.2	9.3	0.11	1.29	1.26	0.029	609	544
TC1	9.3	57	34	7.15	6.1	10.5	17	2.25	2.05	0.199	712	710
TC2	1.9	60	38	6.97	5.6	9.0	10	3.24	3.23	0.015	513	3097
TC3	4.9	54	41	6.66	6.9	10.1	2.7	3.38	3.28	0.102	1144	1554
TC4	3.4	52	44	6.65	6.7	10.0	2.7	3.87	3.78	0.088	1152	932
TC5	2.7	56	42	6.64	5.2	9.0	1.0	3.73	3.72	0.010	1837	1976
TC6	4.6	58	38	6.44	5.1	9.2	1217	4.30	4.27	0.028	2017	1820

^a EC = Electrical conductivity.

^b OC = Organic carbon.

^c IC = Inorganic carbon.

Fig. 1. Principal Component Analysis and White’s non-parametric t-test of (A) sediment component (percent redundancy); (B) total and active trace elements (g kg⁻¹).

Notes: Samples from the Chao Phraya river are labeled CP1-6 and samples from the Tha Chin river are labeled TC1-6. The data are projected using the first two PCs, which explain 100 and 88.3% of the covariance for (A) and (B), respectively.

Table 2. Summary of pyrosequencing data-set and diversity index of the 16S rRNA gene sequences at 0.03% dissimilarity.

Sample	Tagged sequence	No. cleaned sequences	Average length (bp)	No. OTU observed	Chao1	Shannon	Good’s coverage (%)
CP1	AGACGACG	44,102	410	1879	5792	7.161	87.11
CP2	ACATCGAG	16,805	410	1586	3515	6.930	86.50
CP3	TGTGATGT	3761	410	1400	2608	6.880	74.58
CP4	ATGACAGT	64,603	407	2093	6799	7.408	88.85
CP5	ATCAGTCG	12,828	405	1332	3194	6.478	87.20
CP6	ACAGTACA	7632	407	1659	3321	7.106	79.49
TC1	ATGACAGT	55,744	403	2000	7632	7.224	84.62
TC2	AGCAGAGC	30,608	405	1785	4833	7.054	85.70
TC3	AGACGACG	14,560	405	1429	3206	6.693	86.17
TC4	ACTCGTAG	7888	404	1431	2944	6.768	81.16
TC5	ATTGTCAC	10,213	404	1483	3026	6.819	83.15
TC6	ATCAGTCG	27,626	401	1418	3901	6.489	88.35

Fig. 2. The relative abundance and taxonomic profiles of (A) Bacteria in Chao Phraya (CP1-6) and Tha Chin (TC1-6) sediment samples; (B) Proteobacteria in Chao Phraya (CP1-6) and Tha Chin (TC1-6) sediment samples; (C) Heatmap representation of the major bacterial orders.

Fig. 3. Relationships of microbial communities illustrated by Principal Coordinates Analysis (PCoA) of the unweighted UniFrac distance matrix.

Notes: Samples from the Chao Phraya river (circle) are labeled CP1-6 and samples from the Tha Chin river (square) are labeled TC1-6.

Fig. 4. Scatter plot showing relative abundances of bacterial genera from Chao Phraya with Tha Chin rivers.

Notes: Each spot represents a different assigned taxon (genus) and its relative abundance. Spots closer to the x-axis represent genera more abundant in the Chao Phraya, while spots closer to the y-axis are more abundant in the Tha Chin river. The most abundant genera are labeled on the plot. Spots on or near the dashed diagonal have equal or similar abundances found in both samples.