Diversity of bacterial strains in biochar-enhanced Amazon soil and their potential for growth promotion and biological disease control in tomato

CANIATO, Matheus Miranda; CATARINO, Aricléia de Moraes; SOUSA, Thiago Fernandes; SILVA, Gilvan Ferreira da; BICHARA, Karina Pryscilla de Araújo; CRUZ, Jeferson Chagas da; ASSIS, Luiz Alberto Guimarães de; HANADA, Rogério Eiji

doi:10.1590/1809-4392201901072

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Agronomy and Forestry • Acta Amaz. 50 (4) • Oct-Dec 2020 • https://doi.org/10.1590/1809-4392201901072 copy

Diversity of bacterial strains in biochar-enhanced Amazon soil and their potential for growth promotion and biological disease control in tomato

Diversidade de isolados bacterianos em solo amazônico enriquecido com biocarvão e seu potencial para a promoção de crescimento e controle biológico de doenças em tomate

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

The use of bacteria in growth promotion and biological control of plant diseases can minimize environmental contamination caused by the indiscriminate use of pesticides and chemical fertilizers. We aimed to evaluate growth promotion and biological control of Corynespora cassiicola in tomato seedlings mediated by beneficial bacteria isolated from a non-rhizospheric Amazon soil containing different amounts of biochar, and to identify to which groups of bacteria the strains belong. We obtained 200 strains of bacteria from experimental plots containing biochar doses of 0, 40, 80 and 120 t ha^-1. Of these, 53 strains were selected by root colonization tests. Based on growth promotion parameters, 25 strains were screened, identified by molecular characterization and evaluated for indoleacetic acid (IAA) production, phosphate solubilization and biological control. The best dose of biochar for colony formation was 40 t ha^-1, and a regression model indicated 34 t ha^-1 as the optimal dose. The production of IAA was observed in 18 (75%) strains, and two (8%) strains were able to solubilize phosphate. The efficiency in root growth promotion was up to 125%, and the percentage of plant protection ranged from 50 to 59%. Molecular characterization showed that the bacteria used in this study belong to the genera Bacillus and Lysinibacillus.

KEYWORDS:
beneficial bacteria; Corynespora cassiicola; Solanum lycopersicum; target spot

Material	C	N	Ca	Mg	K	P		Zn	Mn
	g kg^-1							mg kg^-1
Fine coal	873.3	8.9	6.2	1.3	2.1	0.2		12.0	Mn	67.0

Strain	PH¹ (cm)	GPE (%)	SD¹ (mm)	GPE (%)	DMAP¹ (g)	GPE (%)	DMR¹ (g)	GPE (%)	TDM¹ (g)	GPE (%)	IAA	P
C-*	12.5 ± 0.5^a	0.0	1.8 ± 0.2^b	0.0	0.0 ± 0.04^a	0.0	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	0.0	-	-
C+**	13.5 ± 0.4^a	8.6	2.1 ± 0.2^a	13.0	0.1 ± 0.06^a	35.7	0.0 ± 0.007^a	75	0.1 ± 0.06^a	39.1	+	-
3T4	13.3 ± 0.4^a	6.7	2.1 ± 0.2^a	12.0	0.0 ± 0.05^a	19.0	0.0 ± 0.005^b	25	0.0 ± 0.05^a	19.6	+	-
4T2	12.9 ± 0.3^a	3.6	2.1 ± 0.1^a	11.3	0.0 ± 0.05^a	16.7	0.0 ± 0.007^a	75	0.1 ± 0.06^a	23.9	-	-
6T1	12.7 ± 0.4^a	1.6	1.8 ± 0.3^b	-2.7	0.0 ± 0.04^a	7.1	0.0 ± 0.005^b	25	0.0 ± 0.05^a	10.8	+	-
15T2	12.4 ± 0.3^a	-0.8	1.7 ± 0.2^b	-9.2	0.0 ± 0.04^a	-9.5	0.0 ± 0.007^a	75	0.0 ± 0.04^a	-2.2	+	-
7T1	13.2 ± 0.3^a	6.3	1.9 ± 0.3^b	1.6	0.0 ± 0.05^a	28.6	0.0 ± 0.007^a	75	0.7 ± 0.06^a	34.8	+	-
25T4	13.2 ± 0.2^a	5.7	1.9 ± 0.3^b	0.5	0.0 ± 0.05^a	19.0	0.0 ± 0.008^a	100	0.1 ± 0.06^a	28.3	+	+
22T3	13.5 ± 0.3^a	8.7	2.0 ± 0.3^a	8.6	0.0 ± 0.05^a	21.4	0.0 ± 0.009^a	125	0.1 ± 0.06^a	32.6	-	-
53T1	13.3 ± 0.3^a	7.1	2.2 ± 0.1^a	17.3	0.0 ± 0.05^a	21.4	0.0 ± 0.007^a	75	0.1 ± 0.06^a	26.0	+	-
23T3	12.7 ± 0.2^a	1.9	1.8 ± 0.1^b	1.1	0.0 ± 0.04^a	0.0	0.0 ± 0.008^a	100	0.0 ± 0.05^a	10.9	+	-
52T1	12.8 ± 0.4^a	2.6	1.8 ± 0.3^b	-2.2	0.0 ± 0.04^a	0.0	0.0 ± 0.008^a	100	0.0 ± 0.05^a	8.7	-	-
114T1	12.8 ± 0.5^a	2.4	1.9 ± 0.4^b	0.5	0.0 ± 0.05^a	11.9	0.0 ± 0.006^b	50	0.0 ± 0.05^a	16.7	+	-
17T3	13.5 ± 0.2^a	8.1	2.1 ± 0.2^a	14.0	0.0 ± 0.05^a	21.4	0.0 ± 0.007^a	75	0.1 ± 0.06^a	28.3	-	-
113T1	12.9 ± 0.2^a	3.3	2.0 ± 0.2^a	7.0	0.0 ± 0.05^a	14.3	0.0 ± 0.007^a	75	0.0 ± 0.05^a	19.6	+	-
117T1	12.6 ± 0.3^a	1.4	1.8 ± 0.2^b	-0.5	0.0 ± 0.04^a	0.0	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	2.2	+	-
47T1	13.1 ± 0.3^a	5.5	1.9 ± 0.3^b	1.6	0.0 ± 0.04^a	4.8	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	2.2	-	-
8T2	12.6 ± 0.4^a	1.2	1.8 ± 0.3^b	0.0	0.0 ± 0.04^a	4.8	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	2.2	+	-
46T1	12.1 ± 0.4^a	-3.1	1.9 ± 0.2^b	0.5	0.0 ± 0.04^a	4.8	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	4.3	+	-
6T3	11.7 ± 0.3^a	-5.8	1.8 ± 0.2^b	-2.2	0.0 ± 0.04^a	7.1	0.0 ± 0.005^b	25	0.0 ± 0.05^a	6.5	-	-
30T2	13.2 ± 0.4^a	5.7	2.0 ± 0.3^a	5.9	0.0 ± 0.04^a	4.8	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	6.5	+	-
80T2	12.8 ± 0.3^a	2.7	2.0 ± 0.2^a	9.7	0.0 ± 0.05^a	14.3	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	13.0	+	-
28T2	12.5 ± 0.3^a	0.1	1.8 ± 0.3^b	-1.1	0.0 ± 0.04^a	4.8	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	4.3	-	-
2T2	12.5 ± 0.3^a	0.2	1.9 ± 0.2^b	0.5	0.0 ± 0.04^a	-2.4	0.0 ± 0.004^b	0.0	0.0 ± 0.04^a	-2.2	+	-
115T1	13.0 ± 0.2^a	4.5	1.9 ± 0.3^b	2.2	0.0 ± 0.04^a	7.1	0.0 ± 0.004^b	0.0	0.0 ± 0.05^a	6.5	+	-
12T4	12.7 ± 0.2^a	2.3	1.8 ± 0.3^b	-3.2	0.0 ± 0.04^a	-4.8	0.0 ± 0.004^b	0.0	0.0 ± 0.04^a	-4.3	-	+
52T2	13.1 ± 0.3^a	4.8	1.9 ± 0.2^b	0.5	0.0 ± 0.05^a	14.3	0.0 ± 0.005^b	25	0.0 ± 0.05^a	13.0	+	-
CV%	14.52	-	16.55	-	17.25	-	17.82	-	16.32	-

Strain	Colonization
1T1	-
2T1	-
3T1	+
4T1	+
5T1	-
6T1	+
7T1	+
8T1	+
9T1	-
10T1	+
11T1	-
12T1	+
13T1	-
14T1	+
15T1	-
16T1	-
17T1	-
18T1	-
19T1	-
20T1	-
21T1	-
22T1	+
23T1	-
24T1	-
25T1	-
26T1	-
27T1	+
28T1	+
29T1	-
30T1	-
31T1	-
32T1	-
33T1	-
34T1	+
35T1	-
36T1	-
37T1	-
41T1	+
46T1	+
47T1	+
51T1	+
52T1	+
53T1	+
102T1	+
108T1	+
109T1	+
113T1	+
114T1	+
115T1	+
117T1	+
1T2	+
2T2	+
3T2	+
4T2	+
5T2	-
6T2	+
7T2	-
8T2	+
9T2	+
10T2	-
11T2	-
12T2	-
13T2	-
14T2	+
15T2	+
16T2	-
17T2	+
18T2	+
19T2	-
20T2	-
21T2	-
22T2	-
23T2	-
24T2	-
25T2	-
26T2	-
27T2	+
28T2	+
29T2	+
30T2	+
31T2	+
32T2	-
33T2	-
34T2	+
35T2	-
36T2	-
37T2	-
38T2	+
39T2	+
40T2	+
41T2	+
42T2	-
43T2	-
45T2	+
52T2	+
63T2	+
72T2	+
79T2	+
80T2	+
85T2	+
1T3	-
2T3	-
3T3	-
4T3	-
5T3	-
6T3	+
7T3	-
8T3	+
9T3	-
10T3	-
11T3	-
12T3	-
13T3	+
14T3	-
15T3	+
16T3	-
17T3	+
18T3	-
19T3	-
20T3	-
21T3	-
22T3	+
23T3	+
24T3	-
25T3	-
26T3	-
27T3	-
28T3	-
29T3	-
30T3	-
31T3	-
32T3	-
33T3	-
34T3	+
35T3	-
36T3	-
37T3	-
38T3	-
39T3	-
40T3	-
41T3	-
42T3	-
43T3	-
44T3	-
45T3	-
46T3	-
47T3	-
48T3	-
49T3	-
62T3	+
1T4	-
2T4	-
3T4	+
4T4	+
5T4	-
6T4	-
7T4	-
8T4	-
9T4	-
10T4	-
11T4	-
12T4	+
13T4	-
14T4	+
15T4	+
16T4	-
17T4	-
18T4	-
19T4	-
20T4	-
21T4	-
22T4	-
23T4	+
24T4	-
25T4	+
26T4	-
27T4	-
28T4	-
29T4	-
30T4	-
31T4	-
32T4	-
33T4	-
34T4	-
35T4	+
36T4	-
37T4	-
38T4	-
39T4	-
40T4	-
41T4	-
42T4	-
43T4	-
44T4	-
45T4	-
46T4	-
47T4	-
48T4	-
49T4	-
50T4	-

Biochar dose (t ha^-1)	Growth promotion				Total
	Positive		Negative
	N	%	N	%
0	25	50	25	50	50 (25%)
40	28	56	22	44	50 (25%)
80	9	18	41	82	50 (25%)
120	8	16	42	84	50 (25%)
Total	70	35	130	65	200 (100%)

Strain	PH¹ (cm)	NL²	DMAP (g)¹	SD (mm)¹
Ctrl-*	11.6 ± 0.4^b	2.0 ± 0.7^d	0.0 ± 0.0^b	2.0 ± 0.2^b
6T3	14.9 ± 0.3^a	3.0 ± 0.6 ^abcd	0.1 ± 0.0^a	2.5 ± 0.2^a
6T2	10.4 ± 0.6^c	2.7 ± 0.6^cd	0.0 ± 0.0^b	1.9 ± 0.3^b
62T3	11.8 ± 0.3^b	2.7 ± 0.6^bcd	0.1 ± 0.0^b	2.1 ± 0.3^b
72T2	11.5 ± 0.4^b	2.3 ± 0.7^cd	0.1 ± 0.0^b	2.0 ± 0.3^b
34T1	11.4 ± 0.7^b	3.3 ± 0.4^abc	0.1 ± 0.0^b	1.9 ± 0.2^b
109T1	10.8 ± 0.3^b	2.3 ± 0.4^cd	0.0 ± 0.0^b	1.9 ± 0.2^b
117T1	13.1 ± 0.3^a	2.7 ± 0.5^cd	0.1 ± 0.0^a	2.0 ± 0.2^b
3T4	13.8 ± 0.2^a	3.7 ± 0.5^abc	0.1 ± 0.0^b	2.1 ± 0.2^b
28T1	11.7 ± 0.2^b	3.3 ± 0.4^abcd	0.1 ± 0.0^b	2.1 ± 0.2^b
30T2	14.5 ± 0.5^a	4.7 ± 0.5^a	0.1 ± 0.0^a	2.5 ± 0.2^a
47T1	14.0 ± 0.5^a	3.0 ± 0.4^abcd	0.1 ± 0.0^a	2.4 ± 0.3^a
80T2	14.0 ± 0.5^a	3.7 ± 0.4^abc	0.1 ± 0.0^a	2.5 ± 0.3^a
10T1	11.8 ± 0.4^b	2.7 ± 0.5^bcd	0.1 ± 0.0^b	1.9 ± 0.3^b
28T2	14.1 ± 0.3^a	3.0 ± 0.4^abcd	0.1 ± 0.0^a	2.4 ± 0.3^a
46T1	14.3 ± 0.6^a	3.3 ± 0.4^abc	0.1 ± 0.0^a	2.3 ± 0.2^a
1T2	10.3 ± 0.2^c	2.0 ± 0.5^d	0.0 ± 0.0^b	1.6 ± 0.3^b
4T2	13.1 ± 0.3^a	2.0 ± 0.6^d	0.1 ± 0.0^a	2.2 ± 0.3^b
4T4	10.2 ± 0.3^c	2.0 ± 0.5^d	0.1 ± 0.0^b	1.7 ± 0.2^b
8T1	10.1 ± 0.3^c	3.0 ± 0.4^abcd	0.0 ± 0.0^b	1.9 ± 0.2^b
85T2	11.6 ± 0.2^b	3.0 ± 0.5^abcd	0.1 ± 0.0^b	2.1 ± 0.2^b
2T2	13.6 ± 0.4^a	3.0 ± 0.4^abcd	0.1 ± 0.0^a	2.6 ± 0.2^a
41T1	11.6 ± 0.5^b	2.3 ± 0.4^cd	0.1 ± 0.0^b	1.9 ± 0.3^b
79T2	11.4 ± 0.2^b	2.3 ± 0.7^cd	0.1 ± 0.0^b	1.9 ± 0.3^b
8T2	13.6 ± 0.3^a	3.7 ± 0.4^abc	0.1 ± 0.0^a	2.2 ± 0.2^a
115T1	14.6 ± 0.3^a	3.7 ± 0.5^abc	0.1 ± 0.0^a	2.3 ± 0.2^a
12T4	14.7 ± 0.4^a	3.3 ± 0.4^abc	0.1 ± 0.0^a	2.6 ± 0.2^a
8T3	12.1 ± 0.4^b	3.0 ± 0.5^abcd	0.1 ± 0.0^b	1.9 ± 0.2^b
12T1	11.3 ± 0.4^b	2.3 ± 0.7^cd	0.0 ± 0.0^b	1.9 ± 0.2^b
6T1	12.9 ± 0.4^a	3.0 ± 0.4^abcd	0.1 ± 0.0^a	2.1 ± 0.2^b
15T4	10.3 ± 0.5^c	2.0 ± 0.6^d	0.0 ± 0.0^b	1.7 ± 0.3^b
15T2	13.0 ± 0.3^a	3.0 ± 0.4^abcd	0.1 ± 0.0^a	1.6 ± 0.2^b
15T3	7.7 ± 0.4^d	2.3 ± 0.6^cd	0.0 ± 0.0^b	1.1 ± 0.3^b
13T3	11.5 ± 0.2^b	2.0 ± 0.5^d	0.1 ± 0.0^b	2.0 ± 0.2^b
7T1	12.9 ± 0.4^a	3.3 ± 0.5^abc	0.1 ± 0.0^a	2.4 ± 0.3^a
52T2	13.2 ± 0.3^a	2.7 ± 0.7^bcd	0.1 ± 0.0^a	2.5 ± 0.2^a
35T4	13.0 ± 0.4^a	2.0 ± 0.5^d	0.1 ± 0.0^b	1.7 ± 0.2^b
25T4	13.2 ± 0.3^a	2.3 ± 0.7^cd	0.1 ± 0.0^a	1.9 ± 0.3^b
22T3	15.7 ± 0.2^a	3.7 ± 0.5^abc	0.1 ± 0.0^a	2.7 ± 0.2^a
53T1	15.1 ± 0.4^a	2.0 ± 0.7^d	0.1 ± 0.0^a	2.1 ± 0.2^b
23T3	13.9 ± 0.3^a	2.3 ± 0.4^cd	0.1 ± 0.0^a	2.4 ± 0.2a
52T1	13.6 ± 0.3^a	4.3 ± 0.5^ab	0.1 ± 0.0^a	2.4 ± 0.3a
22T1	8.6 ± 0.4^d	2.3 ± 0.5^cd	0.0 ± 0.0^b	1.5 ± 0.3^b
102T1	11.5 ± 0.6^b	2.7 ± 0.4^cd	0.1 ± 0.0^b	2.1 ± 0.3b
14T1	10.9 ± 0.3^b	2.0 ± 0.5^d	0.1 ± 0.0^b	1.7 ± 0.2b
27T1	11.8 ± 0.5^b	2.0 ± 0.4^d	0.1 ± 0.0^b	2.1 ± 0.3b
108T1	11.0 ± 0.3^b	3.0 ± 0.5^abcd	0.1 ± 0.0^b	2.4 ± 0.3a
114T1	13.9 ± 0.4^a	3.0 ± 0.6^abcd	0.1 ± 0.0^a	2.4 ± 0.2a
17T3	14.5 ± 0.3^a	2.3 ± 0.4^cd	0.1 ± 0.0^a	2.7 ± 0.2a
17T2	11.0 ± 0.3^b	2.0 ± 0.6^d	0.1 ± 0.0^b	1.9 ± 0.2b
51T1	11.4 ± 0.3^b	3.3 ± 0.5^abc	0.1 ± 0.0^b	2.0 ± 0.3b
39T2	10.1 ± 0.4^c	2.3 ± 0.7^cd	0.0 ± 0.0^b	1.9 ± 0.2b
63T2	11.5 ± 0.4^b	2.7 ± 0.7^cd	0.1 ± 0.0^b	2.1 ± 0.2b
113T1	12.6 ± 0.4^a	3.0 ± 0.5^abcd	0.1 ± 0.0^a	2.4 ± 0.2a
CV%	8.90	-	14.54	16.17

Biochar dose (t ha^-1)	Growth promotion				Total
	Positive		Negative
	N	%	N	%
0	4	40.0	6	60.0	10 (40%)
40	4	50.0	4	50.0	8 (32%)
80	3	62.5	1	37.5	4 (16%)
120	2	66.7	1	33.3	3 (12%)
Total	13	52.0	12	48.0	25 (100%)

Biochar dose (t ha^-1)	Phosphate solubilization				Total
	Positive		Negative
	N	%	N	%
0	0	0	10	100	10 (40%)
40	0	0	8	100	8 (32%)
80	0	0	4	100	4 (16%)
120	2	66.7	1	33.3	3 (12%)
Total	2	8.0	23	92.0	25 (100%)

Strain	GenBank code	Size (bp)	ID Blast %	SDT ID score%*	GenBank code/Related species
8T2	MH547253	1354	99	99.9	KX245015/Bacillus thuringiensis
17T3	MH547254	1256	99	91.9	MG205930/Bacillus thuringiensis
23T3	MH547255	1293	99	95.9	MG205930/Bacillus thuringiensis
115T1	MH547256	1265	99	92.9	KF527213/Lysinibacillus sphaericus
28T2	MH547257	1354	98	98.5	KX057625/Bacillus cereus
53T1	MH547258	1354	98	98.6	KX950679/ Bacillus cereus
80T2	MH547259	908	95	64.0	KX057625/ Bacillus cereus
117T1	MH547261	1354	94	94.3	KX057625/ Bacillus cereus
3T4	MH547260	1355	99	99.3	KX245015 /Bacillus thuringiensis
6T3	MH547262	1356	99	99.4	MF370350/ Bacillus cereus
113T1	MH547263	1311	98	96.9	KX057625/ Bacillus cereus
2T2	MH547265	1354	99	98.8	KF033125/ Bacillus cereus
30T2	MH547266	1353	99	99.1	MF370350/ Bacillus cereus
12T4	MH547264	815	98	58.3	KR999903/ Bacillus flexus
4T2	MH547267	1358	99	91.7	MG984077/Lysinibacillus macroides
6T1	MH547268	815	94	91.4	KY780512/Bacillus cereus
7T1	MH547270	1354	88	87.7	JF701942/Bacillus sp.
46T1	MH547269	1315	96	97.4	KU922484/Bacillus altitudinis
25T4	MH547271	1355	96	96.1	KX268131/Bacillus megaterium
47T1	MH547272	1363	95	95.3	KX057625/Bacillus cereus
114T1	MH547273	768	99	99.5	EU982902/Lysinibacillus sphaericus
22 T3	MH547274	1358	98	98.8	KX816414/Bacillus cereus
52T1	MH547275	1307	95	96.7	KF033125/Bacillus cereus

Biochar dose (t ha^-1)	IAA production				Total
	Positive		Negative
	N	%	N	%
0	7	70.0	3	30.0	10 (40%)
40	6	75.0	2	25.0	8 (32%)
80	2	50.0	2	50.0	4 (16%)
120	2	66.7	1	33.3	3 (12%)
Total	17	68.0	8	32.0	25 (100%)

Biochar dose (t ha^-1)	Resistance induction				Total
	Positive		Negative
	N	%	N	%
0	7	70.0	3	30.0	10 (40%)
40	3	37.5	5	62.5	8 (32%)
80	2	50.0	2	50.0	4 (16%)
120	2	0	1	100	3 (12%)
Total	14	56.0	11	44.0	25 (100%)

Instituto Nacional de Pesquisas da Amazônia Av. André Araujo, 2936 Aleixo, 69060-001 Manaus AM Brasil, Tel.: +55 92 3643-3030, Fax: +55 92 643-3223 - Manaus - AM - Brazil
E-mail: acta@inpa.gov.br

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[1] * Corresponding author: amoraescatarino@gmail.com