Alphaproteobacteria communities depend more on soil types than land managements

Figures & data

Table 1. Crop rotation land management and manuring of arable farming types in conventional (C) and organic (O) systems at the three sites of Karcag (K), Martonvásár (M) and Nyíregyháza (Ny) four years before sampling.

Farming systems		2009	2010	2011	2012
KC	Crop	Maize	Sorghum	Sorghum, winter wheat	Cereal
	Manuring	400 kg ha^−1 NPK^b	300 kg ha^−1 NPK^b	300 kg ha^−1 NPK^b	N 75 kg ha^−1 P 120 kg ha^−1 K 100 kg ha^−1b
KO	Crop	Winter wheat	Sorghum	Sweet clover	Sweet clover
	Manuring	–	–	Green manure	Green manure
MC	Crop	Spring wheat	Maize	Spring wheat	Maize
	Manuring	300 kg ha^−1 NPK400 kg ha^−1 N^a	300 kg ha^−1 NPK300 kg ha^−1 N^a	250 kg ha^−1 NPK^a	300 kg ha^−1 NPK 270 kg ha^−1 N (39%)^a
MO	Crop	Maize	Oil radish	Peas	Cereal
	Manuring	–	Green manure	Green manure	–
NyC	Crop	Sunflower	Sunflower	Rye, hairy vetch	Lupine
	Manuring	–	–	–	Green manure
NyO	Crop	Rye	Rye	Spelt wheat	Alfalfa
	Manuring	–	–	–	–

Legends: ^aComplex NPK fertiliser was used with 15-15-15% active agent. 15% N:10% ammonium nitrogen + 5% urea N; 15% P₂O₅: P content 6.2%; 15% K₂O: K content 12.5%; N fertiliser (calcium ammonium nitrate fertiliser (CAN)) was used which contained 27% N, 5% Ca (7% calcium oxide) and 3% Mg (5% magnesium oxide).

^b300 kg ha⁻¹ NPK fertiliser was applied which contained 34% (N) ammonium nitrate, 18% (P) superphosphate and 60% (K) potassium = no manure).

Figure 1. Principal components (PCA) biplot analysis among the soil samples (Karcag, Martonvásár and Nyíregyháza) from conventional and organic farming systems. (Legends: C = conventional, O = organic systems, K = Karcag, M = Martonvásár, Ny = Nyíregyháza, n = 12, except KC, MC, MO, NYC n = 11 were used, filled circle = KC, circle = KO, filled triangle = MC, triangle = MO, filled square = NyC, square = NyO).

Table 2. The main soil physical properties from conventional and organic farming systems in the three sampling sites.

Soil physical parameters	Farming systems
	KC	KO	MC	MO	NyC	NyO
Sand (%)	7.93 ± 0.45	3.85 ± 0.37	30.04 ± 2.28	32.72 ± 1.60	87.22 ± 4.06	77.89 ± 6.55
Silt (%)	53.87 ± 0.42	50.50 ± 0.58	43.01 ± 0.67	42.43 ± 0.66	6.60 ± 0.75	13.00 ± 2.01
Clay (%)	38.19 ± 0.28	45.66 ± 0.70	26.95 ± 2.77	24.93 ± 1.26	6.18 ± 0.98	9.11 ± 2.97

Legend: C = conventional, O = organic systems, K = Karcag, M = Martonvásár, Ny = Nyíregyháza, n = 12, data are represents the average ± standard deviation.

Table 3. The main soil chemical parameters originated from three different soil types with conventional and organic farming systems.

Soil chemical parameters	Soil types and farming systems
	Clay		Loamy		Sandy
	KC	KO	MC	MO	NyC	NyO
EC (mS cm^−1)	0.17 ± 0.04 n.s.	0.14 ± 0.06	0.27 ± 0.06 **	0.22 ± 0.03	0.03 ± 0.02 n.s.	0.07 ± 0.07
pHH2O	6.77 ± 0.13	7.06 ± 0.27 **	7.75 ± 0.17	7.92 ± 0.14 **	5.54 ± 0.53	6.58 ± 0.42 ***
pHCaCl2	6.60 ± 0.10	6.73 ± 0.33 n.s.	7.71 ± 0.12	7.85 ± 0.10 **	4.81 ± 0.79	6.47 ± 0.33 ***
Humus (%)	3.04 ± 0.15	4.03 ± 0.17 ***	2.65 ± 0.24	2.98 ± 0.26 **	0.71 ± 0.13	0.76 ± 0.23 n.s.
Total N (%)	0.17 ± 0.01	0.20 ± 0.01 ***	0.17 ± 0.01	0.19 ± 0.01 ***	0.04 ± 0.02 n.s.	0.05 ± 0.02
(mg kg^−1)	15.86 ± 8.94 ***	5.96 ± 3.16	8.84 ± 4.64	4.94 ± 0.68 **	4.07 ± 2.15	2.91 ± 1.55 n.s.
(mg kg^−1)	12.59 ± 9.37 n.s.	8.15 ± 2.64	40.24 ± 17.87	5.24 ± 0.99 ***	1.31 ± 0.59	3.05 ± 1.88 **
AL-Na (mg kg^−1)	8.42 ± 1.58	140 ± 116 ***	11.06 ± 3.21	11.19 ± 0.97 n.s.	2.34 ± 1.92	4.32 ± 1.76 **
AL-P2O5 (mg kg^−1)	187 ± 18.87 ***	68.55 ± 15.70	654 ± 46.11	737 ± 261 n.s.	199 ± 81.21 *	129 ± 55.10
AL-K2O (mg kg^−1)	367 ± 33.21 ***	270 ± 25.60	526 ± 58.22	605 ± 89.26 **	221 ± 63.15 **	155 ± 58.53
AL-Ca (m/m%)	0.42 ± 0.01	0.44 ± 0.04 n.s.	1.16 ± 0.96	1.62 ± 0.52 n.s.	0.05 ± 0.09	0.11 ± 0.08 n.s.

Legend: C = conventional, O = organic systems, K = Karcag, M = Martonvásár, Ny = Nyíregyháza, n = 12, data are represents the average ± standard deviation.

*p = < 0.05.

**p = < 0.01.

***p = < 0.001.

n.s. = non-significant between CF vs. OF system between soil types.

Figure 2. The banding pattern of the DGGE UPGMA dendrogram of bacterial communities. (Legends: C = conventional, O = organic systems, K = Karcag, M = Martonvásár, Ny = Nyíregyháza, the codes of farming systems with numbering 1–4 indicated the soil samples (n = 4) which best represent the above area. Numbers in the banding patterns 1–14 indicated the isolated and sequenced bands (thick lines)).

Table 4. The closest phylogenetic relatives of 16S rRNA sequences isolated from DGGE banding patterns.

Sample origin	Band	Closest phylogenetic relatives (Ez Taxon-e)	Similarity (%)	Habitat	Accession Number
MO^a	1	Pseudovibrio denitrificans strain F75075	99	Marine sponge	JF281743
MC^a	2	Devosia sp. R 41.	99	Natural Euphrates poplar forest rhizosphere	KC464823
	3	Ancylobacter rudongensis AS1.1761	99.51	Roots of Spartina anglica	AY056830
KO^a	4	Unc.bact. clone Rhizobiaceae CG 38	100	Pinus massoniana, forest soil	KJ191886
KC^a	5	α-Proteobacterium BAC47	100	GAC-filters	EU180511
	6	α-Proteobacterium clone OP-CG8_2	100	Soil contaminated with zinc and cadmium	JQ649902
	8	Unc.bact. clone Acetobacteraceae C.la-126	98	Soil	JX505010
NyO^a	9	Mesorhizobium sp. JNVU RA14	96	Root nodule of Rhynchosia aurea	KJ000995
	10	Unc.bact. clone Rhodobiaceae	99	Soil	JX504991
	11	Unc.bact. clone α-Proteobacterium	98	Soil	AJ518764
NyC^a	13	Rhizobium sp. HBU50014	99	Root nodules of Trifolium sp.	KX097067
KC^b	7	Unc.bact. clone 16S-P6-3-5C	99	Soil	KC663916
NyO^b	12	Unc.bact. clone Y3-7	100	Subtropical forest soil	AY930170
NyC^b	14	Unc.bact. clone G10-20	99	Forest soil	AY845988

Legend: Unc.bact. = uncultured bacterium clone, C = conventional, O = organic systems, K = Karcag, M = Martonvásár, Ny = Nyíregyháza, GAC-filters = granular activated carbon filter in water treatment.

^aAlphaproteobacteria.

^bBacteria.