Jan 29, 2015 - Aims: Bradyrhizobium from organic fields in Minnesota were isolated .... Carver. Hennepin. Washington. Anoka. Chisago. Wright. Sherburne.
Journal of Applied Microbiology ISSN 1364-5072
ORIGINAL ARTICLE
Predominant populations of indigenous soybeannodulating Bradyrhizobium japonicum strains obtained from organic farming systems in Minnesota M. Wongphatcharachai1, C. Staley1, P. Wang1, K.M. Moncada2, C.C. Sheaffer2 and M.J. Sadowsky1 1 Department of Soil, Water and Climate, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA 2 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
Keywords Bradyrhizobium japnicum, genotyping, indigenous population, organic farms, serotyping, soybean-bradyrhizobia. Correspondence Michael J. Sadowsky, BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St. Paul, MN 55108, USA. E-mail: sadowsky@umn.edu 2014/2436: received 26 November 2014, revised 27 January 2015 and accepted 29 January 2015 doi:10.1111/jam.12771
Abstract Aims: Bradyrhizobium from organic fields in Minnesota were isolated and genotyped to assess diversity of soybean-bradyrhizobia in organic farming systems that can be used to improve soybean productivity. Methods and Results: Soil samples were collected from 25 organic fields in Minnesota during May to July 2012. Soybean (cv. Lambert) was used as a host to trap indigenous bradyrhizobia in each sample. Genetic diversity of Bradyrhizobium strains (n = 733) was determined using the horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (HFERP) DNA fingerprinting technique and the soybean-bradyrhizobia were classified into 79 different genotypes. Of these, 15 dominant genotypes were found and were highly similar (>92% fingerprint similarity) to serotypes USDA 127 (404%), USDA 4 (318%) and USDA 123 (155%), which were the three main populations of soybean-bradyrhizobia in organic fields. Conclusions: Bradyrhizobium japonicum serogroup USDA 4 strains were found to make up a previously unrecognized, predominant rhizobial population in the organic farming soils examined. The relative abundance of strain USDA 4 was negatively correlated with that of USDA 127 and this relationship may be influenced by the levels of NO3-N and other soil edaphic factors. Significance and Impact of the Study: The local community of bradyrhizobia can be affected by applying inoculant bacteria to organic fields. Based on these results, soybean production in organic farms may be improved by displacing strains similar to USDA 4 with those better at nitrogen fixation and competitive ability than indigenous strains.
Introduction Soybean (Glycine max) cultivation is of principal agronomic importance in the United States. In 2009, Minnesota was among the three top soybean producing states (USDA 2010). To date, however, ~93% of soybean crops grown in the U.S. are comprised of genetically modified organisms (GMOs) (USDA 2013). In conventional farms, synthetic fertilizers, pesticides and uniform high-yield hybrid crops are used to achieve enhanced crop productivity. The idea of organic farming systems places a focus on the health of the environment, soils and the ecosystem, 1152
as well as humans, and does not use synthetic fertilizers, pesticides or GMO crops for production. Organic farming methods are regulated at the national and international levels. Based on information from USDA-accredited state and private organic certifiers, Minnesota ranks first in certified organic soybean acres (USDA 2011). According to the USDA’s National Organic Program, one of the most challenging problems for organic farming systems is the limitation of soil nitrogen, since synthetic N compounds cannot be used for production (http:// www.ams.usda.gov/AMSv1.0/nop). Over-use of synthetic fertilizers has been shown to cause serious water
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pollution problems (Comly 1987; Smith et al. 1987; Randall and Mulla 2001; Elmi et al. 2002; WHO 2011). Biological N2-fixation remains a viable option for providing a nitrogen source in organic farming systems for legumes, in place of synthetic fertilizers. This can be achieved by applying Rhizobium or Bradyrhizobium spp. strains, the nitrogen-fixing root- and -stem nodule symbionts of legumes (e.g. soybeans, alfalfa, beans and peas) (Zahran 1999). In the U.S. soybean bradyrhizobia are comprised mainly of two species, Bradyrhizobium japonicum and B. elkanii, with strains of the former being more prevalent in northern states and strains of the latter in the south (Keyser et al. 1984; Dobert et al. 1994; Shiro et al. 2013). The genotypes of soybean bradyrhizobia found in any given soil vary, in part due to the previous inoculant used, soil edaphic factors and to symbiotic interactions with specific soybean varieties (Singleton and Tavares 1986; Shiro et al. 2013). However, relatively few strains have been shown to be highly competitive and effective at carrying-out N2 fixation in most soils (Triplett and Sadowsky 1992). These strains are frequently the ones most often found in nodules from nitrogen-sufficient, highly productive, soybeans found in the field. It has been welldocumented that introduced rhizobia often poorly compete with indigenous strains, as demonstrated by low recovery rates in field crops (Ham et al. 1971; Kvien et al. 1981; Streeter 1994). Moreover, the application of genetically engineered rhizobia or GMO crops is prohibited for use in organic systems. In conventional farms, several studies reported that strains in B. japonicum serocluster 123 are the major indigenous competitors of soybean-bradyrhizobia in the upper Midwest U.S., including Minnesota (Ham et al. 1971; Ellis et al. 1984; Keyser et al. 1984; Schmidt et al. 1986; Cregan et al. 1989). These strains, however, are less effective for N2-fixation than some less competitive strains, such as USDA 110 (Caldwell and Vest 1970; Ellis et al. 1984; Moawad et al. 1984). In contrast, B. elkanii serogroup 31 and 76 strains are predominant in the southeastern United States (Caldwell and Hartwig 1970; Keyser et al. 1984). Thus, the selection and use of highly competitive, efficient nitrogen-fixing, indigenous bradyrhizobial strains can be a useful method to improve soybean productivity on organic farms. Despite the use of legume inoculants on conventional farms and an understanding of indigenous bradyrhizobia in U.S. soils, little work has been done to determine the numbers and types of Bradyrhizobium strains in organic farm soils and whether new inoculants specifically selected for organic systems could be useful for organic soybean systems. The selection and use of highly competitive, efficient nitrogen-fixing, indigenous bradyrhizobial
Diversity of soybean-bradyrhizobia from organic farms
strains can be a useful method to improve soybean productivity on organic farms (Keyser and Li 1992). In this study, we evaluate the serological and genetic diversities of soybean-bradyrhizobia isolated from organic field soils in Minnesota using horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (HFERP) DNA fingerprinting to determine how these populations vary from those previously reported to be present in soils from conventional farming systems (Schmidt et al. 1986; Shiro et al. 2013). In addition, soil nutrient and physicochemical parameters were evaluated to assess relationships between these factors and bradyrhizobial diversity. Results of this study provide novel insights into the bradyrhizobial populations in organic fields and suggest possible means by which to increase organic soybean yields. Materials and methods Soil sampling and isolation of indigenous bradyrhizobia from organic fields Twenty-five soil samples were collected from organic fields at the 0–10 cm depth. Fields were located in 13 counties in Minnesota and in one county in Wisconsin (close to Washington County, Minnesota) during May to July in 2012 (Fig. 1 and Table 1). All fields were certified and were practicing organic farming for at least 4 years before sampling. Soil samples were analysed for the concentration of soybean-bradyrhizobia by using the most probable number (MPN)-growth pouch technique with soybean cv. Lambert as trap host (Somasegaran and Hoben 1985). The remaining soil samples (210 g) were submitted to the Soil Testing Laboratory, University of Minnesota-St. Paul for analysis of soil chemical properties (Table S1). Soybean seeds were surface sterilized as previously described (Somasegaran and Hoben 1985). Briefly, seeds were rinsed with 95% ethanol for 10 s, and immersed in 20% Chlorox bleach for 10 min. Seeds were rinsed exhaustively with sterile water and submerged in water for 30 min at room temperature. Sterile seeds were pregerminated by plating on 1% water agar. Growth pouches were prepared by adding 50 ml of 059 Hoagland’s solution (Hoagland and Arnon 1950) and autoclaved for 30 min. Germinated seeds were placed in sterilized growth pouches, and inoculated with 1 ml of each soil dilution, from 101 through 106, using four replications per dilution. Seeds were incubated in growth chambers at 23°C with 70% humidity and a 16 h photoperiod. Root nodules were harvested after 4 weeks and the concentration of bradyrhizobia in each soil sample, per host plant, was calculated and presented as the MPN per
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Be
Bj 94 11 0
Diversity of soybean-bradyrhizobia from organic farms
Group 1 (9 fields: S1, S2, S5–S11)
(a)
Bj
Bj 4
Bj 127
(b) Kittson
Group 2 (2 fields: S3, S4)
Roseau
Lake of the Woods
Marshall Koochiching Beltrami
Pennington
Bj 4 Bj 1 35
Be 94 (2·0% ) Bj 1 35 ( 3·8% Bj ) 11 0( 5·1 %)
Bj 4 (31·8%)
Cook
Reda Lake
Bj 123
Polk
Lake
Clearwater
Itasca
St.Louis
Norman
Bj 127
Mahnomen
Hubbard
Cass
Becker
Clay
Bj 123 ) (15·8%
Otter Tail (S5, S6)
Morrison
Douglas
Grant
Kanabec Benton
Bj 13 5
Traverse
Bj 4
Stevens
Stearns
Pope
Mi ssis Sherburne sip pi R Wright iver
Big Stone
29
1 Bj
Pine
Mille Lacs
Todd
Bj 129 (1·3%)
Carlton
Aitkin
Crow Wing
Wadena
Wilkin
Bj 127 (40·4%)
3
12
Swift
Lac qui Parle
Mi
Chippewa
nn McLeod esoRenville ta Riv Sibley er
Yellow Medicine
Bj 127 Lincoln Lyon
Redwood
0
Isanti
Bj
Chisago Anoka
Kandiyohi Meeker
Washington
Hennepin
Ramsey
Polk (WI)
Bj 1
23
Carver Scott
Dakota
Bj 127
Goodhue
Nicollet Le Sueur Rice
Wabasha
Brown
Group 3 (8 fields: S16–S23)
Pipestone
Nobles
Cottonwood Watonwam
Jsckson
Martin
Blue Earth Waseca
Faribault
Steele Dodge
Olmsted
Mower
Freeborn
Winona
Group 4 (4 fields: S12–S15)
Fillmore Houston
Bj 110
Rock
Murray
11
Bj 4
Bj 123 Bj 4 Bj 127
Group 5 (2 fields: S24, S25)
Figure. 1 Distribution of serotypes of indigenous soybean-bradyrhizobia isolated from organic farms in Minnesota. (a) Composite distribution among all sites. (b) Sampling locations were grouped based on best management practices (BMP’s) in Minnesota to show the population ratio of indigenous soybean-bradyrhizobia in each area. Group 1, Irrigated and non-irrigated sandy soils; Group 2, Northwestern; Group 3, Southwestern and West Central; Group 4, South Central; Group 5, Southeastern. Red triangles indicate the locations where soybean-bradyrhizobia were taken and yellow triangles indicate the locations where bradyrhizobia could not be obtained in this study. Abbreviation: Bj, Bradyrhizobium japonicum; Be, B. etli. Legends; ( ) Bj USDA 4; ( ) Be USDA 94; ( ) Bj USDA 110; ( ) Bj USDA 123; ( ) Bj USDA 127; ( ) Bj USDA 129 and ( ) Bj USDA 135.
gram of dry soil. Root nodules were used for isolation of indigenous bradyrhizobia. Nodules were rinsed with 95% ethanol for 10 s and surface sterilized with 5% bleach for 10 min, with vigorous shaking. Surface-sterilized nodules were washed with eight changes of sterile, distilled water and each nodule was placed individually into 100 ll of 085% NaCl in wells of microtitre plates. Nodules were crushed with a sterile loop and streaked onto the surface of arabinose-gluconate (AG) agar plates (Sadowsky et al. 1987). Nodule bacteria were purified by streaking onto the same medium. HFERP DNA genotyping of indigenous soybeanbradyrhizobia DNA fingerprints from eight reference strains (Table 2) and about 30 Bradyrhizobium isolates per sample, per host plant, were analysed by using a modification of the HFERP DNA fingerprinting technique as described previously (Johnson et al. 2004). Escherichia coli strain 1154
Pig294, isolated in our laboratory, was used as a control, and an internal ROX-labelled molecular weight marker was included as a control for each sample for inter-gel comparisons (Dombek et al. 2000; Johnson et al. 2004). Briefly, each Bradyrhizobium strain was streaked onto AG medium for single colony isolation. A portion of a single colony of each sample was picked using a 1-ll sterile loop (Fisher Scientific, Waltham, MA) and suspended in 100 ll of 50 mmol l1 NaOH in low 96-well clear PCR plates (Bio-Rad Laboratories, Hercules, CA). The partial colony was suspended vigorously and heated at 95°C for 15 min. Samples were centrifuged at 4°C for 10 min at 640 rev min1 (82 g). A 2-ll aliquot of supernatant for each sample was subjected to HFERP DNA fingerprinting as previously described (Johnson et al. 2004) and PCR was performed using the following conditions: 95°C for 2 min, 30 cycles of 94°C for 3 s, 92°C for 30 s, 50°C for 1 min, 65°C for 8 min and a final extension at 65°C for 8 min. Amplicons were visualized via gel electrophoresis at 70V for 16 h at 4°C
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Diversity of soybean-bradyrhizobia from organic farms
Table 1 Farm locations, soil characteristics, crop rotation practices and nodule number and size of indigenous Bradyrhizobium japonicum strains from 25 organic farms in Minnesota
Application of inoculants
Crops prior to sampling
Nodule number/plant (at 1 : 100 dilution)†
Yes Yes Yes
Kidney bean Kidney bean Soybean
115 125 138 153 158 66
31 30 45
Yes
Soybean
285 82
53
Otter Tail
I: Sandy loam, neutral I: Sandy loam, neutral II: Borup loam, Colvin silty clay loam, slightly basic III: Northcote clay, Fargo clay, slightly basic I: Sandy loam, neutral
Yes
14 June 2012
Otter Tail
IV: Clay loam, neutral
S7 S8 S9 S10 S11 S12
19 08 08 18 18 18
Mille Lacs Morrison Morrison Polk (WI) Polk (WI) Dakota
Green bean Soybean Soybean Green bean Dry bean Soybean
S13
18 May 2012
Dakota
No
Dry bean
S14
18 May 2012
Dakota
No
S15
23 May 2012
Dakota
S16
09 May 2012
S17
30 May 2012
S18 S19 S20
09 May 2012 23 May 2012 30 May 2012
Lac qui Parle Yellow Med Lincoln Murray Redwood
IV: Clay loam, slightly acid V: Loam, neutral VI: Loamy sand, slightly acid VII: Santiago silt loam, neutral VII: Santiago silt loam, neutral VII: Lester loam, Kennebec silt loam, moderately acid) VII: Lester loam, Kennebec silt loam, slightly acid VII: Lester loam, Kennebec silt loam, slightly acid VII: Lester loam, Blooming silt loam, moderately acid VII: Silty clay, neutral
No information No§ Yes Yes Yes Yes No
Dry bean, soybean Green bean
S21 S22 S23 S24
09 09 09 22
Redwood Redwood Redwood Sibley
S25
12 May 2012
Field no.
Sample collection date
County
Soil characteristics*
S1 S2 S3
17 July 2012 17 July 2012 16 May 2012
Hubbard Hubbard Clay
S4
16 May 2012
Clay
S5
14 June 2012
S6
May 2012 June 2012 June 2012 May 2012 May 2012 May 2012
May May May May
2012 2012 2012 2012
Steele
Log10 no. of Bradyrhizobia‡
12 10N
23
02 05N
09
35 40 35 30 28 28
157 105 68 90 88 210
101 95 73 72 63 121
92 44
40
Green bean
108 73
35
Never¶
Dry bean
100 22
38
Never
Soybean
175 176
41
IV: Canisteo clay loam, neutral
Never
Soybean
120 52
39
I: Sandy loam, neutral V: La Prairie loam, slightly acid V: Ves loam/Normania loam, slightly acid IV: Webster clay loam, neutral V: Ves loam, slightly acid V: Normania loam, neutral V: Loam, mix; Crippen, Cordova-Rolfe, slightly acid V: Hayden loam, slightly acid
Never Never No
Soybean Soybean Soybean
45 41 165 31 198 86
34 51 46
Yes No No Never
Dry bean Soybean Soybean Soybean
38 55 50 122
21 43 26 35
No
Soybean Average
130 90 113 73
39 48 60 96
42 43 10
*Soil characteristics were grouped based on USDA textural soil classification. Soil pH descriptions: moderately acid, 55–59; slightly acid, 60–65; neutral, 66–75; slightly basic, 76–80). †Nodule number per plant was reported as x̅ S.D. ‡Population size (log10 MPN g1 dry soil) estimated by the MPN technique using soybean cv. Lambert as trap host. §No; farmers did not use inoculant for the target bean crop and there is no information on past inoculant use. ¶Never; farmers did not use inoculant for the target bean crop and that they have never used inoculant in the past.
with a pump attached for buffer recirculation. Gel images were captured using a Typhoon 8600 scanner (Molecular Dynamics/Amersham Biosciences, Sunnyvale, CA) with a fluorescence acquisition mode. Gel images were analysed using BIONUMERICS ver. 2.5 (Applied Maths, Austin, TX). Phylogenetic analysis was conducted using
the unweighted pair group method with arithmetic means (UPGMA). Genetic diversity was evaluated based on the HFERP DNA fingerprint profiles using SPADE (Species Prediction And Diversity Estimation) software (Chao and Shen 2010) to calculate strain richness (using the abundance-based
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coverage estimator, ACE and Shannon and Simpson diversity indices (Shannon 1948; Simpson 1949). 16S rRNA gene sequencing To identify strains of soybean-bradyrhizobia in group XIII, XIV and XV (Fig. 2), some representatives from Table 2 Reference strains used in this study
each group were chosen for 16S rRNA gene sequence analysis using PCR primers; Bac27F (50 -AGA GTT TGA TCM TGG CTC AG-30 ) and Univ1492R (50 -CGG TTA CCT TGT TAC GAC TT-30 (Lane 1991). PCR amplicons were submitted to the University of Minnesota Genomics Center (UMGC, St. Paul, MN) for DNA sequencing using the Sanger sequencing method and an ABI PRISMTM 3730xl DNA Analyser.
Species
Strains
Sources
Serological analyses using immuno dot-blot assays
Bradyrhizobium japonicum
USDA 4, USDA 110, USDA 127, USDA 135 USDA 122, USDA 123, USDA 129, USDA 76, USDA 94
1
Two representative strains of indigenous soybean-bradyrhizobia in each of 15 genotypic group (n = 30) were selected for immuno dot-blot assays for serological identification as previously described (Cregan et al. 1989; Wongphatcharachai et al. 2013). The representative indigenous isolates and reference Bradyrhizobium strains were grown in AG medium for 2 days to OD600 = 08–12.
(b) B. elkani USDA76 B. elkani USDA94
100
90
80
% Relative similarity 70
20
100
90
80
70
60
50
40
30
20
% Relative similarity
60
(a)
50
Sources: 1, Reference strains belonging to this laboratory. 2, Obtained from the Rhizobium culture collection, United States Department of Agriculture (USDA)-ARS, Beltsville, MD.
40
2 1
30
Bradyrhizobium elkanii
Groups
No. of isolates
% population
No. of farma
I
12
1·95
4
USDA 94
II
23
3·75
6
USDA 135
III IV V VI VII
18 11 12 11 13
2·93 1·79 1·95 1·79 3·12
4 5 3 6 7
USDA 110 USDA 110 USDA 129 USDA 123 USDA 123
VIII
21
3·42
9
USDA 127
IX
71
11·56
18
USDA 123
X
32
5·21
13
USDA 127
XI
35
5·70
12
USDA 127
XII
160
26·06
20
USDA 127
XIII XIV
14 12
2·28 1·95
8 6
†ND †ND
XV
169
27·52
16
‡ND (USDA 4)
Total
614
100
23
Serotype
B. japonicum USDA135
B. japonicum USDA110
B. japonicum USDA122 B. japonicum USDA129
B. japonicum USDA127
B. japonicum USDA123
B. japonicum USDA4
Figure. 2 Dendrograms based on HFERP DNA fingerprinting and serotypes of soybean- nodulating bradyrhizobia isolated from soils of 25 organic farms. (a) all isolates were submitted showing a whole picture of genetic diversity of bradyrhizobia in organic farms. (b) samples which cannot be classified into any groups or fewer than 10 isolates per group were excluded to show the 15 predominant genotypic groups. The black lines ( ) are used to show the reference strains that did not group with any sample and the black triangles ( ) are used to show the reference strains which grouped with samples. Legend: ND = no specific antibody to determine serogroup, †Based on the results of 16S DNA sequencing, ‡Based on the results of HFERP fingerprinting.
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Three replicate 15-ll aliquots of each culture were spotted onto the surface of nitrocellulose membranes and left to air dry for 10 min. The membrane was blocked with 5% fish gelatin (Sigma–Aldrich, St. Louis, MO) in 19 PBST (005% Tween20) at 4°C for 2 h. The membrane was washed once with 19 PBST and incubated for 30 min in a 1 : 400 diluted serotype-specific antibodies with 19 PBST as previously described (Madrzak et al. 1995). The membrane was washed five times with 19 PBST, in 5 min intervals, and incubated for 30 min in a 1 : 5000 diluted goat anti-rabbit antibody-HRP conjugate (Bio-Rad Laboratories) with 19 PBST. The membrane was washed once with 19 PBST, and immunological reactions were detected by incubating with reagents A and B (Pierceâ ECL Plus Western Blotting Substrate, Thermo Scientific) at room temperature for 3 min. The membrane spots were captured by using LABWORKS 4.5 software (UVP products, Upland, CA). Statistical analyses For statistical comparisons of genetic diversity indices, outliers and fields at which bradyrhizobia could not be isolated were excluded from further analyses. Nonparametric unpaired t-test (Mann-Whitney) and Kruskal-Wallis test were used to determine significant differences in comparisons. Spearman rank correlations were also calculated to determine relationships between inoculant application categories, edaphic properties, and bradyrhizobial abundance and diversity. All statistical analyses were performed using SPSS ver. 19 software (SPSS Inc., Chicago, IL) at a = 005. Results Concentrations of bradyrhizobia in soils The concentration of soybean-bradyrhizobia in soils from the 25 farms examined varied from log10 09–53 bradyrhizobia g1 dry soil (Table 1). On average, soils contained log10 43 bradyrhizobia g1 dry soil. Five of the farms in three counties (S3, S4 in Clay; S19 in Murray; S20, S22 in Redwood) contained populations of soybeanbradyrhizobia greater than the average, with log10 45, 53, 51, 46 and 43 bradyrhizobia g1dry soil, respectively, and the greatest concentration of bradyrhizobia was found in Clay County (S4). Bradyrhizobial concentrations did not differ significantly due to inoculant application practices (P > 005). However, concentrations were significantly greater when soybeans were planted prior to sampling (P = 0008, Table 3). The average number of nodules per plant was 113 73 nodules at the 100-fold-diluted soil suspensions
Diversity of soybean-bradyrhizobia from organic farms
(Table 1). The number of nodules observed was significantly and positively correlated with the bradyrhizobial concentration in the soil (r = 0509, P = 0018). The greatest number of nodules per plant was found in soils from site S4 in Clay County, with 285 82 nodules per plant. Of note, soybean nodules from two fields in Otter Tail County (sites S5 and S6) were small in size and bradyrhizobia could not be obtained after surface sterilization. These were likely ineffective nodules. The number of nodules observed did not differ significantly by crop prior to sampling or inoculant application practices (P = 0129 and 0871, respectively). Genetic diversity of soybean-bradyrhizobia from organic farms Evaluation of genetic diversity of all the isolates was determined by using the HFERP DNA fingerprinting technique. Results of this analysis revealed that the soybean-bradyrhizobia (n = 733) could be classified into 79 different genotypes at >92% similarity (Fig. 2a). This similarity value was previously shown to represent clonal isolates (Johnson et al. 2004). Genetic diversity and richness of soybean-bradyrhizobia were not significantly different as a result of crop planting prior to sampling, inoculant application practices, or locations (P > 005; Table 3). After excluding the ungrouped unique strains (n = 119, samples which could not be classified into any groups or contained fewer than 10 isolates per group), soybean-bradyrhizobia were classified into 15 predominant genotypic groups (I - XV) based on HFERP DNA fingerprints (Fig. 2a,b). Soils from organic farming systems in Minnesota contained three main populations. Group IX accounted for 116% of isolates typed and was found in soils at 18 farms. This group also included the reference strain B. japonicum USDA 123. Group XII accounted for 261% of isolates typed and was present at 20 farms in all counties, except in Otter Tail county where soybean-bradyrhizobia could not be obtained in this study. Group XV accounted for 275% of isolates and also included the reference B. japonicum strain USDA 4. This genotype was obtained from 16 farms in 10 counties, except from Mille Lacs, Lac qui Parle and Yellow Medicine farms (Table 4). Soil chemical properties and genetic diversity Correlation analysis of soil chemical properties and genetic diversity revealed that the percentage of soil organic matter was significantly and negatively correlated with the Shannon diversity index (r = 0512,
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1158
plant
bradyrhizobia
135 70
(n = 14)
93 45
(n = 10)
P = 0129
(n = 14)
30 09
(n = 10)
P = 0008
Common
beans
P value
(n = 2)
P = 0100
(n = 2)
P = 0617
(n = 4)
(n = 4)
(n = 4)
126 05
(n = 8) 59 02
(n = 8)
128 55
(n = 8)
35 05
(n = 4)
(n = 2) 66 05
(n = 2)
106 67
(n = 2)
37 10
39 05
20 05
78 05
221 90
P < 0001
(n = 2)
61 02 P = 0761
(n = 2)
19 08
(n = 8)
16 04
(n = 2)
18 01
(n = 7)
49 05
17 08
(n = 9)
(n = 9)
(n = 9)
86 52
29 09
67 03
(n = 6)
P = 0440
(n = 2)
191 174
(n = 4)
254 120
(n = 8)
123 106
(n = 2)
145 50
(n = 7)
212 134
P = 0095
(n = 6) P = 0247
ND
(n = 6)
P = 0871
(n = 6)
P = 0346
(n = 8) 116 54
(n = 8)
250 153
(n = 8)
18 04
184 78
(n = 8)
P = 0644
18 04
P = 0684
(n = 9)
196 140
17 07 (n = 9)
(n = 14)
171 111
ACE
(n = 14)
18 05
H’
16 02
ND
(n = 8)
ND
121 47
125 60
37 07
ND§
(n = 8)
(n = 10)
(n = 10)
40 06
110 75
34 10
P = 0770
(n = 10)
66 04
(n = 14)
66 02
pH (soil)
P = 0151
(n = 2)
85 35
(n = 4)
240 194
(n = 8)
93 67
(n = 2)
82 05
(n = 7)
224 141
P = 0242
(n = 6)
837 62
(n = 8)
202 178
(n = 8)
176 104
P = 0116
(n = 9)
211 174
(n = 14)
122 85
strains
unidentified
Percent of
P = 0185
(n = 2)
50 14
(n = 4)
128 45
(n = 8)
71 36
(n = 2)
95 21
(n = 7)
100 52
P = 0329
(n = 6)
77 16
(n = 8)
110 58
(n = 8)
99 29
P = 0315
(n = 9)
97 97
(n = 14)
86 41
No. of strains
P = 0428
(n = 2)
529 119
(n = 4)
440 339
(n = 8)
245 234
(n = 2)
29 40
(n = 7)
298 374
P = 0857
(n = 6)
360 269
(n = 8)
291 306
(n = 8)
271 333
P = 0590
(n = 9)
365 337
(n = 14)
260 272
USDA4
(n = 9)
(n = 9)
(n = 8)
(n = 8) (n = 6)
P = 0394
0 (n = 2)
(n = 4)
44 88
P = 0280
(n = 2)
37 52
(n = 4)
183 297
0 (n = 8)
0 (n = 2)
0 (n = 2) 0 (n = 8)
(n = 7)
50 88
P = 0638
(n = 7)
47 67
P = 0521
19 45
87 217
28 62 0 (n = 6)
(n = 8)
39 79
P = 0087
(n = 8)
31 62
P = 0105
111 207
(n = 14)
43 73
11 27
(n = 14)
USDA110
08 31
USDA94
Relative abundance of serotypes
Bold texts indicate significant difference at 005 levels. *The mean difference between groups was analysed by Mann-Whitney Test (a = 005 level). †The mean difference between groups was analysed by one way-ANOVA, Kruskal-Wallis Test (a = 005 level). ‡Locations were grouped as shown in Fig. 1. §ND, not determined. ¶No; farmers did not use inoculant for the target bean crop and there is no information on past inoculants use. **Never; farmers did not use inoculant for the target bean crop and that they have never used inoculants in the past.
P value
Group 5
Group 4
Group 3
Group 2
Group 1
Locations†,‡
P value
Never**
No¶
Yes
Inoculants application practices†
Soybean
40 08
Crop prior to sampling*
nodules per
No. of
Conc. of
Genetic diversity
P = 0858
(n = 2)
210 69
(n = 4)
127 122
(n = 8)
162 142
(n = 2)
248 174
(n = 7)
132 182
P = 0468
(n = 6)
137 73
(n = 8)
210 194
(n = 8)
1273 127
P = 0486
(n = 9)
14. 4 168
(n = 14)
168 130
USDA123
(n = 4)
P = 0042
(n = 2) P = 0060
0 (n = 2)
(n = 4) 224 03
64 74
0 (n = 8)
P = 0395
0 (n = 2)
0 (n = 4)
(n = 8)
107 181
(n = 2)
75 26
(n = 7) 0 (n = 2)
06 16 (n = 7)
P = 0734
(n = 6)
60 100
(n = 8)
62 177
(n = 8)
21 35
P = 0028
0 (n = 9)
(n = 14)
75 140
USDA135
13 23
P = 0097
0 (n = 6)
(n = 8)
38 58
(n = 8)
05 14
P = 0086
(n = 9)
34 56
(n = 14)
03 11
USDA129
142 84
(n = 8)
486 128
(n = 2)
648 189
(n = 7)
454 316
P = 0167
(n = 6)
426 221
(n = 8)
283 152
(n = 8)
506 292
P = 0038
(n = 9)
303 243
(n = 14)
475 183
USDA127
Table 3 Comparison of Bradyrhizobium concentrations, number of nodules and population diversity of bradyrhizobia in relation to crop prior to sampling, inoculant application and location of the farm
Diversity of soybean-bradyrhizobia from organic farms M. Wongphatcharachai et al.
Journal of Applied Microbiology 118, 1152--1164 © 2015 The Society for Applied Microbiology
36
29
Hubbard Clay
Clay Otter Tail
Otter Tail Mille Lacs
Morrison Morrison
Polk Polk
Dakota Dakota
Dakota Dakota
Lac qui Parle
Yellow
Med Lincoln
Murray Redwood
Redwood Redwood
Redwood Sibley
Steele
S2 S3
S4 S5
S6 S7
S8 S9
S10 S11
S12 S13
S14 S15
S16
S17
S18
S19 S20
S21 S22
S23 S24
S25 Total
Journal of Applied Microbiology 118, 1152--1164 © 2015 The Society for Applied Microbiology
4
1 18
– –
– –
– –
–
–
–
9 3
– –
5 –
– –
– –
– –
– –
–
III
5
– 11
– –
– –
– –
–
–
–
4 –
– 2
– –
1 –
– 3
– –
– –
1
IV
3
1 12
– –
– –
– –
–
–
–
9 –
– –
– –
– 2
– –
– –
– –
–
V
6
– 11
– –
2 4
– –
–
1
–
– 1
– 2
– –
– –
– 1
– –
– –
–
VI
7
2 13
– 3
– –
– 1
–
1
–
2 1
– –
– –
– –
– –
– –
– 3
–
VII
9
2 21
– –
– –
– 1
–
–
–
– –
– –
2 1
1 2
– –
8 –
– 1
3
VIII
18
5 71
– 2
4 7
2 1
4
7
2
1 1
– 3
– –
5 4
– 7
4 –
– 10
2
IX
13
1 32
– –
1 –
2 1
1
1
3
2 –
2 –
– –
3 10
– 3
– –
– 2
–
X
12
2 35
– –
– –
4 4
–
3
–
– 1
– –
– 1
6 3
– 4
4 –
– 2
1
XI 1
20
1 160
7 7
12 11
16 –
10
17
11
2 2
6 1
7 16
6 –
– 1
13 –
– 13
XII
6
1 14
– –
– –
1 2
4
–
–
– –
5 –
– –
1 –
– –
– –
– –
–
XIII
6
4 12
– 1
– 1
– 2
–
–
3
– –
1 –
– –
– –
– –
– –
– –
–
XIV
16
7 169
– 18
8 2
9 12
9
–
–
– 18
17 6
7 1
– 2
– –
– –
33 2
18
XV
23
27 614
14 31
27 25
34 24
28
34
25
29 27
31 17
21 19
24 26
0 20
32 0
33 35
31
Total
4 119
0 2
3 5
1 5
1
2
5
2 5
9 18
11 5
10 7
– 14
3 –
1 3
3
unidentified strains§
Diversity from all 25 organic fields‡‡
11 15
2 6
5 5
6 8
5
7
5
7 7
5 6
4 4
8 7
0 7
5 0
1 8
7
No. of groups‡
No. of
315 1894
–
2 67
91 75
93 361
75
18
91
124 19
312 39
89 265
249 268
ND 403
109 ND††
–1 18
219
Richness (ACE)
288
242 –
069 132
158 168
149 205
151
162
179
185 159
195 273
189 119
236 23
ND 245
172 ND
013 192
162
Shannon index
Genetic diversity¶
012
012 –
05 036
026 023
03 021
026
028
021
02 034
023 008
017 047
012 014
ND 011
023 ND
094 021
032
Simpson’s index
*Total number of indigenous soybean–nodulating bradyrhizobia of each farm submitted for HFERP DNA fingerprinting. †Number of indigenous soybean-nodulating bradyrhizobia in each group and field after excluding the ungroup strains. ‡No. of predominant genetic groups in each farm based on HFERP DNA fingerprinting at 92% relative similarity. §Not all of the unidentified strains were singletons. Several of the unidentified strains shared the same genotype but were represented by fewer than 10 isolates. ¶Genetic diversities were calculated based on a total number of bacterial entries submitted to HFERP DNA fingerprinting. **Number of different genotypes in each field before excluding the ungrouped strains. ††ND, not determined. ‡‡Diversity from all 25 organic fields was calculated based on HFERP fingerprinting before excluding the ungrouped strains (Fig. 2a).
6
4
14 33
30 30
35 29
Number of fields in each group
4
–
– 23
6
–
– 12
– –
– –
31 733
– –
– 3
7 –
– –
– –
– –
1 –
– 3
– –
– –
– 1
– –
3 –
– –
– –
– 2
– –
–
–
5
II
– –
I
–
30
31 32
40 35
32 24
34 33
0 34
35 0
34 38
34
Hubbard
S1
Total entries*
County
Field no.
Number of soybean-Bradyrhizobium isolates in each genotypic group†
Table 4 Genetic diversity and number of soybean-nodulating bradyrhizobia in each group isolated from soils from 25 organic fields in Minnesota
044
071 –
026 038
046 049
042 061
045
045
053
054 046
053 077
055 038
067 066
ND 07
048 ND
004 053
046
Evenness
79
15 –
2 6
7 7
7 13
6
9
8
9 10
13 19
8 7
14 14
0 16
8 0
2 11
10
No. of genotypes**
M. Wongphatcharachai et al. Diversity of soybean-bradyrhizobia from organic farms
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Diversity of soybean-bradyrhizobia from organic farms
M. Wongphatcharachai et al.
P = 0021), evenness (r = 0556, P = 0011), relative abundance of unidentified strains (r = 0798, P < 0001) and the number of different strains (r = 0510, P = 0022) (Table S2). Distribution of serotypes of soybean-bradyrhizobia in organic fields Serological analyses were performed by using immunospot blot assays to identify serotypes of each predominant genotypic group (Table 5). The B. japonicum USDA 127 strains (part of serocluster 123) made up the largest percentage of the population (404%; group VIII, X, XI and XII) followed by B. japonicum USDA 4 (318%; group XIII, XIV and XV) and USDA 123 strains (158%; group VI, VII and IX). Isolates in groups XIII and XIV were identified by using 16S rRNA gene sequencing (~ 1300 bp) and strains were found to be 100% identical to B. japonicum strain USDA 4, thus samples in those two groups were reported as serotype USDA 4 strains.
This serotype was frequently detected among organic farms in Minnesota (318% of isolates) and was obtained from 18 farms in 11 counties (except Mille Lacs and Yellow Medicine). Application of soybean inoculants did not significantly affect serotype distributions (P > 005). The distribution of serotype USDA 127 and USDA 135 strains were significantly greater at farms where soybean was the crop in the year prior to sampling, compared to farms where common bean was planted as the previous crop at P = 0038 and 0028, respectively. The relative abundance of serotype USDA 127 strains was significantly different among the locations (P = 0042, Table 3). The relative abundances of several serotypes were inter-correlated. For example, the relative abundance of USDA 4 strains was negatively correlated with abundances of USDA 127 and 135 (r = 0641 and 0571; P = 0001 and 0006, respectively), and the abundances of strains in serotypes USDA 127 and 135 were positively correlated (r = 0532, P = 0006).
Table 5 Serological assignment (via immuno dot-blot assays) of 614 isolates of Bradyrhizobium japonicum strains isolated from 25 organic fields in Minnesota Number of isolates and percentage (%) in each serotype Farm no.
Counties
S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 S21 S22 S23 S24 S25 Total
Hubbard Hubbard Clay Clay Otter Tail Otter Tail Mille Lacs Morrison Morrison Polk (WI) Polk (WI) Dakota Dakota Dakota Dakota Lac qui Parle Yellow Med Lincoln Murray Redwood Redwood Redwood Redwood Sibley Steele
No. of strain 31 33 35 32 – – 20 24 26 21 19 31 17 29 27 25 34 28 34 24 27 25 14 31 27 614
USDA 4* 18 (581) 33 (100) 2 (57) – – – –
USDA 94 5 (161) – – – – – 1 (50)
1 2 7 1 23 6
(42) (77) (333) (53) (742) (353)
– 18 (667) 3 (120) – 13 10 16 8 3
(464) (294) (667) (296) (120)
– 19 (613) 12 (444) 195 (318)
USDA 110
– 3 (115) – – – 3 (176) – – – – – – – – – – – – 12 (20)
1 (32) – – – – – – – 2 (77) 5 (238) – – – 18 3 – – – – – – – – – 2 31
(621) (111)
(74) (51)
USDA 123 3 – 13 4 – – 10 5 4 – – – 5 3 3 2 9 4 2 2 6 11 – 5 7 97
USDA 127*
(65)
5 (161) –
(371) (125)
18 (514) 25 (781) – –
(500) (208) (154)
(294) (103) (111) (80) (265) (143) (59) (83) (222) (440) (161) (259) (158)
8 16 15 9 18 8 1 4 3 14 21 11 22 6 13 11 7 7 6 248
(400) (667) (577) (429) (947) (258) (59) (138) (111) (560) (618) (393) (647) (250) (482) (440) (500) (226) (222) (404)
USDA 129
USDA 135
– – – – – – 1 1 – – – – 2 4 – – – – – – – – – – – 8
– – 2 (57) 3 (94)
(50) (42)
(118) (138)
– – – 1 (42) – – – – – – – 6 (240) 4 (118) – – – – –
(13)
7 (500) – – 23 (38)
*The relative abundance of USDA 4 was negatively correlated with USDA 127 (r = 0641, P = 0001). Number in parenthesis indicates percentage (%) of serotype in each group.
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Soil chemical properties and distribution of serotypes Soil pH was significantly and positively correlated with the relative abundance of USDA 127 strains (r = 0582, P = 0004) and inversely correlated with the relative abundance of USDA 4 (r = 0469, P = 0024). Interestingly, the concentration of nitrate-nitrogen (NO3-N) was significant positively correlated with the relative abundance of strains in serotype USDA127 (r = 0720, P < 0001), and inversely correlated with the relative abundance of serotype USDA 4 (r = 0441, P = 0040; Table S2). Grouping of soil samples based on farm locations (Fig. 1) indicated that the relative abundance of strains in serotype USDA 127 was significantly greater at farms in Group 3, compared to soil samples in Group 4 (P = 0011). Moreover, soil pH and concentration of NO3-N was also significantly greater at farms in Group 3 with P = 0027 and 0007, respectively (Table S3). Discussion DNA fingerprinting methods are commonly used in bacterial biogeography and epidemiology studies (Fajardo-Cavazos and Nicholson 2006). The rep-PCR DNA fingerprinting technique, using the BOX A1R primer, has been used to amplify specific genome regions located between adjacent BOX repetitive elements (154 bp), and is commonly found in a number of gram positive and negative bacterial species (Martin et al. 1992; Ishii and Sadowsky 2009). This technique has proven to be a valuable tool for genotyping due to relative simplicity and reproducibility as well as high discriminatory power for clustering inter- and intra-specific bacterial genotypes (Olive and Bean 1999). In this study, the HFERP DNA fingerprinting technique was modified to include an internal standard to circumvent issues of inter-gel variability (Johnson et al. 2004). Moreover, HFERP fingerprinting output can be easily analysed by computer assisted methods making HFERP fingerprinting a practical tool for use in environmental microbial studies (Johnson et al. 2004). It has been reported that Bradyrhizobium serocluster 123 strains comprise a major component of field populations found in conventional soybean farms in the Midwest U.S. (Schmidt et al. 1986). Based on differences in their somatic antigens (Date and Decker 1965), this serocluster is defined by three serotypes, represented by strains USDA 123, USDA 127 and USDA 129 (Schmidt et al. 1986). Strains in serocluster 123, especially strain USDA 123, have shown exceptional competitive ability. These strains, however, are reported to be less effective for N2-fixation than other strains, such as USDA 110, and may negatively affect soybean productivity (Caldwell
Diversity of soybean-bradyrhizobia from organic farms
and Vest 1970; Ellis et al. 1984; Moawad et al. 1984). Therefore, displacement of members of serocluster 123 with more effective B. japonicum strains may significantly increase soybean productivity, as shown by using inoculant strains USDA 110, 122 (CB1809) and 138 (Kvien et al. 1981; Kogan et al. 1987). However, these latter strains are more likely to lack competitive ability against indigenous strains, as relatively few were identified in this study. In contrast with what was reported by Shiro et al. (2013), B. elkanii was found in only about 20% of the population in four farms. This result is consistent with other studies that have shown that B. elkanii strains are more prevalent in southern U.S. soils than those in the north (Keyser et al. 1984), at least using modern soybean cultivars. Serological testing using antibodies against USDA 122, 123, 127, and 129 can provide false-positive results due to cross-reactivity, as previously reported (Date and Decker 1965; Schmidt et al. 1986). Therefore, in this study, the results of HFERP DNA fingerprinting profiles together with serological assays using cross-adsorbed, serotype-specific antisera were performed to identify and confirm the serological identity of nodule isolates. It should be noted that only 5 of 32 isolates (156%) from farm S1 in Hubbard County were located in the same group with the reference strain B. japonicum USDA 122 (Fig. 2a). Strain USDA 122 is a parent strain of a commercial inoculant CB1809, and inoculation with this strain has been documented as being effective at promoting N2-fixation with most soybean cultivars (Keyser and Griffin 1987). This is also a member of serocluster 123 (Schmidt et al. 1986). The lack of USDA 122 populations in organic fields in this study is similar to what has been shown for non-organic fields (Keyser et al. 1984). Interestingly, B. japonicum strain USDA 4 was found to comprise a previously unrecognized, predominant population of indigenous soybean-bradyrhizobia in organic farm fields. We hypothesize that elevated abundance of this strain may be due to its highly competitive nature in organic farming systems, in contrast with what has been reported in several studies done at conventional farms (Keyser et al. 1984; Schmidt et al. 1986; Cregan et al. 1989; Shiro et al. 2013). Strain USDA 4, the type strain for this serotype, was originally isolated from a soybean field in Iowa in 1932 (Van Berkum and Fuhrmann 2000) and is not frequently isolated from conventional farm fields. Among all the samples in this study, soil pH was related to the distribution of two of the most abundant serotypes strains, USDA 4 and 127, and it was also significantly associated with inoculant application practice. Serotype strain USDA 4 may represent a previously
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M. Wongphatcharachai et al.
unrecognized, dominant and indigenous serotype in these soils that is displaced due to biological and/or chemical changes associated with conventional farm managements. In this study, genetic diversity and relative abundance of serotypes did not differ significantly by inoculant application practices, suggesting that inoculation strategies used by farmers may not displace indigenous bradyrhizobial strains. The results of soil chemical properties revealed that most of the farms contained the essential nutrients, nitrogen (N), phosphorous (P) and potassium (K) at elevated concentrations. The influence of high concentrations of P and K on legume-rhizobium symbiosis also remains unclear. Soil nitrogen concentrations in organic farms are not well-understood, since the amount of nitrogen is dependent upon the previous legume crops, crop rotations, as well as manure history. However, the amount of NO3-N recommended should not exceed 25 ppm and nitrate testing has now evolved as accepted best management practices (BMPs) to determine and improve the accuracy of the amount of nitrogen needed for agriculture farms in Minnesota (Rehm and Schmitt 2002). In contrast, it is well-documented that nitrate is a potent inhibitor of nodulation and nodule activity in soybean. In the presence of nitrate, the number of nodules formed on soybean are often reduced and delayed (Streeter 1988). While nodule trapping used in this study was done under controlled conditions in the laboratory, the diversity of indigenous soybean-bradyrhizobia recovered on soybeans may be different in field conditions using other cultivars. However, the technique does give a good estimate of Bradyrhizobium concentration and rough approximation of diversity in field soils, and is an accepted practice for this type of analysis. That said, our next goal is to measure bradyrhizobial population density and diversity directly at organic farms sites using several different soybean trap cultivars. Result from this study may be useful for strain selection for future studies e.g. N2-fixation assays and field-based yield experiments. Further characterization of the competitive ability of these strains and their efficiency at N2-fixation may also be a useful benefit to organic farmers, since it can provide strategies to improve soybean production without application of synthetic fertilizers. In summary, high levels of B. japonicum USDA 4 strains were found to be predominant populations in organic farms in Minnesota. This may highlight difference in soil edaphic factors in organic vs conventional soybean farms. The relative abundance of USDA 4 strains was negatively correlated with the abundances of strains in serogroup 127 and levels of NO3-N in soils, and these may also contribute to this difference. A long1162
term study for N2-fixation with selected and improved indigenous soybean-bradyrhizobial strains would be important to establish new inoculants for organic farms. Acknowledgements This work was support, in part, from a grant 201151300-30743 from USDA-NIFA. The authors would also like to thank Patrick Elia from USDA-ARS, Beltsville, MD for providing Bradyrhizobium japonicum USDA 122, USDA 123 and USDA 129 reference strains, and the organic farmers in Minnesota and Wisconsin who participated in our study. Authors’ contributions MW and MS designed the study of diversity of soybeanbradyrhizobia in organic farms and MW performed HFERP fingerprinting, serological assay, statistical analysis and drafted the manuscript. CS and PW helped wrote the manuscript and gave valuable suggestions for data analysis, and CS performed statistical analysis. KMM and CCS contacted the farmers, collected soil samples from organic farms, and provided soybean seeds for the MPN method. MJS supervised the study design, data analyses and helped write the manuscript. All authors read and approved the final manuscript. Conflict of interest The author(s) declare that they have no competing interests. References Caldwell, B.E. and Hartwig, E.E. (1970) Serological distribution of soybean root nodule bacteria in soils of southeastern USA. Agron J 62, 621–622. Caldwell, B.E. and Vest, G. (1970) Effects of Rhizobium japonicum strains on soybean yields. Crop Sci 10, 19–21. Chao, A. and Shen, T.-J. (2010) Program SPADE (species prediction and diversity estimation). Program and User’s Guide published at http://chao.stat.nthu.edu.tw. Comly, H.H. (1987) Landmark article Sept 8, 1945: cyanosis in infants caused by nitrates in well-water By Hunter H. Comly. JAMA 257, 2788–2792. Cregan, P.B., Keyser, H.H. and Sadowsky, M.J. (1989) Host plant effects on nodulation and competitiveness of the Bradyrhizobium japonicum serotype strains constituting serocluster 123. Appl Environ Microbiol 55, 2532–2536. Date, R.A. and Decker, A.M. (1965) Minimal antigenic constitution of 28 strains of Rhizobium japonicum. Can J Microbiol 11, 1–8.
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Supporting Information Additional Supporting Information may be found in the online version of this article: Table S1 Soil chemical properties of organic fields in Minnesota. Table S2 Statistical correlations of soil chemical properties compared with genetic diversity and relative abundance of serotypes. Table S3 Correlations of soil pH, NO3-N concentration, and relative abundance of serotype USDA 127 strains in different locations of organic farms in Minnesota.
Journal of Applied Microbiology 118, 1152--1164 © 2015 The Society for Applied Microbiology