Title
Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla.
Authors and e-mail address
Yong-Po Zhao 1,2,Sheng Lin 1,2,Leixia Chu1,3, JiangTao Gao1,2,SaadiaAzeem1,3,Wenxiong Lin 1,2*,
*Corresponding author
Affiliations
1. College of Life Sciences, Fujian Agricultural and ForestryUniversity, Fuzhou35002, China;
2. Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and ForestryUniversity, Fuzhou35002, China
3. Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and ForestryUniversity, Fuzhou35002, China
Full address for correspondence
*Corresponding author: Wenxiong Lin,Agroecological Institute, Fujian Agriculture and ForestryUniversity, Fuzhou35002, Fujian, People's Republic of China.
Phone +86-591-83737535 Fax +86-591-83769440
E-mail address
Supplementary Figure S1. Comparison of the bacterial communities at the class (a), order (b) and family(c)level.CK, NP and RP refer to the control soil without planting any crop, newly planted soil and replanted soil, respectively. Sequences that could not be classified into any known group are labeled ‘‘other’’.Data are representative of 3 independent experiments±s.d.. The figure is representativeof 3 independent experiments. Statistical analysis wasprovided by student’s t-test, wherea,b,cP＜0.05.
Supplementary Table S1.The bacteria which had a significant negative correlation with theincrease of continuous cropping years
Representative population（negative correlation） / Main Ecological Function / Rate ofdecrease (%)Dehalobacterium / carbon cycle1, dehalogenation2,3 / 100.00%
Bilophila / unknown / 100.00%
Desulfovibrio / sulfur cycle4 , nitrogen cycle5-7 / 100.00%
Oscillospira / carbon cycle8, degrade dimethyl sulfide9 / 99.48%
Ruminococcus / carbon cycle10-13 / 98.62%
Cupriavidus / carbon cycle14, nitrogen cycle15, degrade soil contaminant16 / 90.65%
Nevskia / degrade soil contaminant17 / 42.40%
Lactobacillus / beneficial bacteria18, degradingorganic matter19 / 27.05%
Pediococcus / carbon cycle20, beneficial bacteria21 / 22.03%
A4 / unknown / 21.85%
Rhodanobacter / degrade soil contaminant22,23
nitrogen cycle22,24,25 / 16.67%
Paenibacillus / nitrogen cycle26
beneficial bacteria26-29 / 9.09%
Fimbriimonas / carbon cycle30 / 8.70%
Kaistobacter / unknown / 3.38%
Lysobacter / beneficial bacteria31-33
degrade soil contaminant34 / 2.72%
Rate of decrease (%)= (the relative abundances in control soil without planting any crop - the relative abundances in replanted soil)/the relative abundances in control soil without planting any crop×100%
Supplementary Table S2.The bacteria which had a significant positive correlation with the increase of continuous cropping years
Representative population（positive correlation） / Main Ecological Function / Rate of increase (%)Mycobacterium / degrade polycyclic aromatic hydrocarbon35 / 1.47%
Pseudomonas / plant growth promoting
rhizobacteria36-38or pathogen39 / 7.27%
Rhodoplanes / nitrogen cycle (denitrification)40, Phototrophic bacteria41,42 / 15.75%
Phenylobacterium / degrade soil contaminant43,44 / 15.95%
Opitutus / unknown / 17.31%
Luteimonas / nitrogen cycle (denitrification)45,46 / 18.75%
Ralstonia / pathogen47 / 21.18%
Chthonomonas / carbon cycle30 / 31.96%
Candidatus-Solibacter / acidophilic bacteria48,49 / 38.84%
Burkholderia / beneficial bacteria50,51,pathogen52 / 42.28%
Methylophaga / unknown / 50.57%
Halomonas / nitrogen cycle(denitrification)53,54, degrade aromatic compounds54 / 96.40%
Nitrospira / nitrogen cycle55,56 / 119.20%
DA101 / unknown / 121.20%
Janthinobacterium / pathogen57,58 / 121.90%
Candidatus-Koribacter / acidophilic bacteria48,59 / 124.10%
Thalassospira / pathogen60, nitrogen cycle (denitrification)61 / 124.20%
Chromobacterium / pathogen62,63 / 136.80%
Acinetobacter / acidophilic bacteria64,plant growth promoting rhizobacteria 65 / 154.30%
Rate of increase (%)= (the relative abundances in replanted soil- the relative abundances in control soil without planting any crop)/the relative abundances in control soil without planting any crop×100%
Supplementary Table S3.The identification and functional analysis of fungi in rhizosphere soil of different-years of planting P. heterophylla
numerical order / Representative population / Main Ecological Function1 / Achaeta camerani / Unknown
2 / Achaeta unibulba / Unknown
3 / Gibberella intermedia / pathogenic fungi66
4 / Uncultured Fusarium sp / pathogenic fungi orsaprophyticfungi67
5 / Trichoderma reesei strain, / saprophyticfungi68, carbon cycle69
6 / Cryptococcus humicolus / carbon cycle70,71
7 / Fusarium oxysporum / pathogenic fungi72
8 / Athelia rolfsii / pathogenic fungi73
9 / Uncultured fungus / Unknown
10 / Hemienchytraeus sp. / Unknown
11 / Uncultured fungus / Unknown
12 / Rhyacodrilus coccineus / Unknown
13 / Enchytraeidae sp. / Unknown
14 / Cladosporium sp. / pathogenic fungi74
15 / Uncultured fungus / Unknown
16 / Uncultured fungus / Unknown
References
1Mägli, A., Wendt, M. & Leisinger, T. Isolation and characterization of Dehalobacterium formicoaceticum gen. nov. sp. nov., a strictly anaerobic bacterium utilizing dichloromethane as source of carbon and energy. Arch. Microbiol.166, 101-108 (1996).
2Krausova, V. I., Robb, F. T. & González, J. M. Biodegradation of dichloromethane in an estuarine environment. Hydrobiologia559, 77-83 (2006).
3Koenig, J., Lee, M. & Manefield, M. Aliphatic organochlorine degradation in subsurface environments. Rev. Environ. Sci. Bio.14, 49-71 (2015).
4Heidelberg, J. F. et al. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol.22, 554-559 (2004).
5McCready, R., Gould, W. & Cook, F. Respiratory nitrate reduction by Desulfovibrio sp. Arch. Microbiol.135, 182-185 (1983).
6Boopathy, R. & Kulpa, C. Nitroaromatic compounds serve as nitrogen source for Desulfovibrio sp.(B strain). Can. J. Microbiol.39, 430-433 (1993).
7McCready, R., Gould, W. & Barendregt, R. Nitrogen isotope fractionation during the reduction of NO3-to NH4+ by Desulfovibrio sp. Can. J. Microbiol.29, 231-234 (1983).
8Mackie, R. I. et al. Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches. Appl. Environ. Microb.69, 6808-6815 (2003).
9Ye, T. R., Cai, H. Y., Liu, X. & Jiang, H.L. Dominance of Oscillospira and Bacteroides in the bacterial community associated with the degradation of high-concentration dimethyl sulfide under iron-reducing condition. Ann. Microbiol., 1-8 (2016).
10Pettipher, G. L. & Latham, M. J. Characteristics of enzymes produced by Ruminococcus flavefaciens which degrade plant cell walls. J. Gen. Microbiol.110, 21-27 (1979).
11Koike, S. & Kobayashi, Y. Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol. Lett.204, 361-366 (2001).
12Pettipher, G. L. & Latham, M. J. Characteristics of enzymes produced by Ruminococcus flavefaciens which degrade plant cell walls. Microbiology110, 21-27 (1979).
13Weimer, P. J. Why don’t ruminal bacteria digest cellulose faster? J. Dairy Sci.79, 1496-1502 (1996).
14Pérez-Pantoja, D. et al. Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134. Appl. Environ. Microb.81, 3914-3924 (2015).
15Amadou, C. et al. Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res.18, 1472-1483 (2008).
16Zhu, B. et al. Survival and chlorpyrifos-degradation of strain Cupriavidus taiwanensis Lux-X1 in different type soils. J. Food Agric. Environ.11, 873-876 (2013).
17Chooklin, C. S., Phertmean, S., Cheirsilp, B., Maneerat, S. & Saimmai, A. Utilization of palm oil mill effluent as a novel and promising substrate for biosurfactant production by Nevskia ramosa NA3. Songklanakarin J. Sci. Technol.35, 167-176 (2013).
18Chen, Y.S. & Yanagida, F. Characteristics and effects of temperature and surfactants on bacteriocin-like inhibitory substance production of soil-isolated Lactobacillus animalis C060203. Curr. Microbiol.53, 384-387 (2006).
19Moldes, A. B. et al. Ex situ treatment of hydrocarbon-contaminated soil using biosurfactants from Lactobacillus pentosus. J. Agr. Food Chem.59, 9443-9447 (2011).
20Mundt, J. O., Beattie, W. G. & Wieland, F. R. Pediococci residing on plants. J. Bacteriol.98, 938-942 (1969).
21Peraza-Gómez, V., Luna-González, A., González-Prieto, J. M., Fierro-Coronado, A. & González-Ocampo, H. A. Protective effect of microbial immunostimulants and antiviral plants against WSSV in Litopenaeus vannamei cultured under laboratory conditions. Aquaculture420, 160-164 (2014).
22Green, S. J. et al. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Appl. Environ. Microb.78, 1039-1047 (2012).
23Nalin, R., Simonet, P., Vogel, T. M. & Normand, P. Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int. J. Syst. Evol. Micr.49, 19-23 (1999).
24Kostka, J. E. et al. Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J. Bacteriol.194, 4461-4462 (2012).
25Van Den Heuvel, R., Van Der Biezen, E., Jetten, M., Hefting, M. & Kartal, B. Denitrification at pH 4 by a soil-derived Rhodanobacter-dominated community. Environ. Microbiol.12, 3264-3271 (2010).
26McSpadden Gardener, B. B. Ecology of Bacillus and Paenibacillus spp. in agricultural systems. Phytopathology94, 1252-1258 (2004).
27Budi, S. W. et al. Hydrolytic enzyme activity of Paenibacillus sp. strain B2 and effects of the antagonistic bacterium on cell integrity of two soil-borne pathogenic fungi. Appl. Soil Ecol.15, 191-199 (2000).
28Timmusk, S., Nicander, B., Granhall, U. & Tillberg, E. Cytokinin production by Paenibacillus polymyxa. Soil Biol. Biochem.31, 1847-1852 (1999).
29Hong, T.Y. & Meng, M. Biochemical characterization and antifungal activity of an endo-1, 3-β-glucanase of Paenibacillus sp. isolated from garden soil. Appl. Microbiol. Biot.61, 472-478 (2003).
30Lee, K. C. et al. Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. ISME J.8, 1522-1533 (2014).
31Islam, M. T., Hashidoko, Y., Deora, A., Ito, T. & Tahara, S. Suppression of damping-off disease in host plants by the rhizoplane bacterium Lysobacter sp. strain SB-K88 is linked to plant colonization and antibiosis against soilborne peronosporomycetes. Appl. Environ. Microb.71, 3786-3796 (2005).
32Folman, L. B., Postma, J. & van Veen, J. A. Characterisation of Lysobacter enzymogenes (Christensen and Cook 1978) strain 3.1 T8, a powerful antagonist of fungal diseases of cucumber. Microbiol. Res.158, 107-115 (2003).
33QIAN, G. L., HU, B. S., JIANG, Y. H. & LIU, F. Q. Identification and characterization of Lysobacter enzymogenes as a biological control agent against some fungal pathogens. Agr. Sci. China.8, 68-75 (2009).
34Wang, G.L. et al. Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil. Int. J. Syst. Evol. Micr.61, 674-679 (2011).
35Child, R. et al. Polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates: their association with plant roots. Appl. Microbiol. Biot.75, 655-663 (2007).
36Gal, M., Preston, G. M., Massey, R. C., Spiers, A. J. & Rainey, P. B. Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol. Ecol.12, 3109-3121 (2003).
37Walsh, U. F., Morrissey, J. P. & O'Gara, F. Pseudomonas for biocontrol of phytopathogens: from functional genomics to commercial exploitation. Curr Opin Biotechnol12, 289-295 (2001).
38Howell, C. & Stipanovic, R. Control of Rhizoctonia solani on cotton seedlings with Pseudomonas fluorescens and with an antibiotic produced by the bacterium. Phytopathology69, 480-482 (1979).
39Ellis, C., Karafyllidis, I. & Turner, J. G. Constitutive activation of jasmonate signaling in an Arabidopsis mutant correlates with enhanced resistance to Erysiphe cichoracearum, Pseudomonas syringae, and Myzus persicae. Mol. Plant Microbe. In.15, 1025-1030 (2002).
40Hiraishi, A. & Ueda, Y. Rhodoplanes gen. nov., a New Genus of Phototrophic Bacteria Including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov. Int. J. Syst. Bacteriol.44, 665-673 (1994).
41Hiraishi, A. & Ueda, Y. Rhodoplanes gen. nov., a new genus of phototrophic bacteria including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov. Int. J. Syst. Evol. Micr.44, 665-673 (1994).
42Takaichi, S., Sasikala, C., Ramana, C. V., Okamura, K. & Hiraishi, A. Carotenoids in Rhodoplanes species: variation of compositions and substrate specificity of predicted carotenogenesis enzymes. Curr. Microbiol.65, 150-155 (2012).
43Lingens, F. et al. Phenylobacterium immobile gen. nov., sp. nov., a gram-negative bacterium that degrades the herbicide chloridazon. Int. J. Syst. Bacteriol.35, 26-39 (1985).
44Eberspächer, J. & Lingens, F. in The Prokaryotes5,250-256 (Springer, 2006).
45Finkmann, W., Altendorf, K., Stackebrandt, E. & Lipski, A. Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int. J. Syst. Evol. Micr.50, 273-282 (2000).
46Lipski, A. & Stackebrandt, E. S. Luteimonas. Bergey's Manual of Systematics of Archaea and Bacteria.1–3.
47Salanoubat, M. et al. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature415, 497-502 (2002).
48Montana, J. S., Jiménez, D. J., Hernández, M., Ángel, T. & Baena, S. Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome. Antonie van Leeuwenhoek101, 205-215 (2012).
49Challacombe, J. F. et al. Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076. PloS one6, e24882 (2011).
50Jiang, C. Y., Sheng, X. F., Qian, M. & Wang, Q. Y. Isolation and characterization of a heavy metal-resistant Burkholderia sp. from heavy metal-contaminated paddy field soil and its potential in promoting plant growth and heavy metal accumulation in metal-polluted soil. Chemosphere72, 157-164 (2008).
51Van, V. T., Berge, O., Ke, S. N., Balandreau, J. & Heulin, T. Repeated beneficial effects of rice inoculation with a strain of Burkholderia vietnamiensison early and late yield components in low fertility sulphate acid soils of Vietnam. Plant Soil218, 273-284 (2000).
52LiPuma, J. J., Spilker, T., Coenye, T. & Gonzalez, C. F. An epidemic Burkholderia cepacia complex strain identified in soil. The Lancet359 (2002).
53González-Domenech, C. M., Martínez-Checa, F., Béjar, V. & Quesada, E. Denitrification as an important taxonomic marker within the genus Halomonas. Syst. Appl. Microbiol.33, 85-93 (2010).
54García, M. T., Mellado, E., Ostos, J. C. & Ventosa, A. Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds. Int. J. Syst. Evol. Micr.54, 1723-1728 (2004).
55Lücker, S. et al. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl. Acad. Sci.107, 13479-13484 (2010).
56Daebeler, A. et al. Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil. ISME J.8, 2397-2410 (2014).
57Lincoln, S. P., Fermor, T. R. & Tindall, B. Janthinobacterium agaricidamnosum sp. nov., a soft rot pathogen of Agaricus bisporus. Int. J. Syst. Evol. Micr.49, 1577-1589 (1999).
58Pudełko, K. The Occurrence of Soft Rot (Janthinobacterium Agaricidamnosum) In Mushroom (Agaricus Bisporus) Crops. J. Plant Prot. Res.53, 148-153 (2013).
59Ward, N. L. et al. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl. Environ. Microb.75, 2046-2056 (2009).
60Sun, X., He, Y., Xu, N., Xia, Y. & Liu, Z. Isolation and identification of two strains of pathogenic bacteria and their effects on the volatile metabolites of Gracilariopsis lemaneiformis (Rhodophyta). J. Appl. Phycol.24, 277-284 (2012).
61Decleyre, H., Heylen, K., Van Colen, C. & Willems, A. Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers. Front Microbiol.6 (2015).
62Dessaux, Y., Elmerich, C. & Faure, D. Violacein: a molecule of biological interest originating from the soil-borne bacterium Chromobacterium violaceum. La revue de médecine intern.25, 659-662 (2004).
63Broadbent, P. & Baker, K. F. Behaviour of Phytophthora cinnamomi in soils suppressive and conducive to root rot. Crop Pasture Sci.25, 121-137 (1974).
64Baumann, P. Isolation of Acinetobacter from soil and water. J. Bacteriol.96, 39-42 (1968).
65Silambarasan, S. & Vangnai, A. S. Biodegradation of 4-nitroaniline by plant-growth promoting Acinetobacter sp. AVLB2 and toxicological analysis of its biodegradation metabolites. J. Hazard Mater.302, 426-436 (2016).
66Marin, S., Sanchis, V., Vinas, I., Canela, R. & Magan, N. Effect of water activity and temperature on growth and fumonisin B1 and B2 production by Fusarium proliferatum and F. moniliforme on maize grain. Lett. Appl. Microbiol.21, 298-301 (1995).
67Lightner, D. V. & Fontaine, C. A mycosis of the American lobster, Homarus americanus, caused by Fusarium sp. J Invertebr Pathol25, 239-245 (1975).
68Nevalainen, H., Suominen, P. & Taimisto, K. On the safety of Trichoderma reesei. J. Biotechnol.37, 193-200 (1994).
69Yang, D. et al. Genome sequence and annotation of Trichoderma parareesei, the ancestor of the cellulase producer Trichoderma reesei. Genome announcements3, e00885-00815 (2015)
70Park, D., Lee, D. S., Kim, Y. M. & Park, J. M. Bioaugmentation of cyanide-degrading microorganisms in a full-scale cokes wastewater treatment facility. Bioresource Technol.99, 2092-2096 (2008).
71Middelhoven, W. J., Koorevaar, M. & Schuur, G. W. Degradation of benzene compounds by yeasts in acidic soils. Plant Soil145, 37-43 (1992).
72Zhao, Y. P. et al. Interaction of Pseudostellaria heterophylla with Fusarium oxysporum f. sp. heterophylla mediated by its root exudates in a consecutive monoculture system. Sci. Rep.5, 8197; DOI:10.1038/srep08197 (2015).
73Baminger, U., Subramaniam, S. S., Renganathan, V. & Haltrich, D. Purification and characterization of cellobiose dehydrogenase from the plant pathogen Sclerotium (Athelia) rolfsii. Appl. Environ. Microb.67, 1766-1774 (2001).
74Alvarez, A. & Nishijima, W. Postharvest diseases of papaya. Plant Dis.71, 681-686 (1987).