Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale

Barberán, A., Bates, S.T., Casamayor, E.O., and Fierer, N. 2012. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J., 6, 343–351.

PubMed  Google Scholar 

Bastian, M., Heymann, S., and Jacomy, M. 2009. Gephi: an open source software for exploring and manipulating networks. Proc. Int. AAAI Conf. Web Soc. Media, 3, 361–362. Retrieved from https://ojs.aaai.org/index.php/ICWSM/article/view/13937.

Google Scholar 

Becerra-Rivera, V.A. and Dunn, M.F. 2019. Polyamine biosynthesis and biological roles in rhizobia. FEMS Microbiol. Rev., 366, fnz084.

CAS  Google Scholar 

Berry, D. and Widder, S. 2014. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front. Microbiol., 5, 219.

PubMed  PubMed Central  Google Scholar 

Bokulich, N.A., Kaehler, B.D., Rideout, J.R., Dillon, M., Bolyen, E., Knight, R., Huttley, G.A., and Caporaso, J.G. 2018. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome, 6, 90.

PubMed  PubMed Central  Google Scholar 

Bolyen, E., Rideout, J.M., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al Ghalith, A.G., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., et al. 2018. QIIME 2: reproducible, interactive, scalable, and extensible microbiome data science. Nat. Biotechnol., 37, 852–857.

Google Scholar 

Boukhatem, Z.F., Merabet, C., and Tsaki, H. 2022. Plant growht promoting actinobacteria, the most promising candidates as bioinoculants?. Front. Agron., 4, 849911.

Google Scholar 

Cao Y. 2022. Package ‘microbiomeMarker’: microbiome biomarker analysis toolkit. R package version 1.2.2. https://github.com/yiluheihei/microbiomeMarker.

Google Scholar 

Chi, S.C., Mothersole, D.J., Dilbeck, P., Niedzwiedzki, D.M., Zhang, H., Qian, P., Vasilev, C., Grayson, K.J., Jackson, P.J., Martin, E.C., et al. 2015. Assembly of functional photosystem complexes in Rhodobacter sphaeroides incorporating carotenoids from the spirilloxanthin pathway. Biochim. Biophys. Acta, 1847, 189–201.

CAS  PubMed  Google Scholar 

Chowdhury, C., Sinha, S., Chun, S., Yeates, T.O., and Bobik, T.A. 2014. Diverse bacterial microcompartment organelles. Microbiol. Mol. Biol. Rev., 78, 438–468.

PubMed  PubMed Central  Google Scholar 

Clarke, K.R. and Ainsworth, M. 1993. A method of linking multivariate community structure to environmental variables. Mar. Ecol. Prog. Ser., 92, 205–219.

Google Scholar 

Collins, M.D. and Jones, D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev., 45, 316–354.

CAS  PubMed  PubMed Central  Google Scholar 

Csárdi, G. and Nepusz, T. 2006. The igraph software package for complex network research. InterJ. Complex Syst., 1695, 1–9.

Google Scholar 

Cram, J.A., Xia L.C., Needham D.M., Sachdeva R., Sun F., and Fuhrman J.A. 2015. Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes. ISME J., 9, 2573–2586.

PubMed  PubMed Central  Google Scholar 

de Menezes, A.B., Prendergast-Miller, M.T., Richardson, A.E., Toscas, P., Farrell, M., Macdonald, L.M., Baker, G., Wark, T., and Thrall, P.H. 2015. Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters. Environ. Microbiol., 17, 2677–2689.

CAS  PubMed  Google Scholar 

Ding, B., Niu, J., Shang, F., Yang, L., Chang, T., and Wang, J. 2019. Characterization of the geranylgeranyl diphosphate synthase gene in Acyrthosiphon pisum (Hemiptera: Aphididae) and its association with carotenoid biosynthesis. Front. Physiol., 10, 1398.

PubMed  PubMed Central  Google Scholar 

Douglas, G.M., Maffei, V.J., Zaneveld, J., Yurgel, S.N., Brown, J.R., Taylor, C.M., Huttenhower, C., Langille, M.G.I. 2020. PICRUSt2: an improved and extensible approach for metagenome inference. Nat. Biotechnol., 38, 685–688.

CAS  PubMed  PubMed Central  Google Scholar 

El-Tarabily, K., AlKhajeh, A.S., Ayyash, M.M., Alnuaimi, L.H., Sham, A., ElBaghdady, K.Z., Tariq, S., and AbuQamar, S.F. 2019. Growth promotion of Salicornia bigelovii by Micromonospora chalcea UAE1, and endophytic 1-aminocyclopropane-1-carboxylic acid deaminase-producing actinobacterial isolate. Front. Microbiol., 10, 1694.

PubMed  PubMed Central  Google Scholar 

Expósito, R.G., Postma, J., Raaijmakers, J.M., and Bruijn, I.D. 2015. Diversity and activity of Lysobacter species from disease suppressive soils. Front. Microbiol., 6, 1243.

Google Scholar 

Faust, K. and Raes, J. 2012. Microbial interactions: from networks to models. Nat. Rev. Microbiol., 10, 538–550.

CAS  PubMed  Google Scholar 

Fierer, N. and Jackson, R.B. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA, 103, 626–631.

CAS  PubMed  PubMed Central  Google Scholar 

Hartmann, A., Rothballer, M., and Schmid, M. 2008. Lorenz Hiltner; a pioneer in rhizosphere microbial ecology & soil bacteriology research. Plant Soil, 312, 7–14.

CAS  Google Scholar 

Herridge, D.F., Peoples, M.B., and Boddey, R.M. 2008. Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil, 311, 1–18.

CAS  Google Scholar 

Hobley, L., Kim, S.H., Maezato, Y., Wyllie, S., Fairlamb, A.H., Stanley-Wall, N.R., and Michael, A.J. 2014. Norspermidine is not a selfproduced trigger for biofilm disassembly. Cell, 156, 844–854.

CAS  PubMed  PubMed Central  Google Scholar 

Jiménez, J.A., Novinscak, A., and Filion, M. 2020. Inoculation with plant-growth-promoting rhizobacterium Pseudomonas fluorescens LBUM677 impacts the rhizosphere microbiome of three oilseed crops. Front. Microbiol., 11, 569366.

PubMed  PubMed Central  Google Scholar 

Jin, D., Kong, X., Li, H., Luo, L., Zhuang, X., Zhuang, G., Deng, Y., and Bai, Z. 2016. Patulibacter brassicae sp. nov., isolated from rhizosphere soil of chinese cabbage (Brassica campestris). Int. J. Syst. Evol. Microbiol., 66, 5056–5060.

Google Scholar 

Jin, J., Wang, G.H., Liu, X.B., Liu, J.D., Chen, X.L., and Herbert, S.J. 2009. Temporal and spatial dynamics of bacterial community in the rhizosphere of soybean genotypes grown in a black soil. Pedosphere, 19, 808–816.

CAS  Google Scholar 

Katoh, K., Misawa, K., Kuma, K., and Miyata, T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res., 30, 3059–3066.

CAS  PubMed  PubMed Central  Google Scholar 

Killiny, N. and Nehela, Y. 2020. Citrus polyamines: structure, biosynthesis, and physiological functions. Plants, 9, 426.

CAS  PubMed Central  Google Scholar 

Kim, H.S., Kim, Y.H., Yoo, O.J., and Lee, J.J. 1996. Aclacinomycin X, a novel anthracycline antibiotic produced by Streptomyces galilaeus ATCC 31133. Biosci. Biotech. Biochem., 60, 906–908.

CAS  Google Scholar 

Kraut-Cohen, J., Shapiro, O.H., Dror, B., and Cytryn, E. 2021. Pectin induced colony expansion of soil-derived Flavobacterium strains. Front. Microbiol., 12, 651891.

PubMed  PubMed Central  Google Scholar 

Kuffner, M., Puschenreiter, M., Wieshammer, G., Gorfer, M., and Sessitsch, A. 2008. Rhizosphere bacteria affect growth and metal uptake of heavy metal accumulating willows. Plant Soil, 304, 35–44.

CAS  Google Scholar 

Langfelder, P. and Horvath, S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.

PubMed  PubMed Central  Google Scholar 

Langille, M.G.I., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., Reyes, J.A., Clemente, J.C., Burkepile, D.E., Thurber, R.L.V., Knight, R., et al. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol., 31, 814–821.

CAS  PubMed  PubMed Central  Google Scholar 

Lankau, R.A., George, I., and Miao, M. 2022. Crop performance is predicted by soil microbial diversity across phylogenetic scales. Ecosphere, 13, e4029.

Google Scholar 

Liang, J., Sun, S., Ji, J., Wu, H., Meng, F., Zhang, M., Zheng, X., Wu, C., and Zhang, Z. 2014. Comparison of the rhizosphere bacterial communities of zigongdongdou soybean and a high-methionine transgenic line of this cultivar. PLoS ONE, 9, e103343.

PubMed  PubMed Central  Google Scholar 

Liu, C., Sun, Z., Shen, S., Lin, L., Li, T., Tian, B., and Hua, Y. 2013. Identification and characterization of the geranylgeranyl diphosphate synthase in Deinococcus radiodurans. Lett. Appl. Microbiol., 58, 219–224.

PubMed  Google Scholar 

Lozupone, C.A., Hamady, M., Kelley, S.T., and Knight, R. 2007. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol., 73, 1576–1585.

CAS  PubMed  PubMed Central  Google Scholar 

Lozupone, C., Lladser, M., Knights, D., Stombaugh, J., and Knight, R. 2011. UniFrac: an effective distance metric for microbial community comparison. ISME J., 5, 169–172.

PubMed  Google Scholar 

Luster, J., Göttlein, A., Nowack, B., and Sarret, G. 2009. Sampling, defining, characterising and modeling the rhizosphere-the soil science tool box. Plant Soil, 321, 457–482.

CAS  Google Scholar 

Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res., 27, 209–220.

CAS  PubMed  Google Scholar 

Mcdonald, D., Price, M.N., Goodrich, J., Nawrocki, E.P., DeSantis, T.Z., Probst, A., Andersen, G.L., Knight, R., and Hugenholtz, P. 2012. An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME, J. 6, 610–618.

Google Scholar 

Mehrani, M., Sobotka, D., Kowal, P., Ciesielski, S., and Makinia, J. 2020. The occurrence and role of Nitrospiria in nitrogen removal systems. Bioresour. Technol., 303, 122936.

CAS  PubMed  Google Scholar 

Mendes, L.W., Kuramae, E.E., Navarrete, A.A., van Veen, J.A., and Tsai, S.M. 2014. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J., 8, 1577–1587.

CAS  PubMed  PubMed Central  Google Scholar 

Meng, J., Xu, Y., Li, S., Li, C., Zhang, X., Dong, D., and Chen, P. 2010. Soybean growth and soil microbial populations under conventional and conservational tillage systems. J. Crop Improv., 24, 337–348.

Google Scholar 

Mizrahi-Man, O., Davenport, E.R., and Gilad, Y. 2013. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS ONE, 8, e53608.

CAS  PubMed  PubMed Central  Google Scholar 

Naik, D., Smith, E., and Cumming, J.R. 2009. Rhizosphere carbon deposition, oxidative stress and nutritional changes in two poplar species exposed to aluminum. Tree Physiol., 29, 423–436.

CAS  PubMed 

留言 (0)

沒有登入
gif