Puentes-Tellez PE and Salles JF. (2019) Dynamics of abundant and rare bacteria during degradation of lignocellulose from sugarcane biomass. Microbial Ecology, under review

van der Loos LM, Eriksson BK, Salles JF. (2019) The macroalgal holobiont in a changing sea. Trends in Microbiology, in press

Brinker, P., Weig, A., Rambold, G.,  Feldhaar, H.,  Tragust, S., (2019) Microbial community composition of nest-carton and adjoining soil of the ant Lasius fuliginosus and the role of host secretions in structuring microbial communities. Fungal Ecology, 38: 44-53

Brinker, P., Fontaine, M. C., Beukeboom, L. W. & Salles, J. F., (2019) Host, symbionts, and the microbiome: The missing tripartite interaction. Trends in Microbiology, xx: xx

Dini-Andreote, F., Jia, X., Salles, J. F. (2019) Molecular methods to study microbial succession in soil. In: Microbial Ecology: Current advances from genomics, metagenomics and other “omics”, Caister Academic Press: Norfolk, UK, p. 27-44

Gurung, K. , Wertheim, B. and Salles, J. F. (2019) The microbiome of pest insects: it is not just bacteria. Entomol Exp Appl, 167: 156-170.

Xing J, Wang H, Brookes P, Salles JF, Xu J. (2019) pH and microbial diversity constrain the survival of E.coli in soil. Soil Biology and Biochemistry, 128:139-149


Carrió EM, Dini-Andreote F, Brossi MJL, Salles JF and Olff H. (2018) Organic amendment under increasing agricultural intensification: effects on soil bacterial communities and plant productivity. Frontiers in Microbiology, 9: 2612

Cortes-Tolalpa L, Norder J, van Elsas JD, Salles JF. (2018) Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. Applied and Biotechnology Microbiology, 102: 2913-2927

Dini-Andreote F, van Elsas JD, Olff H, Salles JF. (2018) Transition in land colonization reflects a multi-trait switch in microbiomes. Nature Scientific Reports, 8:9451

Jia X, Dini-Andreoete F and Salles JF. (2018) Community Assembly Processes of the Rare Biosphere. Trends in Microbiology, 9:738-747

Jimenez DJ, Chaib de Mares M and Salles JF. (2018) Temporal expression dynamics of plant biomass-degrading enzymes by a synthetic bacterial consortium growing on sugarcane bagasse. Frontiers in Microbiology, 9:299

Jurburg SD, Natal-da-Luz T, Raimundo J, Morais P, Sousa JP, van Elsas JD, Salles JF. (2018) Bacterial communities in soil become sensitive to drought under intensive grazing. STOTEN, 618: 1638-1646. DOI: 10.1016/j.scitotenv.2017.10.012

Leite DCA, Salles JF, Calderon EN, Castro CB, Bianchini A, Marques A, van Elsas JD, Peixoto RS. (2018) Coral bacterial-core abundance and network complexity as proxies for anthropogenic pollution. Frontiers in Microbiology, 9: 833.

Leite DCA, Salles JF, Calderon EN, van Elsas JD, Peixoto RS. (2018) Specific plasmids patterns and high rates of bacterial co-occurrence within the coral holobiont. Ecology and Evolution, 8: 1818-1832. DOI: 10.1002/ece3.3717

Mallon CA, Le Roux X, Van Doorn GS, Dini-Andreote F, Poly F, Salles JF. (2018) The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche. ISMEj, 12:728-741 10.1038/s41396-017-0003-y

Nunes IM, Jurburg SD, Jacquiod S, Brejnrod A, Salles JF, Priemé A, Sørensen SJ. (2018) Functional response groups of a soil bacterial community exposed to extreme heat. Biology and Fertility of Soils, 54: 189-202. DOI:10.1007/s00374-017-1255-4

Puentes-Tellez PE and Salles JF. (2018) Construction of an effective minimal active microbial consortia for lignocellulose degradation. Microbial Ecology, 76: 419-429. DOI: 10.1007/s00248-017-1141-5

Veelen HPJ, Salles JF and Tieleman BI. (2018) Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. ISMEj, 12: 1375-1388

Wang M, Veldsink JH, Dini-Andreote F, Salles JF. (2018) Distributional patterns of the abundance and structure of the N-cycling microbial communities associated with plant roots along a salt marsh primary succession. Antoine van Leeuwenhoek, 111: Pages: 2061-2078


Cortes-Tolalpa L, Salles JF and van Elsas JD. (2017) Bacterial synergism in lignocellulose biomass degradation – complementary roles of degraders as influenced by complexity of the carbon source. Frontiers in Microbiology, 8:14 DOI 10.3389/fmicb.2017.01628

El-Aidy S, Ramsteijn AS, Dini-Andreote F, van Eijk R, Houwing DJ, Salles JF, Olivier JDA. (2017) Serotonin Transporter Genotype Modulates the Gut Microbiota composition in Young Rats, an effect augmented by early life stress. Frontiers in Cellular Neuroscience, 11:222. DOI: 10.3389/fncel.2017.00222

Garcia, E.D., R. Lopez, B., de-Bashan, L.E., Hirsch, A.M., Maymon, M. & Bashan, Y. (2017) Functional metabolic diversity of the bacterial community in undisturbed resource island soils in the southern Sonoran Desert. Land Degradation and Development. doi: 10.1002/ldr.2905

Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer SW, Salles JF, van Elsas JD. (2017) Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia. Trends in microbiology 25:788-796. DOI: 10.1016/j.tim.2017.05.012

Jurburg SD, Nunes IM, Stegen JC, Le Roux X, Premie A, Sorensen SJ, Salles JF. (2017) Autogenic succession in soil microbes. Nature Scientific reports, 7:45691. DOI: 10.1038/srep45691

Jurburg SD, Nunes I, Brejnrod A, Jacquoid S, Priemé A, Sørensen SJ, van Elsas JD, Salles JF. (2017) Legacy effects on recovery of soil microbial communities from perturbation. Frontiers in Microbiology, 8:1832. DOI: 10.3389/fmicb.2017.01832

López-Lozano NE, Pereira E Silva MC, Poly F, Guillaumaud N, van Elsas JD, Salles JF. (2017) Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils. Antonie van Leeuwenhoek, 110: 1453-1465. DOI:10.1007/s10482-017-0898-3

Salles JF, Pereira e Silva MC, Dini-Andreote F, Dias ACF, Guillaumaud N, Poly F, van Elsas JD. (2017) Successional patterns of key genes and processes involved in the microbial nitrogen cycle in a salt marsh chronosequence. Biogeochemistry, 132(1-2), 185-201. DOI: 10.1007/s10533-017-0296-y

da Silva TF, Vollú RE, Marques JM, Salles JF, Seldin L. (2017) The bacterial community associated with rose-scented geranium (Pelargonium graveolens) leaves responds to anthracnose symptoms. Plant and Soil, in press doi:10.1007/s11104-016-3102-z

Tilstra A, Dini-Andreote F, Eriksson BK, Salles JF, Pen I, Osinga R, Wild C. (2017) Light modulates thermal stress responses of the hard coral Stylophora pistillata. PeerJ, 5, e3802. DOI: 10.7717/peerj.3802

Veelen HPJ, Salles JF and Tieleman BI. (2017) Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks. Microbiome, 5: 17. DOI 10.1186/s40168-017-0371-6

Vink, S.N., Jordan, N.R., Aldrich-Wolfe, L. , Huerd, S.C., Shaeffer, C.C. & Kinkel, L.L. (2017) Soil conditioning affects interactions between native and invasive exotic perennials of semi-natural grasslands. Journal of Applied Ecology, 54, 1526–1533

Wang M, Li E, Liu C, Jousset A, Salles JF. (2017) Functionality of root-associated bacteria along a salt marsh primary succession. Frontiers in Microbiology, 8:17. DOI 10.3389/fmicb.2017.02102

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Küsel k, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z and Hol G W H (2017) Where less may be more: how the rare biosphere pulls ecosystems strings. ISME journal, in press doi:10.1038/ismej.2016.174


Adam E, Groenenboom AE, Kurm V, Rajewska M, Schmidt R, Tyc O, Weidner S, Berg G, de Boer W, Salles JF. 2016. Controlling the microbiome: microhabitat adjustments for successful biocontrol strategies in soil and human gut. Frontiers in microbiology, 7-1079

Cortes-Tolalpa L, Jiménez D J, Brossi MJL, Salles JF & van Elsas JD. 2016. Different inocula produce distinctive microbial consortia with similar lignocellulose degradation capacity.
Applied Microbiology and Biotechnology, 100:7713-7725

Dini-Andreote F, Brossi MJL, van Elsas JD, Salles JF. 2016. Reconstructing the genetic potential of the microbially-mediated nitrogen cycle in a salt marsh ecosystem. Frontiers in microbiology, 7-902.

Dini-Andreote F, Pylro VS, Baldrian P, van Elsas JD, Salles JF. 2016. Ecological succession reveals signatures of marine–terrestrial transition in salt marsh fungal communities. ISME journal, 10:1984–1997

Wang M, Yang P and Salles JF. 2016. Exploring the root-associated bacterial community turnover along a primary succession in salt marsh. Frontiers in Plant Science, 6:1188. doi: 10.3389/fpls.2015.01188


Dini-Andreote F, Stegen J, van Elsas JD, Salles JF. 2015. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. PNAS, 112: E1326-E1332. Faculty of 1000 recommendation

van Elsas JD, Semenov, AV, Pereira e Silva MC, Salles JF. 2015. Lessons of the impact of genetically engineered micro-organisms on natural ecosystems like soil. Proceedings of the OECD Conference on Biosafety and environmental uses of micro-organisms, p. 47-58.

Grizard S, Versteegh MA, Ndithia HK, Salles JF, Tieleman BI. 2015. Shifts in bacterial communities of eggshells and antimicrobial activities in eggs during incubation in a ground-nesting passerine. PloS One, 10: e0121716.

Jurburg SD and Salles JF. 2015. Functional redundancy and ecosystem function: the soil microbiota as a case study. In: Lo Y-H, Blanco JA and Royhttp S (eds), Biodiversity in Ecosystems – Linking Structure and Function. In Tech, Croatia. pp:29-49. (total of 216 downloads).

Mallon CA, van Elsas JD, Salles JF. 2015. An Ecological Framework for Microbial Invasions: Examining the Phases of Invasion and the Mechanisms Driving Invasion Resistance. Trends in Microbiology, 23:719-729.


Dini-Andreote F, Pereira e Silva MC, Triado-Margarit X, Casamayor E, van Elsas JD, Salles JF. 2014. Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning. ISME journal, 8: 1989-2001.

Grizard S, Dini-Andreote F, Tieleman BI, Salles JF. 2014. Dynamics of bacterial and fungal communities associated with eggshells during incubation. Ecology and Evolution, 4: 1140-1157

Salles JF and Mallon CA. 2014. Invasive plant species set up their own niche. New Phytologist, 204:435–437.

Semenov AV, Pereira e Silva MC, Salles JF, Schmitt H, van Elsas JD. 2014. Quantitative assessment of soil functioning across a representative range of Dutch soils. Ecological indicators, 39: 88-93