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As integrated multi-trophic aquaculture (IMTA) gains momentum, the use of halophyte plants to phytoremediate aquaculture effluents has received growing attention, particularly in aquaponics. It is, therefore, important to obtain a more in-depth knowledge of the microbial communities present in the root systems of these plants, both in their natural environment (sediment) and in aquaponics, in order to understand their nutrient removal potential. The present study used denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing to assess the bacterial community present in the endosphere and rhizosphere of three halophyte plants: <jats:italic>Halimione portulacoides<\/jats:italic>, <jats:italic>Salicornia ramosissima<\/jats:italic> and <jats:italic>Sarcocornia perennis<\/jats:italic>. Species-specific effects were recorded in the profile and diversity of the bacterial communities present in halophyte roots, with significant differences also recorded for the same halophyte species grown in contrasting environments (sediment <jats:italic>vs<\/jats:italic>. aquaponics). In aquaponics the most abundant groups belonged to the orders <jats:italic>Rhodocyclales<\/jats:italic>, <jats:italic>Campylobacterales<\/jats:italic>, <jats:italic>Rhodobacterales<\/jats:italic> and <jats:italic>Desulfobacterales<\/jats:italic>, while in the natural environment (sediment) the most abundant groups belonged to the orders <jats:italic>Rhizobiales<\/jats:italic>, <jats:italic>Sphingomonadales<\/jats:italic> and <jats:italic>Alteromonadales<\/jats:italic>. An overall enrichment in bacterial taxa involved in nutrient cycling was recorded in the roots of halophytes grown in aquaponics (such as <jats:italic>Denitromonas<\/jats:italic>, <jats:italic>Mesorhizobium<\/jats:italic>, <jats:italic>Colwellia<\/jats:italic>, <jats:italic>Dokdonella<\/jats:italic> and <jats:italic>Arcobacter<\/jats:italic>), thereby highlighting their potential to reduce the nutrient loads from aquaculture effluents.<\/jats:p>","DOI":"10.1038\/s41598-020-66093-8","type":"journal-article","created":{"date-parts":[[2020,6,22]],"date-time":"2020-06-22T10:03:36Z","timestamp":1592820216000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Aquaponics using a fish farm effluent shifts bacterial communities profile in halophytes rhizosphere and endosphere"],"prefix":"10.1038","volume":"10","author":[{"given":"Vanessa","family":"Oliveira","sequence":"first","affiliation":[]},{"given":"Patr\u00edcia","family":"Martins","sequence":"additional","affiliation":[]},{"given":"Bruna","family":"Marques","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6143-3390","authenticated-orcid":false,"given":"Daniel F. 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