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This study evaluated four media-based biofloc aquaponic designs over two years (encompassing two full fish production cycles and four tomato growing seasons) to investigate system failures, including plant wilting, necrosis, and the underlying physical and microbial stressors. In the first year, plant wilt was primarily linked to poor drainage and sludge accumulation in coupled systems, resulting in root-zone hypoxia and a 21% reduction in yield compared to decoupled systems. In response, system modifications were implemented in the second year, including the implementation of radial flow settlers upstream of filters and timer-controlled pumps, which improved oxygenation and solids management. These interventions reversed previous trends: coupled systems had\u2009&gt;\u200945% higher yields than decoupled systems. However, wilting still occurred in a subset of plants during the second year. Root-zone analysis showed that wilted plants exhibited 65% lower dissolved oxygen levels than non-wilted, and a tendency for higher relative abundance of potential pathogens and parasitic organisms (\n                    <jats:italic>Pythium graminicola<\/jats:italic>\n                    and\n                    <jats:italic>Xiphinema rives<\/jats:italic>\n                    ). In contrast, healthy root zones were associated with greater abundance of plant growth-promoting bacteria (PGPB), particularly taxa with known biocontrol potential. These findings highlight the importance of maintaining oxygen-rich root environments and effective solids management to support long-term aquaponic productivity.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0349411","type":"journal-article","created":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T17:23:10Z","timestamp":1779124990000},"page":"e0349411","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Physical and microbial root-zone factors underlying tomato wilt in long-term biofloc aquaponic 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