{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T13:53:45Z","timestamp":1790949225683,"version":"4.1.0"},"reference-count":46,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:00:00Z","timestamp":1790899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:00:00Z","timestamp":1790899200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","award":["HATCH 1021870: TEX09714, 2024-68012-41750"],"award-info":[{"award-number":["HATCH 1021870: TEX09714, 2024-68012-41750"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2022-67013-36836, 2023-67013-40174"],"award-info":[{"award-number":["2022-67013-36836, 2023-67013-40174"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Fungal hyphae form spatially confined interfaces in soil that mediate close associations with bacteria, collectively referred to as the hyphosphere. Despite its recognized ecological importance, experimental access to hyphosphere-associated microbial communities under realistic soil and plant-associated conditions has remained limited. Here, we present a soil-mimetic microcosm that enables controlled recovery of hyphosphere bacterial communities embedded within plant-associated soil. The system integrates field-derived soil, a native soil microbial inoculum, living cotton seedlings, and a spatially constrained fungal inoculum housed within sterile cell-strainer assemblies, permitting hyphal extension into soil while preserving a recoverable fungal-soil boundary. Using the soil-borne plant pathogen\n                      <jats:italic toggle=\"yes\">Fusarium oxysporum<\/jats:italic>\n                      f. sp.\n                      <jats:italic toggle=\"yes\">vasinfectum<\/jats:italic>\n                      as a model filamentous fungus, we show that the microcosm enables reproducible recovery of hypha-associated soil microaggregates containing physically attached bacterial cells. Full-length 16S rRNA profiling revealed pronounced reductions in bacterial richness and evenness in hyphosphere samples relative to bulk and rhizosphere soils (Shannon diversity, Kruskal-Wallis\n                      <jats:italic toggle=\"yes\">H<\/jats:italic>\n                      = 15.25,\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      = 0.0016, with genus richness declining by 87% in bulk soil and 24% in rhizosphere soil contexts), consistent with recruitment of a restricted subset of the surrounding microbiota. Ordination analyses demonstrated clear compositional separation between soil and hyphosphere compartments (PERMANOVA\n                      <jats:italic toggle=\"yes\">F<\/jats:italic>\n                      = 7.14,\n                      <jats:italic toggle=\"yes\">R<\/jats:italic>\n                      <jats:sup>2<\/jats:sup>\n                      = 0.572,\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      = 0.001), with hyphosphere communities of bulk and rhizosphere origin converging to similar composition despite differing starting soils (\n                      <jats:italic toggle=\"yes\">R<\/jats:italic>\n                      <jats:sup>2<\/jats:sup>\n                      = 0.128,\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      = 0.307). Phylogenetic turnover analyses (\u03b2NTI) indicated phylogenetic structuring (exceeding the +2 threshold), whereas taxonomic analyses identified a conserved set of bacterial genera consistently associated with hyphae, alongside compartment-specific taxa influenced by soil and plant context. Together, these findings establish the novel hyphal release-and-capture microcosm as a reproducible, ecologically grounded platform for studying hyphosphere-associated bacterial communities in plant-associated soils.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Soil fungi recruit distinct bacterial communities along their hyphae, forming a specialized microhabitat known as the hyphosphere. Despite its ecological importance, studying hyphosphere-associated bacteria under realistic plant-soil conditions has remained experimentally difficult. Here, we present a soil-mimetic hyphal release-capture microcosm that enables controlled reconstruction and recovery of bacterial communities assembled along fungal hyphae in intact plant-associated soils. Using the cotton wilt pathogen\n                        <jats:italic toggle=\"yes\">Fusarium oxysporum<\/jats:italic>\n                        f. sp.\n                        <jats:italic toggle=\"yes\">vasinfectum<\/jats:italic>\n                        , we show that fungal hyphae reproducibly recruit reduced and compositionally distinct bacterial assemblages from surrounding soils through strong deterministic selection. Because this pathogen is a regulated quarantine organism for which field inoculation is restricted, this system provides a tractable experimental platform for studying hyphosphere assembly under controlled yet ecologically relevant conditions. This approach provides new opportunities to investigate fungal-bacterial interactions, microbial community assembly, and plant-associated soil microbiomes at spatially resolved hyphal interfaces.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.01096-26","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T13:00:47Z","timestamp":1790946047000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["A hyphal release-capture soil microcosm for recovering hyphosphere bacterial communities"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4734-513X","authenticated-orcid":true,"given":"Gayan","family":"Abeysinghe","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01f5ytq51","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant Pathology and Microbiology, Texas A&M University","place":["College Station, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elek","family":"Nagy","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01f5ytq51","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant Pathology and Microbiology, Texas A&M University","place":["College Station, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanya","family":"Wagner","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01f5ytq51","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant Pathology and Microbiology, Texas A&M University","place":["College Station, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shravan","family":"Parunandi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01f5ytq51","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant Pathology and Microbiology, Texas A&M University","place":["College Station, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Santos","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01f5ytq51","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant Pathology and Microbiology, Texas A&M University","place":["College Station, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muthukumar","family":"Bagavathiannan","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01f5ytq51","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Soil and Crop Sciences, Texas A&M University","place":["College Station, 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