Capturing the spatial structure of the benthic microbiome under an intensive aquaculture scenario in Chilean Patagonia

BMC Microbiology, vol. 25, pp. 752

Abstract

BACKGROUND: Identifying the microbial taxa that structure assemblages in response to local disturbances along the Chilean Patagonian coast is critical for understanding community reorganization and ecological risk in this vulnerable marine environment. Here, we examined benthic microbial interactions across sixteen sites spanning 42-44°S in the Inner Sea of Chiloé and adjacent fjord systems. Using co-occurrence network analysis, we characterized spatial interaction patterns and identified keystone taxa whose relationships with environmental variables may serve as ecological indicators. The presence of keystone taxa supports the concept of microbial "seed banks," which sustain community stability and ecosystem functionality under stress. Networks revealed structured communities dominated by niche-specialist taxa, consistent with ecological processes of niche differentiation and environmental filtering. RESULTS: The benthic environment was found to harbor niche-specialist taxa, including Flavobacteriaceae, Gemmataceae, Humimicrobiaceae, Clostridiaceae, and Sulfurovaceae, typically associated with organic enrichment and anthropogenic influence. These microbial families showed strong correlations with environmental gradients such as nitrate, phosphate, silicate, pH, salinity, and phaeopigments. Alpha-diversity analyses revealed greater microbial richness in FZ compared to the ISC, likely reflecting higher environmental heterogeneity and long-term adaptation to dynamic and fluctuating conditions. Beta-diversity analyses further supported the presence of distinct microbial assemblages between the two zones. Multivariate statistics and co-occurrence network analyses demonstrated that FZ communities display enhanced taxonomic interactions and greater network complexity, suggesting increased ecological stability. In contrast, microbial networks in the ISC exhibited reduced connectivity, potentially indicative of environmental stressors disrupting microbial spatial organization and network resilience. Moreover, the identification of indigenous bacterial isolates provided evidence for the presence of opportunistic host-associated pathogens, highlighting the utility of microbial biomarkers in detecting early ecological responses to human impacts. CONCLUSION: Microbial co-occurrence patterns in northern Patagonian sediments reveal shifts in community assembly and increased network complexity that may enhance resilience to perturbations. The detection of strains harboring opportunistic pathogen biomarkers highlights risks under intense anthropogenic pressures. Monitoring keystone taxa thus offers early warning of functional decline. Broader spatio-temporal assessments remain essential to clarify microbial dynamics and their implications for ecosystem health and antimicrobial resistance.

Authors 12

1. Ana María Zárate

   Universidad Autónoma de Chile

   Affiliation as printed

   Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autonoma de Chile, Temuco, Chile. ana.zarate@uautonoma.cl

   Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autonoma de Chile, Temuco, Chile

2. Leticia Barrientos

   Universidad Autónoma de Chile

   Affiliation as printed

   Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autonoma de Chile, Temuco, Chile

3. July Z. Florez

   Universidad de Playa Ancha de Ciencias de la Educación · Universidad de Los Lagos

   Affiliation as printed

   Centro i-mar, CeBiB & MASH, Universidad de Los Lagos, Puerto Montt, 5480000, Chile. july.florezguerrero@ulagos.cl

   Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaiso, 2340000, Chile. july.florezguerrero@ulagos.cl

   Centro i-mar, CeBiB & MASH, Universidad de Los Lagos, Puerto Montt, 5480000, Chile

4. Alejandro H. Buschmann

   Universidad de Los Lagos

   Affiliation as printed

   Centro i-mar, CeBiB & MASH, Universidad de Los Lagos, Puerto Montt, 5480000, Chile

5. Iván E Pérez-Santos

   University of Concepción · Universidad de Los Lagos

   Affiliation as printed

   COPAS COASTAL, Universidad de Concepción, Concepción, 4030000, Chile

   Centro i-mar, Universidad de Los Lagos, Puerto Montt, 5480000, Chile

6. Pablo Bruna

   Universidad de La Frontera

   Affiliation as printed

   Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar , Temuco, 01145, Chile

7. Benjamín Leyton-Carcaman

   Universidad de La Frontera

   Affiliation as printed

   Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar , Temuco, 01145, Chile

8. Pedro A. Inostroza Aachen Institute for Environmental Research

   University of Gothenburg · RWTH Aachen University

   Affiliation as printed

   Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 40530, Sweden

   Institute for Environmental Research, RWTH Aachen University, Aachen, 52074, Germany

9. Daniel Lundin

   Linnaeus University

   Affiliation as printed

   Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, 39182, Sweden

10. Carles Borrego

    Universitat de Girona · Catalan Institute for Water Research

    Affiliation as printed

    Catalan Institute for Water Research , (ICRA-CERCA), Girona, 17003, Spain

    Grup de Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona, Girona, E-17001, Spain

11. José Luís Balcázar

    Catalan Institute for Water Research

    Affiliation as printed

    Catalan Institute for Water Research , (ICRA-CERCA), Girona, 17003, Spain

12. Maria Vila‐Costa

    Institute of Environmental Assessment and Water Research

    Affiliation as printed

    Institute of Environmental Assessment and Water Research , (IDAEA-CSIC), Barcelona, 08034, Spain