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Nomosatryo S, Lipus D, Bartholomäus A, Henny C, Ridwansyah I, Sujarta P, Yang S, Wagner D, Kallmeyer J. The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani. FEMS Microbiol Ecol 2025; 101:fiae162. [PMID: 39689918 PMCID: PMC11707878 DOI: 10.1093/femsec/fiae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 11/16/2024] [Accepted: 12/16/2024] [Indexed: 12/19/2024] Open
Abstract
Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here, we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different sites across the lake, its tributary rivers and their river mouths to assess diversity and community structure using 16S rRNA gene sequencing. Our results reveal distinct communities in lake and river sediments, supporting the observed geochemical differences. Taxonomic assessment showed the potential impact of anthropogenic pressure along the northern, urbanized shore, as river and river mouth samples revealed high abundances of Bacteroidota, Firmicutes, and Cyanobacteria, which could be attributed to pollution and eutrophication. In contrast, lake sediment communities were dominated by Thermodesulfovibrionia, Methanomethylicia, Bathyarchaeia, and Thermoplasmata, suggesting sulfate reducing, thermophilic, acidophilic bacteria and methanogenic archaea to play an important role in tropical lake systems. This study provides novel insights into ecological functions of tropical lakes and contributes to the optimization of management strategies of Lake Sentani, ensuring its holistic preservation in the future.
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Affiliation(s)
- Sulung Nomosatryo
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
- Research Center for Limnology and Water Resources, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Jakarta-Bogor KM 46, Cibinong, Bogor 16911, Indonesia
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
- Department of Biological and Chemical Sciences, College of Life Sciences, Thomas Jefferson University, Philadelphia, PA 19144, United States
| | - Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
| | - Cynthia Henny
- Research Center for Limnology and Water Resources, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Jakarta-Bogor KM 46, Cibinong, Bogor 16911, Indonesia
| | - Iwan Ridwansyah
- Research Center for Limnology and Water Resources, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Jakarta-Bogor KM 46, Cibinong, Bogor 16911, Indonesia
| | - Puguh Sujarta
- Cendrawasih University, Department of Biology, Faculty of Mathematics and Natural Sciences, Jl. Kamp. Wolker, Waena, Jayapura 99358, Indonesia
| | - Sizhong Yang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
- University of Potsdam, Institute of Geosciences, 14476, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
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Soriano B, Hafez AI, Naya-Català F, Moroni F, Moldovan RA, Toxqui-Rodríguez S, Piazzon MC, Arnau V, Llorens C, Pérez-Sánchez J. SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian Approach. Genes (Basel) 2023; 14:1650. [PMID: 37628701 PMCID: PMC10454057 DOI: 10.3390/genes14081650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Gut microbiomes of fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to (i) infer information of how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and (ii) predict how the diversity and functional profile of that microbiome would change under other variable conditions. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of Bayesian network scenarios created by SAMBA using data from a microbial synthetic community, and the pan-microbiome of gilthead sea bream (Sparus aurata) in different feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems as it can be used for modelling microbiome-host network relationships of any vertebrate organism, including humans, in any system and/or ecosystem.
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Affiliation(s)
- Beatriz Soriano
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia and CSIC (UVEG-CSIC), 46980 Paterna, Spain;
| | - Ahmed Ibrahem Hafez
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
| | - Fernando Naya-Català
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - Federico Moroni
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - Roxana Andreea Moldovan
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain
| | - Socorro Toxqui-Rodríguez
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - María Carla Piazzon
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
| | - Vicente Arnau
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia and CSIC (UVEG-CSIC), 46980 Paterna, Spain;
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
| | - Carlos Llorens
- Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain; (A.I.H.); (R.A.M.); (C.L.)
| | - Jaume Pérez-Sánchez
- Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain; (F.N.-C.); (F.M.); (S.T.-R.); (M.C.P.)
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Bruen M, Hallouin T, Christie M, Matson R, Siwicka E, Kelly F, Bullock C, Feeley HB, Hannigan E, Kelly-Quinn M. A Bayesian Modelling Framework for Integration of Ecosystem Services into Freshwater Resources Management. ENVIRONMENTAL MANAGEMENT 2022; 69:781-800. [PMID: 35171345 PMCID: PMC9012763 DOI: 10.1007/s00267-022-01595-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/10/2022] [Indexed: 05/09/2023]
Abstract
Models of ecological response to multiple stressors and of the consequences for ecosystem services (ES) delivery are scarce. This paper describes a methodology for constructing a BBN combining catchment and water quality model output, data, and expert knowledge that can support the integration of ES into water resources management. It proposes "small group" workshop methods for elucidating expert knowledge and analyses the areas of agreement and disagreement between experts. The model was developed for four selected ES and for assessing the consequences of management options relating to no-change, riparian management, and decreasing or increasing livestock numbers. Compared with no-change, riparian management and a decrease in livestock numbers improved the ES investigated to varying degrees. Sensitivity analysis of the expert information in the BBN showed the greatest disagreements between experts were mainly for low probability situations and thus had little impact on the results. Conversely, in our applications, the best agreement between experts tended to occur for the higher probability, more likely, situations. This has implications for the practical use of this type of model to support catchment management decisions. The complexity of the relationship between management measures, the water quality and ecological responses and resulting changes in ES must not be a barrier to making decisions in the present time. The interactions of multiple stressors further complicate the situation. However, management decisions typically relate to the overall character of solutions and not their detailed design, which can follow once the nature of the solution has been chosen, for example livestock management or riparian measures or both.
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Affiliation(s)
- Michael Bruen
- University College Dublin, CWRR, Belfield, Dublin 4, Ireland.
| | | | | | - Ronan Matson
- Inland Fisheries Ireland, 3044 Lake Drive, Citywest Business Campus, Dublin, Ireland
| | - Ewa Siwicka
- University of Auckland, Auckland, New Zealand
| | - Fiona Kelly
- Inland Fisheries Ireland, 3044 Lake Drive, Citywest Business Campus, Dublin, Ireland
| | - Craig Bullock
- University College Dublin, APEP, Richview, Dublin 4, Ireland
| | - Hugh B Feeley
- University College Dublin, SBES, Belfield, Dublin 4, Ireland
| | - Edel Hannigan
- University College Dublin, SBES, Belfield, Dublin 4, Ireland
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