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Miyamoto H, Kawachi N, Kurotani A, Moriya S, Suda W, Suzuki K, Matsuura M, Tsuji N, Nakaguma T, Ishii C, Tsuboi A, Shindo C, Kato T, Udagawa M, Satoh T, Wada S, Masuya H, Miyamoto H, Ohno H, Kikuchi J. Computational estimation of sediment symbiotic bacterial structures of seagrasses overgrowing downstream of onshore aquaculture. ENVIRONMENTAL RESEARCH 2023; 219:115130. [PMID: 36563976 DOI: 10.1016/j.envres.2022.115130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 05/02/2023]
Abstract
Coastal seagrass meadows are essential in blue carbon and aquatic ecosystem services. However, this ecosystem has suffered severe eutrophication and destruction due to the expansion of aquaculture. Therefore, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found near the shore downstream of the onshore aquaculture facility. To evaluate the characteristics of the sediment for growing seagrass, physicochemical properties and bacterial ecological evaluations of the sediment were conducted. Evaluation of chemical properties in seagrass sediments confirmed a significant increase in total carbon and a decrease in zinc content. Association analysis and linear discriminant analysis refined bacterial candidates specified in seagrass overgrown- and nonovergrown-sediment. Energy landscape analysis indicated that the symbiotic bacterial groups of seagrass sediment were strongly affected by the distance close to the seagrass-growing aquaculture facility despite their bacterial population appearing to fluctuate seasonally. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal sediment symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the sediment symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan.
| | | | - Atsushi Kurotani
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Wataru Suda
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Kenta Suzuki
- RIKEN, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan
| | - Chie Shindo
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Motoaki Udagawa
- Keiyo Gas Energy Solution Co. Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0329, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Hiroshi Masuya
- RIKEN, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan; Miroku Co.Ltd.: Kitsuki, Oita, 873-0021, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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Insights into Bacterial Communities and Diversity of Mangrove Forest Soils along the Upper Gulf of Thailand in Response to Environmental Factors. BIOLOGY 2022; 11:biology11121787. [PMID: 36552296 PMCID: PMC9775068 DOI: 10.3390/biology11121787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
The comprehensive data for the dynamic adaptation of bacterial community structure in response to environmental factors is important for the maintenance of the mangrove ecosystem. This aspect was investigated with soils and surface water from six mangrove forests in six provinces along the Upper Gulf of Thailand shoreline. Mangrove soils were variable with respect to pH (acidic to slightly alkaline) and had low amounts of organic matter (OM). Illumina next-generation sequencing attested that the number of observed species as well as the bacterial diversity and richness among all sites were not significantly different. The gamma-, alpha-Proteobacteria, Desulfobacteria, Bacteroidia, Anaerolineae, Bathyarchaeia, Acidobacteriae, Nitrososphaeria, Clostridia, and Thermoplasmata were more abundant bacterial classes present in all sites. Soil OM was the major factor that mostly modulated the bacterial community structure, while salinity influenced the number of observed species and bacterial richness. These results provide informative data on the bacterial community, in response to both environmental factors and heavy metal pollutants, that is prominent for sustainable development and management of mangrove forests.
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Kegler HF, Hassenrück C, Kegler P, Jennerjahn TC, Lukman M, Jompa J, Gärdes A. Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities. PeerJ 2018; 6:e4555. [PMID: 29761035 PMCID: PMC5944435 DOI: 10.7717/peerj.4555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/09/2018] [Indexed: 12/30/2022] Open
Abstract
Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment can alter bacterial communities that may be important for coral reef ecosystem function.
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Affiliation(s)
- Hauke F. Kegler
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
- Faculty of Biology and Chemistry (FB2), University of Bremen, Bremen, Germany
| | - Christiane Hassenrück
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Pia Kegler
- Department of Ecology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Tim C. Jennerjahn
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Muhammad Lukman
- Department of Marine Science, Universitas Hasanuddin, Makassar, Indonesia
| | - Jamaluddin Jompa
- Department of Marine Science, Universitas Hasanuddin, Makassar, Indonesia
| | - Astrid Gärdes
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
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Wang H, Wang B, Dong W, Hu X. Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures. Sci Rep 2016; 6:34588. [PMID: 27698451 PMCID: PMC5048299 DOI: 10.1038/srep34588] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/15/2016] [Indexed: 01/05/2023] Open
Abstract
Crude oil is a complex mixture of hydrocarbons with different structures; its components vary in bioavailability and toxicity. It is important to understand how bacterial communities response to different hydrocarbons and their co-acclimation in the process of degradation. In this study, microcosms with the addition of structurally different hydrocarbons were setup to investigate the successions of bacterial communities and the interactions between different bacterial taxa. Hydrocarbons were effectively degraded in all microcosms after 40 days. High-throughput sequencing offered a great quantity of data for analyzing successions of bacterial communities. The results indicated that the bacterial communities responded dramatically different to various hydrocarbons. KEGG database and PICRUSt were applied to predict functions of individual bacterial taxa and networks were constructed to analyze co-acclimations between functional bacterial groups. Almost all functional genes catalyzing degradation of different hydrocarbons were predicted in bacterial communities. Most of bacterial taxa were believed to conduct biodegradation processes via interactions with each other. This study addressed a few investigated area of bacterial community responses to structurally different organic pollutants and their co-acclimation and interactions in the process of biodegradation. The study could provide useful information to guide the bioremediation of crude oil pollution.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Bin Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Wenwen Dong
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
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Li C, Lesnik KL, Fan Y, Liu H. Millimeter scale electron conduction through exoelectrogenic mixed species biofilms. FEMS Microbiol Lett 2016; 363:fnw153. [PMID: 27279626 DOI: 10.1093/femsle/fnw153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2016] [Indexed: 02/03/2023] Open
Abstract
The functioning of many natural and engineered environments is dependent on long distance electron transfer mediated through electrical currents. These currents have been observed in exoelectrogenic biofilms and it has been proposed that microbial biofilms can mediate electron transfer via electrical currents on the centimeter scale. However, direct evidence to confirm this hypothesis has not been demonstrated and the longest known electrical transfer distance for single species exoelectrogenic biofilms is limited to 100 μm. In the present study, biofilms were developed on electrodes with electrically non-conductive gaps from 50 μm to 1 mm and the in situ conductance of biofilms was evaluated over time. Results demonstrated that the exoelectrogenic mixed species biofilms in the present study possess the ability to transfer electrons through electrical currents over a distance of up to 1 mm, 10 times further than previously observed. Results indicate the possibility of interspecies interactions playing an important role in the spatial development of exoelectrogenic biofilms, suggesting that these biological networks might remain conductive even at longer distance. These findings have significant implications in regards to future optimization of microbial electrochemical systems.
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Affiliation(s)
- Cheng Li
- Department of Biological and Ecological Engineering, Oregon State University, 116 Gilmore Hall, Corvallis, OR 97333, USA
| | - Keaton Larson Lesnik
- Department of Biological and Ecological Engineering, Oregon State University, 116 Gilmore Hall, Corvallis, OR 97333, USA
| | - Yanzhen Fan
- Department of Biological and Ecological Engineering, Oregon State University, 116 Gilmore Hall, Corvallis, OR 97333, USA
| | - Hong Liu
- Department of Biological and Ecological Engineering, Oregon State University, 116 Gilmore Hall, Corvallis, OR 97333, USA
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Nielsen LP, Risgaard-Petersen N. Rethinking sediment biogeochemistry after the discovery of electric currents. ANNUAL REVIEW OF MARINE SCIENCE 2014; 7:425-442. [PMID: 25251266 DOI: 10.1146/annurev-marine-010814-015708] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The discovery of electric currents in marine sediments arose from a simple observation that conventional biogeochemistry could not explain: Sulfide oxidation in one place is closely coupled to oxygen reduction in another place, centimeters away. After experiments demonstrated that this resulted from electric coupling, the conductors were found to be long, multicellular, filamentous bacteria, now known as cable bacteria. The spatial separation of oxidation and reduction processes by these bacteria represents a shortcut in the conventional cascade of redox processes and may drive most of the oxygen consumption. In addition, it implies a separation of strong proton generators and consumers and the formation of measurable electric fields, which have several effects on mineral development and ion migration. This article reviews the work on electric currents and cable bacteria published through April 2014, with an emphasis on general trends, thought-provoking consequences, and new questions to address.
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Affiliation(s)
- Lars Peter Nielsen
- Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark; ,
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Malvankar NS, King GM, Lovley DR. Centimeter-long electron transport in marine sediments via conductive minerals. ISME JOURNAL 2014; 9:527-31. [PMID: 25050525 DOI: 10.1038/ismej.2014.131] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 11/09/2022]
Abstract
Centimeter-long electron conduction through marine sediments, in which electrons derived from sulfide in anoxic sediments are transported to oxygen in surficial sediments, may have an important influence on sediment geochemistry. Filamentous bacteria have been proposed to mediate the electron transport, but the filament conductivity could not be verified and other mechanisms are possible. Surprisingly, previous investigations have never actually measured the sediment conductivity or its basic physical properties. Here we report direct measurements that demonstrate centimeter-long electron flow through marine sediments, with conductivities sufficient to account for previously estimated electron fluxes. Conductivity was lost for oxidized sediments, which contrasts with the previously described increase in the conductivity of microbial biofilms upon oxidation. Adding pyrite to the sediments significantly enhanced the conductivity. These results suggest that the role of conductive minerals, which are more commonly found in sediments than centimeter-long microbial filaments, need to be considered when modeling marine sediment biogeochemistry.
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Affiliation(s)
- Nikhil S Malvankar
- 1] Department of Physics, University of Massachusetts, Amherst, Amherst, MA, USA [2] Department of Microbiology, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Gary M King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Amherst, MA, USA
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