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Lalitha N, Ronald BSM, Chitra MA, Jangam AK, Katneni VK, Suganya PN, Senthilnayagam H, Senthilkumar TMA, Muralidhar M. Exploration of the candidate beneficial bacteria for Penaeus vannamei culture by core microbiome analysis using amplicon sequencing. Lett Appl Microbiol 2023; 76:ovad087. [PMID: 37541955 DOI: 10.1093/lambio/ovad087] [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: 05/26/2023] [Revised: 06/28/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Globally, Penaeus vannamei is the vital species in aquaculture production. Beneficial bacterial exploration of gut, sediment, and water were investigated in P. vannamei culture using Illumina Miseq sequencing of 16S RNA V3-V4 hypervariable regions. Predominant phyla identified were Proteobacteria, Tenericutes, Bacteroidetes in gut; Proteobacteria, Bacteroidetes, Planctomycetes in sediment and Cyanobacteria, Proteobacteria, and Planctomycetes in water. In total, 46 phyla, 509 families and 902 genera; 70 phyla, 735 families and 1255 genera; 55 phyla, 580 families and 996 genera were observed in gut, sediment and water, respectively. Diversity of microbial communities in respect of observed Operational Taxonomic Units, diversity indices (Shannon and Simpson), richness index (Chao1) were significantly high P (<0.05) in 60 DoC in gut and 30 DoC in sediment. Beta diversity indicated separate clusters for bacterial communities in gut, sediment and water samples and formation of distinct community profiles. Core microbiome in P. vannamei rearing ponds over a time consisted of 9, 21, and 20 OTUs in gut, rearing water and sediment, respectively. This study helps to intervene with suitable beneficial microbes to establish an aquaculture system thereby contributes to enhance the productivity, improve water quality and pond bottom condition, and control the pathogenic agents at each stage of the culture.
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Affiliation(s)
- Natarajan Lalitha
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Murugesan Ananda Chitra
- Centre for Animal Health Studies, Madhavaram Milk Colony, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| | - Ashok Kumar Jangam
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Vinaya Kumar Katneni
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Panjan Nathamuni Suganya
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Hemalatha Senthilnayagam
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Moturi Muralidhar
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
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2
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Vasquez-Cardenas D, Hidalgo-Martinez S, Hulst L, Thorleifsdottir T, Helgason GV, Eiriksson T, Geelhoed JS, Agustsson T, Moodley L, Meysman FJR. Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria. Front Microbiol 2022; 13:1034401. [PMID: 36620049 PMCID: PMC9814725 DOI: 10.3389/fmicb.2022.1034401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.
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Affiliation(s)
- Diana Vasquez-Cardenas
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium,*Correspondence: Diana Vasquez-Cardenas,
| | | | - Lucas Hulst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | | | | | | | | | | | - Leon Moodley
- NORCE Norwegian Research Centre, Randaberg, Norway
| | - Filip J. R. Meysman
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium
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Quero GM, Piredda R, Basili M, Maricchiolo G, Mirto S, Manini E, Seyfarth AM, Candela M, Luna GM. Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02120-7. [PMID: 36205738 DOI: 10.1007/s00248-022-02120-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host's tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.
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Affiliation(s)
- Grazia Marina Quero
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy.
| | - Roberta Piredda
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano (Bari), Italy
| | - Marco Basili
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
- Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Giulia Maricchiolo
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Messina, Italy
| | - Simone Mirto
- Institute of Anthropic Impacts and Sustainability in Marine Environment, National Research Council (IAS-CNR), Palermo, Italy
| | - Elena Manini
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Anne Mette Seyfarth
- Department of Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Marco Candela
- Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Gian Marco Luna
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
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4
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Patil MP, Woo HE, Lee IC, Nakashita S, Kim K, Kim JO, Kim K. A microcosm study of microbial community profiles during sediment remediation using pyrolyzed oyster shells. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115229. [PMID: 35544980 DOI: 10.1016/j.jenvman.2022.115229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The accumulation of organic and inorganic components in sediments leads to a deterioration in the environment and an imbalance in the coastal ecosystem. Currently, capping is the most effective technology for remediating polluted sediment and restoring ecosystems. A microcosm experiment was designed using pyrolyzed oyster shell (POS). These were mixed in with coastal sediment or added as a capping layer. The results showed that POS effectively decreased pollutants, including PO4-P and NH4-N. Metagenomics analysis was performed using 16S rRNA gene sequencing and the most abundant phyla identified in the POS treated and untreated sediments were Proteobacteria, followed by Firmicutes, Bacteroidetes, Chloroflexi, Fusobacteria, Nitrospirae, and Spirochaetes. The relative abundance of Proteobacteria members of the Class Gammaproteobacteria significantly increased, but Deltaproteobacteria gradually decreased throughout the experiment in POS-covered sediment. This suggests that the POS effectively promoted a shift from anaerobic to facultative anaerobic or aerobic microbial communities in the sediment. Dominant species of facultative anaerobic or microaerophilic bacteria from the order Chromatiales and phylum Nitrospirae were observed in the POS-covered sediment. Based on these study results, it can be concluded that POS is an effective covering material for sediment remediation and restores the microbial communities in sediments.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - In-Cheol Lee
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - Shinya Nakashita
- Graduate School of Advanced Science and Engineering, Hiroshima University, Kagamiyama 1-4-1, Higashi-Hiroshima, 739-8527, Hiroshima, Japan
| | - Kyeongmin Kim
- Graduate School of Advanced Science and Engineering, Hiroshima University, Kagamiyama 1-4-1, Higashi-Hiroshima, 739-8527, Hiroshima, Japan; Coastal and Estuarine Sediment Dynamics Group, Port and Airport Research Institute, 3-1-1 Nagase, Yokosuka, 239-0826, Kanagawa, Japan
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea; School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea.
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea.
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5
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Reda RM, Maricchiolo G, Quero GM, Basili M, Aarestrup FM, Pansera L, Mirto S, Abd El-Fattah AH, Alagawany M, Abdel Rahman AN. Rice protein concentrate as a fish meal substitute in Oreochromis niloticus: Effects on immune response, intestinal cytokines, Aeromonas veronii resistance, and gut microbiota composition. FISH & SHELLFISH IMMUNOLOGY 2022; 126:237-250. [PMID: 35654384 DOI: 10.1016/j.fsi.2022.05.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The potential of rice protein concentrate (RPC) to substitute fishmeal (FM) protein in the diet of Oreochromis niloticus was assessed in a five-month-long feeding trial. Fishmeal protein was replaced by RPC at rates of 0% (control), 25%, 50%, and 75% (RPC0, RPC25, RPC50, and RPC75, respectively). RPC25 had no significant effect on antioxidant capacity (total antioxidant capacity; superoxide dismutase, catalase, and glutathione peroxidase activities) and immune indices (lysozyme, nitric oxide, antiprotease, and bactericidal activities) after one, two, and five months of feeding, while the values for these parameters were significantly lower in the RPC75 group compared to those in the RPC0 group. The RPC25 group showed higher mRNA levels of the intestinal cytokines IL-1β, IL-10β, TGF-β, and TNF-α than the control group. In fish affected by Aeromonas veronii, the highest significant cumulative mortality was recorded in the RPC75 group, followed by the RPC50, RPC25, and control groups. Gut microbiome analyses showed a reduction in microbial diversity in response to the addition of RPC, regardless of the RPC content, and the composition of the community of the RPC samples differed from that of the control. RPC-enriched diets resulted in higher relative abundances of Bacteroidetes and Fusobacteria in the gut compared to that in the gut of the control fish. In summary, RPC can be used to replace up to 25% of the FM protein in the diet of O. niloticus, while improving the antioxidant capacity, immunocompetence, and disease resistance of the fish.
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Affiliation(s)
- Rasha M Reda
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt.
| | - Giulia Maricchiolo
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (IRBIM-CNR), Messina, Italy
| | - Grazia Marina Quero
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Ancona, Italy
| | - Marco Basili
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Ancona, Italy
| | - Frank M Aarestrup
- Department of Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Lidia Pansera
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (IRBIM-CNR), Messina, Italy
| | - Simone Mirto
- Institute of Anthropic Impact and Sustainability in Marine Environment, National Research Council (CNR-IAS), Palermo, Italy
| | - Amir H Abd El-Fattah
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt
| | - Mahmoud Alagawany
- Department of Poultry, Faculty of Agriculture, Zagazig University, P.O. Box 44511, Zagazig, Egypt
| | - Afaf N Abdel Rahman
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt
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6
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Patil MP, Woo HE, Kim JO, Kim K. Field study on short-term changes in benthic environment and benthic microbial communities using pyrolyzed oyster shells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153891. [PMID: 35182647 DOI: 10.1016/j.scitotenv.2022.153891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
To evaluate the effect of pyrolyzed crushed oyster shells (PCOS) on the remediation of sediments and microbial diversity, a field study was conducted in Buksin Bay, Tongyeong City, Republic of Korea. It was observed that after treatment with PCOS, the concentration of H2S in the sediment of the control site was 287 mg/L. Furthermore, it decreased up to 0 mg/L and remained so until the end of the field study, that is for a period of six months. Moreover, the concentrations of NO2-N + NO3-N, NH4-N, and PO4-P decreased sharply, and the oxidation-reduction potential (ORP) increased after PCOS treatment in pore water and overlying water. Regarding the diversity of microbial communities, the predominance of bacteria from phylum Chlorobi was observed in highly reduced (-410 mV; ORP) sediment, which is well known for the production of H2S. After PCOS treatment, the relative abundance of Chlorobi was sharply suppressed. On the other hand, the predominance of bacteria from the phyla Proteobacteria and Bacteroidetes was observed, and their relative abundance in the PCOS-treated sediment increased throughout the experiment, based on 16S rRNA sequencing. The results demonstrate that the abundance of bacterial communities in the PCOS-treated sediments of Buksin Bay is important for marine ecological functioning, especially for pollutant transformation.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea; School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea.
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea.
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7
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Kaur G, Krol M, Brar SK. Geothermal heating: Is it a boon or a bane for bioremediation? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117609. [PMID: 34182401 DOI: 10.1016/j.envpol.2021.117609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/14/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
There has been a worldwide interest in renewable energy technologies, as a means of decreasing reliance on fossil fuels, minimizing climate change effects, and reducing greenhouse emissions. One such technology is geothermal heating where the constant subsurface temperature is used to cool or heat building interiors via heat pumps. In Canada, the use of geothermal heating has become a popular option for heating and cooling buildings, and it is anticipated that, in the near term, most large buildings will include geothermal heating as part of their climate control strategy. However, little is known about the environmental impacts of geothermal heating on the subsurface environment. The present review will examine the effect of geothermal heating on groundwater flow and remediation efforts, whereby the heat generated by geothermal systems may help with urban pollution. "Geothermal Remediation" could leverage the subsurface heating resulting from geothermal systems to accelerate biodegradation of certain petroleum-based pollutants at brown-field sites, while providing building(s) with sustainable heating and cooling. This idea coincides with the rising momentum towards sustainable and green remediation in Europe and the United States. To ensure that Geothermal Remediation is achievable, the effect of heat on bioremediation needs to be examined. This review provides an insight into what we know about heat effects on bioremediation activities and subsurface transport.
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Affiliation(s)
- Gurpreet Kaur
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Magdalena Krol
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario, M3J 1P3, Canada.
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8
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Basili M, Campanelli A, Frapiccini E, Luna GM, Quero GM. Occurrence and distribution of microbial pollutants in coastal areas of the Adriatic Sea influenced by river discharge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117672. [PMID: 34380232 DOI: 10.1016/j.envpol.2021.117672] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The transport of a variety of pollutants from agricultural, industrial and urbanised areas makes rivers major contributors to the contamination of coastal marine environments. Too little is known of their role in carrying pathogens to the coast. We used DNA-based metabarcoding data to describe the microbial community composition in seawater and sediment collected in front of the estuary of the Tronto, the Chienti and the Esino, three Italian rivers with different pollution levels that empty into the north-central Adriatic Sea, and to detect and measure within these communities the relative abundance of microbial pollutants, including traditional faecal indicators and alternative faecal and sewage-associated pollutants. We then applied the FORENSIC algorithm to distinguish human from non-human sources of microbial pollution and FAPROTAX to map prokaryotic clades to established metabolic or other ecologically relevant functions. Finally, we searched the dataset for other common pathogenic taxa. Seawater and sediment contained numerous potentially pathogenic bacteria, mainly faecal and sewage-associated. The samples collected in front of the Tronto estuary showed the highest level of contamination, likely sewage-associated. The pathogenic signature showed a weak but positive correlation with some nutrients and strong correlations with some polycyclic aromatic hydrocarbons. This study confirms that rivers transport pathogenic bacteria to the coastal sea and highlights the value of expanding the use of HTS data, source tracking and functional identification tools to detect microbial pollutants and identify their sources with a view to gaining a better understanding of the pathways of sewage-associated discharges to the sea.
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Affiliation(s)
- Marco Basili
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Alessandra Campanelli
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Emanuela Frapiccini
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Gian Marco Luna
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Grazia Marina Quero
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy.
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9
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Hamoutene D, Hua K, Lacoursière-Roussel A, Page F, Baillie SM, Brager L, Salvo F, Coyle T, Chernoff K, Black M, Wong D, Nelson E, Bungay T, Gaspard D, Ryall E, Mckindsey CW, Sutherland TF. Assessing trace-elements as indicators of marine finfish aquaculture across three distinct Canadian coastal regions. MARINE POLLUTION BULLETIN 2021; 169:112557. [PMID: 34089964 DOI: 10.1016/j.marpolbul.2021.112557] [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: 03/03/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Several trace-elements have been identified as indicators of finfish aquaculture organic enrichment. In this study, sediment sampling at finfish farms was completed as part of an Aquaculture Monitoring Program in three distinct Canadian regions. Despite diverse datasets, multivariate analyses show a consistent clustering of known direct (Cu and Zn) and indirect (Cd, Mo and U) tracers of aquaculture activities with sediment organic matter (OM) and/or total dissolved sulfides concentrations. OM content was also a predictor of Cu, Zn, Mo and U concentrations according to decision tree analyses. Distance from cages did not emerge as a strong driver of differences among sampling points; however, a tendency towards negative associations is clear especially for Zn. Enriched stations as determined after geochemical normalization were mostly localized within 150 m of net-pens. Selected trace-elements (in particular Zn) can be useful indicators of aquaculture organic enrichment in different ecosystems and valuable tools for monitoring programs.
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Affiliation(s)
- D Hamoutene
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada.
| | - K Hua
- Aquaculture, Biotechnology and Aquatic Animal Health Science Branch, Fisheries and Oceans Canada, Ottawa, ON K1A 0E6, Canada
| | - A Lacoursière-Roussel
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - F Page
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - S M Baillie
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - L Brager
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - F Salvo
- Northwest Atlantic Fisheries Center, Fisheries and Oceans Canada, St. John's, NL A1C 5X1, Canada
| | - T Coyle
- Pacific Enterprise Science Center, Fisheries and Oceans Canada, Vancouver, BC V7V 1N6, Canada
| | - K Chernoff
- Pacific Enterprise Science Center, Fisheries and Oceans Canada, Vancouver, BC V7V 1N6, Canada
| | - M Black
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - D Wong
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - E Nelson
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - T Bungay
- Northwest Atlantic Fisheries Center, Fisheries and Oceans Canada, St. John's, NL A1C 5X1, Canada
| | - D Gaspard
- Pacific Enterprise Science Center, Fisheries and Oceans Canada, Vancouver, BC V7V 1N6, Canada
| | - E Ryall
- Aquaculture, Biotechnology and Aquatic Animal Health Science Branch, Fisheries and Oceans Canada, Ottawa, ON K1A 0E6, Canada
| | - C W Mckindsey
- Institut Maurice Lamontagne, Fisheries and Oceans Canada, 850 Route de la mer, Mont-Joli, QUE G5H 3Z4, Canada
| | - T F Sutherland
- Pacific Enterprise Science Center, Fisheries and Oceans Canada, Vancouver, BC V7V 1N6, Canada
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10
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Frühe L, Dully V, Forster D, Keeley NB, Laroche O, Pochon X, Robinson S, Wilding TA, Stoeck T. Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms. Front Microbiol 2021; 12:637811. [PMID: 33995296 PMCID: PMC8116884 DOI: 10.3389/fmicb.2021.637811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Nigel B Keeley
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Research, Bergen, Norway
| | - Olivier Laroche
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Shawn Robinson
- St. Andrews Biological Station, Department of Fisheries and Oceans, St. Andrews, NB, Canada
| | | | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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11
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Nguyen TT, Paulsen JE, Landfald B. Seafloor deposition of water-based drill cuttings generates distinctive and lengthy sediment bacterial community changes. MARINE POLLUTION BULLETIN 2021; 164:111987. [PMID: 33515825 DOI: 10.1016/j.marpolbul.2021.111987] [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: 08/17/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
The spatial extent and persistence of bacterial change caused by deposition of water-based drill cuttings on the seafloor were explored by a community-wide approach. Ten centimeter sediment cores were sampled along transects extending from ≤15 m to 250 m from three nearby drilling sites in the southern Barents Sea. Eight months, 8 years and 15 years, respectively, had passed since the completion of the drillings. At locations heavily affected by drill cuttings, the two most recent sites showed distinct, corresponding deviances from native Barents Sea bacterial community profiles. Otherwise marginal groups, including Mollicutes and Clostridia, showed significant increases in relative abundance. Beyond 100 m from the boreholes the microbiotas appeared undisturbed, as they did at any distance from the 15-years old borehole. The extent of the biological distortion, as indicated by the present microbial study, agreed with previously published macrofaunal surveys at the same drilling sites.
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Affiliation(s)
- Tan T Nguyen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, PO Box 6050 Langnes, 9037 Tromsø, Norway.
| | | | - Bjarne Landfald
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, PO Box 6050 Langnes, 9037 Tromsø, Norway.
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12
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Song C, Zhang J, Chen X, Hu G, Fan L, Yang G, Li T, Qiu L, Chen J, Fang L. Effects of fenvalerate concentrations and its chiral isomers on bacterial community structure in the sediment environment of aquaculture ponds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:14498-14507. [PMID: 33215281 DOI: 10.1007/s11356-020-11651-w] [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: 05/18/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
To investigate the effect of chiral pesticide fenvalerate (FV) on the micro-ecological environment of aquaculture pond sediment, we used an indoor static experiment to observe the effects of FV added at different concentrations with different chiral isomers on the changes in the sediment bacterial community. The 16S rDNA high-throughput sequencing technique was used to conduct sequencing and analysis of the bacterial community structure as well as changes in aquaculture pond sediments after 4 weeks of cultivation. The results showed that the microbial alpha diversity indices (Sobs and Shannon indices) of the treated groups were significantly lower than those of the control group after 4 weeks (P < 0.05), and the values in the high-concentration group were significantly lower than those of the low-concentration group (P < 0.05). In terms of bacterial group composition, the proportion of abundance of Proteobacteria and Acidobacteria in the treated groups were greater than in the control group after 4 weeks, while the proportion of abundance of Bacteroidetes and Verrucomicrobia were lower. In the high-concentration FV treatment group, the proportion of abundance of Bacteroidetes, Acidobacteria, Chloroflexi, Nitrospinae, unclassified_k_norank, Ignavibacteriae, and Nitrospirae were significantly different from those of the other groups (P < 0.05). Principal coordinate analysis (PCoA) and ANONISIM/Adonis analysis showed that the cis-enantiomer had a stronger effect on the bacterial community as the concentration of FV increased. In addition, the linear discriminant analysis effect size (LEfSe) and linear discriminant analysis (LDA) results revealed differences in the level of enrichment of bacterial groups caused by FV at different concentrations and isomer levels. Collectively, this study showed that FV residue has a pronounced effect on bacterial communities in sediment, which becomes more significant with increasing exposure concentration. The effects of the cis- and trans-enantiomers of FV on the sediment environment are different; the cis-enantiomer has a stronger effect on the bacterial community.
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Affiliation(s)
- Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
| | - Jingwei Zhang
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
| | - Xi Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
| | - Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
| | - Guang Yang
- Fisheries Engineering Institute, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Tian Li
- Fisheries Engineering Institute, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People's Republic of China.
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China.
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China.
| | - Longxiang Fang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture and Rural Affairs, Wuxi, People's Republic of China
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
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13
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Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages. Microorganisms 2021; 9:microorganisms9020455. [PMID: 33671759 PMCID: PMC7927081 DOI: 10.3390/microorganisms9020455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.
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14
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Biomonitoring of the Application of Monoculture and Integrated Multi-Trophic Aquaculture (IMTA) Using Macrobenthic Structures at Tembelas Island, Kepulauan Riau Province, Indonesia. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8110942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sustainable aquaculture needs to be considered when it comes to the utilization of water resources. The aim of this study was to apply biomonitoring using macrobenthic structures on both spatial and temporal applications of monoculture and integrated multi-trophic aquaculture (IMTA) at Tembelas Island, Kepulauan Riau Province, Indonesia. Samples of sediment were taken from three fish farm locations, namely from an IMTA site, a monoculture site, and a reference site. Macrobenthic organisms obtained through rinsing, sieving, and sorting were then identified under a stereo-microscope. Diversity of the macrobenthic assemblages was analyzed with a Shannon-Wiener index (H’). Equitability was expressed through Pielou’s evenness index. Finally, Bray-Curtis’ non-metric multi-dimensional scaling (NMDS) was used for similarities derived from log (X+1) transformed macrobenthic abundance to provide a visual representation of differences in their structure between sites over time. Results showed polychaetes exhibited differences in both variation and abundance of genera between the farm and reference site. The assemblage of macrobenthos at the IMTA site consisted of 9 genera of gastropods, 3 genera of bivalves, 5 genera of polychaetes, and 2 genera of crustaceans. At the monoculture site, 12 genera of gastropods, 4 genera of bivalves, 8 genera of polychaetes, 1 genera of crustaceans, and 1 genera of ophiuroid were observed. A relatively high abundance was observed at the reference site, with 27 genera of gastropods, 11 genera of bivalves, 3 genera of polychaetes, and 1 genera of crustacean. The favorable water conditions and possible absence of waste input from aquaculture resulting in a more suitable habitat for macrobenthic life may explain this relative abundance. Some of them were recognised as opportunistic taxa, i.e., Capitella sp., Heteromastus sp., and Lumbrinereis sp. Based on the diversity and evenness indices and the MNDS ordination, it can be concluded that the application of IMTA systems results in a suppressed or reduced potential impact on environmental disturbance due to aquacultural activities.
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15
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Shen X, Xu M, Li M, Zhao Y, Shao X. Response of sediment bacterial communities to the drainage of wastewater from aquaculture ponds in different seasons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137180. [PMID: 32065893 DOI: 10.1016/j.scitotenv.2020.137180] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Bacterial communities play an important role in diffuse sediment pollution in aquaculture farms. Previous studies have revealed the short-term influence of wastewater drainage on the bacterial communities but the seasonal response of the sediment bacterial communities to wastewater drainage from aquaculture farms remains unclear. This study used the 16S rRNA approach to explore the profiles of bacterial communities over four seasons in a typical crab aquaculture farm that included a pond and an outlet ditch. Nineteen sediment samples and an equal number of water samples were collected and analysed during spring, summer, autumn, and winter during 2018-19. Our results showed that Proteobacteria, Chloroflexi, and Bacteroides were the predominant phyla in aquaculture pond sediment with the relative abundance of 28.95%, 17.32%, and 15.31%, respectively. The relative abundance of Proteobacteria and Bacteroides was higher in autumn and winter, and the relative abundance of Chloroflexi was highest in spring. The Shannon diversity index value ranged from 6.17 to 9.30 and showed significant positive correlation (P < 0.01) with the concentrations of TN, NH4+-N, and TP in the water. The variation in the bacterial community and relative abundance in outlet ditch sediment were consistent with those in the pond sediment. Our results show that determinisation of the bacterial community composition in the outlet ditch sediment provides a novel tool to monitor watersheds sensitive to the influence of aquacultures.
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Affiliation(s)
- Xiaoxiao Shen
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China
| | - Ming Xu
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China
| | - Ming Li
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China
| | - Yongjun Zhao
- College of Biological Chemical Science and Engineering, Jiaxing University, Jiaxing 314001, PR China.
| | - Xiaohou Shao
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China.
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