1
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Li Z, Liu Q, Sheng Y. Effect of organic matter on the environmental behavior of sulfur and heavy metals in mariculture sediments during the aging process. MARINE POLLUTION BULLETIN 2024; 203:116420. [PMID: 38692006 DOI: 10.1016/j.marpolbul.2024.116420] [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: 09/26/2023] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Organic matter (OM) significantly impacts the environmental behavior of sulfur and heavy metals. In this study, the effects of OM on the migration and transformation of sulfur and heavy metals in mariculture sediments were investigated. The results indicated that baiting had a strong impact on the accumulation of acid volatile sulfur (AVS) (P < 0.05) and increased the environmental risk of sulfide in sediments. The addition of bait promoted the generation of chromium (II)-reducible sulfur (CRS); however, the resistance of AVS to CRS conversion increased with increasing bait addition. The addition of bait considerably influenced Cd accumulation. The acid-soluble fractions of Cr and Cu and the oxidizable fraction of Cd were primarily affected by the bait addition (coefficient of variation>15 %). An increase in the reducible fraction promoted the conversion of AVS to CRS, which reduced the degree of sediment aging. Higher OM levels reduced the diversity and abundance of the bacterial communities. The sulfate respiration functional microbiota was particularly affected by OM.
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Affiliation(s)
- Zhaoran Li
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Qunqun Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yanqing Sheng
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
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2
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Reynolds R, Hyun S, Tully B, Bien J, Levine NM. Identification of microbial metabolic functional guilds from large genomic datasets. Front Microbiol 2023; 14:1197329. [PMID: 37455725 PMCID: PMC10348482 DOI: 10.3389/fmicb.2023.1197329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/26/2023] [Indexed: 07/18/2023] Open
Abstract
Heterotrophic microbes play an important role in the Earth System as key drivers of major biogeochemical cycles. Specifically, the consumption rate of organic matter is set by the interaction between diverse microbial communities and the chemical and physical environment in which they reside. Modeling these dynamics requires reducing the complexity of microbial communities and linking directly with biogeochemical functions. Microbial metabolic functional guilds provide one approach for reducing microbial complexity and incorporating microbial biogeochemical functions into models. However, we lack a way to identify these guilds. In this study, we present a method for defining metabolic functional guilds from annotated genomes, which are derived from both uncultured and cultured organisms. This method utilizes an Aspect Bernoulli (AB) model and was tested on three large genomic datasets with 1,733-3,840 genomes each. Ecologically relevant microbial metabolic functional guilds were identified including guilds related to DMSP degradation, dissimilatory nitrate reduction to ammonia, and motile copiotrophy. This method presents a way to generate hypotheses about functions co-occurring within individual microbes without relying on cultured representatives. Applying the concept of metabolic functional guilds to environmental samples will provide new insight into the role that heterotrophic microbial communities play in setting rates of carbon cycling.
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Affiliation(s)
- Ryan Reynolds
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Sangwon Hyun
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Benjamin Tully
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
- Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Jacob Bien
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Naomi M. Levine
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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3
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Gregory BRB, Bell MA, Sproule A, Shields SW, Overy DP, Blais JM. Exploring within-ecodistrict lake organic matter variability and identifying possible environmental contaminant biomarkers using sedimentomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:161981. [PMID: 36739015 DOI: 10.1016/j.scitotenv.2023.161981] [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: 11/28/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Sedimentomics methods offer insight into the physiological parameters that influence freshwater sediment organic matter (sedOM). To date, most sedimentomics studies characterized variations across large spatial and environmental gradients; here we examine whether sedimentomics methods capture subtle sedOM variations within a relatively homogeneous study area in southwestern Nova Scotia, Canada. Additionally, we explore the lake sedimentome for candidate biomarkers related to ongoing carnivorous animal farming in the region. Sediment cores were recovered from seven lakes across a trophic (oligo- to eu- trophic) and anthropogenic land use gradient (carnivorous animal farming in catchment, downstream of farming, no farming nearby). Subsamples that dated prior to 1910 (pre-carnivorous animal farming) and later than 2010 (during carnivorous animal farming) were analyzed using UHPLC-HRMS in both negative (ESI-) and positive (ESI+) electrospray ionization modes. Cluster analysis (k-means) showed replicate samples from a given lake clustered distinctly from one another in both ESI modes, indicating sedOM captured subtle variations between lake systems. PCA combined with multiple linear regression indicated carnivorous animal farming and OM source explained most of the observed variation in lake sedOM. Principal component analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) of ESI- and ESI+ data sets identified 103 unique candidate biomarkers. Ten strong candidate biomarkers were identified using graphical methods; more research is required for biomarker verification and molecular characterization. Our results indicate sedimentomics could be used in environmentally homogeneous areas, offering insight into the controls of sedOM cycling. Additionally, we identified prospective biomarkers related to carnivorous animal farming that could be used to understand relative contributions of farming to ongoing eutrophication issues in southwestern Nova Scotia.
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Affiliation(s)
- B R B Gregory
- Department of Biology, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON K1N 6N5, Canada.
| | - M A Bell
- Statistics Canada, 100 Tunney's Pasture Driveway, Ottawa, ON K1A 0T6, Canada
| | - A Sproule
- Agriculture and Agri-food Canada, K.W. Neatby Bldg, Ottawa, ON K1Y 4X2, Canada
| | - S W Shields
- Agriculture and Agri-food Canada, K.W. Neatby Bldg, Ottawa, ON K1Y 4X2, Canada
| | - D P Overy
- Agriculture and Agri-food Canada, K.W. Neatby Bldg, Ottawa, ON K1Y 4X2, Canada
| | - J M Blais
- Department of Biology, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON K1N 6N5, Canada
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4
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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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5
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Gao J, Feng W, Yang F, Liu J, Fan W, Wang Y, Zhang Q, Yang W. Effects of water quality and bacterial community composition on dissolved organic matter structure in Daihai lake and the mechanisms. ENVIRONMENTAL RESEARCH 2022; 214:114109. [PMID: 35981612 DOI: 10.1016/j.envres.2022.114109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/25/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
The migration of organic matter in salinized lakes was critical in maintaining ecological balance and material circulation process of inland shallow lakes. To clarify the ecological and microbial mechanism of material transport and transformation, the microbial community structure and the characteristics of dissolved organic matter (DOM) in the sediment of Daihai Lake, a typical saline lake at the Yellow River Basin, were explored with three-dimensional excitation and emission matrix fluorescence (3DEEM), parallel factor analysis (PARAFAC) and 16 S rRNA techniques. The correlation between environmental factors, DOM composition and the bacterial community structure were also studied for identifying the key factors of community formation. DOM in the lake demonstrated both terrigenous and endogenous characteristics. Protein-like materials accounted for 74% of the total fluorescence intensity in the sediment, where 1127 species, 671 genera, 468 families, 157 classes, 317 orders, 59 phyla of microorganisms were detected. Among the top 10 abundant taxa of each level, Firmicutes, Actinobacterota, Acidimicrobiia and Alphaproteobacteria had the greatest influence on the composition and structure of DOM (|R| > 0.7, p < 0.01). Microbial metabolism was a key process of transforming sediment organic matter from terrestrial humic-like to protein-like matter, accounting for 81% of total fluorescence signal in saline lake samples, while salinity, temperature, dissolved oxygen and electrical conductivity also had significant impacts during the process (|R|>0.7, p < 0.05). The research provides fundamental data and enlightenment for the improvement of the saline inland lake environment.
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Affiliation(s)
- Jiayue Gao
- School of Space and Environment, Beihang University, Beijing, 100191, China
| | - Weiying Feng
- School of Space and Environment, Beihang University, Beijing, 100191, China; Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China.
| | - Fang Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Jing Liu
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Wenhong Fan
- School of Space and Environment, Beihang University, Beijing, 100191, China; Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China
| | - Ying Wang
- School of Space and Environment, Beihang University, Beijing, 100191, China; Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China
| | - Qi Zhang
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Wenhuan Yang
- School of Energy and Environment, Inner Mongolia University of Science and Technology, Baotou, 014010, China
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6
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Da Silva RRP, White CA, Bowman JP, Ross DJ. Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture. MARINE POLLUTION BULLETIN 2022; 182:113957. [PMID: 35872476 DOI: 10.1016/j.marpolbul.2022.113957] [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: 05/04/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO4. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.
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Affiliation(s)
- R R P Da Silva
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia.
| | - C A White
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
| | - J P Bowman
- Tasmanian Institute of Agriculture (TIA), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - D J Ross
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
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7
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Sediment Characteristics—A Key Factor for Fish Farm Site Selection: Examples from Croatia. MINERALS 2022. [DOI: 10.3390/min12060696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The rapid development and intensive production of aquaculture have brought to light various environmental problems. In particular, fish farming adversely affects the benthic environments through the accumulation of organic matter (OM), which leads to the degradation of aquatic sediments and associated biotic communities. To prevent environmental degradation, proper site selection for fish farming is a prerequisite for sustainable aquaculture practices. An important physical factor in selecting a site for fish farming is sediment structure. Coarser sediments are preferred, while their mineral composition is rarely discussed. To investigate relationships between sediment characteristics and the content of OM, sediments were collected from three different sites with different aquaculture practices under different climatic and environmental conditions and analyzed during the one-year monitoring period. Grain size distribution, mineral composition, carbonate content, and organic matter content were determined for three fish farm sites (Ilova, River, Krka River, and Pelješac) and their reference sites. Preliminary results from all studied sites showed that sediment texture in combination with natural mineral composition is one of the key factors for the accumulation of OM in the sediment. In particular, the mineral composition of the fine-grained sediment should be known when conducting an environmental impact assessment of fish farms.
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8
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Manirakiza B, Zhang S, Addo FG, Isabwe A, Nsabimana A. Exploring microbial diversity and ecological function of epiphytic and surface sediment biofilm communities in a shallow tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151821. [PMID: 34808175 DOI: 10.1016/j.scitotenv.2021.151821] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities in epiphytic biofilms and surface sediments play a vital role in the biogeochemical cycles of the major chemical elements in freshwater. However, little is known about the diversity, composition, and ecological functions of microbial communities in shallow tropical lakes dominated by aquatic macrophytes. In this study, epiphytic bacterial and eukaryotic biofilm communities on submerged and floating macrophytes and surface sediments were investigated in Lake Rumira, Rwanda in August and November 2019. High-throughput sequencing data revealed that members of the phyla, including Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Chloroflexi, Bacteriodetes, Verrumicrobia, and Myxomycota, dominated bacterial communities, while the microeukaryotic communities were dominated by Unclassified (uncl) SAR(Stramenopiles, Alveolata, Rhizaria), Rotifers, Ascomycota, Gastrotricha, Platyhelminthes, Chloroplastida, and Arthropoda. Interestingly, the eukaryotic OTUs (operational taxonomic units) number and Shannon indices were significantly higher in sediments and epiphytic biofilms on Eicchornia crassipes than Ceratophyllum demersum (p < 0.05), while no differences were observed in bacterial OTUs number and Shannon values among substrates. Redundancy analysis (RDA) showed that water temperature, pH, dissolved oxygen (DO), total nitrogen (TN), and electrical conductivity (EC) were the most important abiotic factors closely related to the microbial community on C. demersum and E. crassipes. Furthermore, co-occurrence networks analysis (|r| > 0.7, p < 0.05) and functional prediction revealed more complex interactions among microbes on C. demersum than on E. crassipes and sediments, and those interactions include cross-feeding, parasitism, symbiosis, and predatism among organisms in biofilms. These results suggested that substrate-type and environmental factors were the strong driving forces of microbial diversity in epiphytic biofilms and surface sediments, thus shedding new insights into microbial community diversity in epiphytic biofilms and surface sediments and its ecological role in tropical lacustrine ecosystems.
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Affiliation(s)
- Benjamin Manirakiza
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China; University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Antoine Nsabimana
- University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
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9
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Tyagi I, Tyagi K, Bhutiani R, Chandra K, Kumar V. Bacterial diversity assessment of world's largest sewage-fed fish farms with special reference to water quality: a Ramsar site. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42372-42386. [PMID: 33813698 DOI: 10.1007/s11356-021-13756-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world's largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0-50%), Pseudomonas (0-15%), Sulfurospirillum (0-9%), Cloacibacterium (0-6%), hgcI clade (7-29%), C39 (0-9%), V6 (3-36%), Fluiivicola (1-6%) and Cyanobium (3-8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.
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Affiliation(s)
- Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Rakesh Bhutiani
- Department of Environmental Sciences, Gurukul Kangri Vishwavidyalaya, Haridwar, 249404, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India.
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10
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Laroche O, Pochon X, Wood SA, Keeley N. Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments. Mol Ecol Resour 2021; 21:2264-2277. [PMID: 33971078 DOI: 10.1111/1755-0998.13426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
Characterization of microbial assemblages via environmental DNA metabarcoding is increasingly being used in routine monitoring programs due to its sensitivity and cost-effectiveness. Several programs have recently been developed which infer functional profiles from 16S rRNA gene data using hidden-state prediction (HSP) algorithms. These might offer an economic and scalable alternative to shotgun metagenomics. To date, HSP-based methods have seen limited use for benthic marine surveys and their performance in these environments remains unevaluated. In this study, 16S rRNA metabarcoding was applied to sediment samples collected at 0 and ≥1,200 m from Norwegian salmon farms, and three metabolic inference approaches (Paprica, Picrust2 and Tax4Fun2) evaluated against metagenomics and environmental data. While metabarcoding and metagenomics recovered a comparable functional diversity, the taxonomic composition differed between approaches, with genera richness up to 20× higher for metabarcoding. Comparisons between the sensitivity (highest true positive rates) and specificity (lowest true negative rates) of HSP-based programs in detecting functions found in metagenomic data ranged from 0.52 and 0.60 to 0.76 and 0.79, respectively. However, little correlation was observed between the relative abundance of their specific functions. Functional beta-diversity of HSP-based data was strongly associated with that of metagenomics (r ≥ 0.86 for Paprica and Tax4Fun2) and responded similarly to the impact of fish farm activities. Our results demonstrate that although HSP-based metabarcoding approaches provide a slightly different functional profile than metagenomics, partly due to recovering a distinct community, they represent a cost-effective and valuable tool for characterizing and assessing the effects of fish farming on benthic ecosystems.
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Affiliation(s)
- Olivier Laroche
- Institute of Marine Research, Tromsø, Norway.,Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Nigel Keeley
- Institute of Marine Research, Tromsø, Norway.,Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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11
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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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12
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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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Meng Q, Han Y, Zhu H, Yang W, Bello A, Deng L, Jiang X, Wu X, Sheng S, Xu Y, Xu X. Differences in distribution of functional microorganism at DNA and cDNA levels in cow manure composting. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110161. [PMID: 31954219 DOI: 10.1016/j.ecoenv.2019.110161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Denitrification and nitrification processes are the two prominent pathways of nitrogen (N) transformation in composting matrix. This study explored the dynamics of denitrifying and nitrifying bacteria at different composting stages of cow manure and corn straw using functional gene sequencing at DNA and cDNA levels. Corresponding agreement among OTUs, NMDS, mental test and network analyses revealed that functional bacteria community compositions and responses to physicochemical factors were different at DNA and cDNA levels. Specifically, some OTUs were detected at the DNA level but were not observed at cDNA level, differences were also found in the distribution patterns of nitrifying and denitrifying bacteria communities at both levels. Furthermore, co-occurrence network analysis indicated that Pseudomonas, Paracoccus and Nitrosomonas were identified as the keystone OTUs at the DNA level, while Paracoccus, Agrobacterium and Nitrosospira were keystone OTUs at the cDNA level. Mantel test revealed that TN, C/N and moisture content significantly influenced both the denitrifying bacteria and ammonia-oxidizing bacteria (AOB) communities at the DNA level. NO3--N, NH4+-N, TN, C/N, and moisture content only registered significant correlation with the nosZ-type denitrifiers and ammonia-oxidizing bacteria (AOB) communities at the cDNA level. Structural equation model (SEM) showed that TN, NH4+-N, and pH were direct and significantly influenced the gene abundance of denitrifying bacteria. Howbeit, TN, NH4+-N, and NO3--N had significant direct effects on amoA gene abundance.
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Affiliation(s)
- Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Han
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Haifeng Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaotong Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Siyuan Sheng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yingying Xu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
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Florez JZ, Camus C, Hengst MB, Marchant F, Buschmann AH. Structure of the epiphytic bacterial communities of Macrocystis pyrifera in localities with contrasting nitrogen concentrations and temperature. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101706] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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15
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Furey PC, Liess A, Lee S. Substratum-associated microbiota. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2019; 91:1326-1341. [PMID: 31523907 DOI: 10.1002/wer.1226] [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: 05/28/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
This survey of 2018 literature on substratum-associated microbiota presents brief highlights on research findings from primarily freshwaters, but includes those from a variety of aquatic ecosystems. Coverage of topics associated with benthic algae and cyanobacteria, though not comprehensive, includes new methods, taxa new to science, nutrient dynamics, trophic interactions, herbicides and other pollutants, metal contaminants, nuisance, bloom-forming and harmful algae, bioassessment, and bioremediation. Coverage of bacteria, also not comprehensive, focused on methylation of mercury, metal contamination, toxins, and other environmental pollutants, including oil, as well as the use of benthic bacteria as bioindicators, in bioassessment tools and in biomonitoring. Additionally, we cover trends in recent and emerging topics on substratum-associated microbiota of relevance to the Water Environment Federation. PRACTITIONER POINTS: This review of literature from 2018 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Topics covered that focus on algae and cyanobacteria include findings on new methods, taxa new to science, nutrient dynamics, trophic interactions, herbicides and other pollutants, metal contaminants, nuisance, bloomforming and harmful algae, bioassessment, and bioremediation. Topics covered that focus on bacteria include findings on methylation of mercury, metal contamination, toxins and other environmental pollutants, including oil, as well as the us e of benthic bacteria as bioindicators, in bioassessment tools and in biomonitoring. A brief presentation of new, noteworthy and emerging topics on substratum-associated microbiota, build on those from 2017, to highlight those of particular relevance to the Water Environment Federation.
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Affiliation(s)
- Paula C Furey
- Department Biology, St. Catherine University, St. Paul, Minnesota, USA
| | - Antonia Liess
- Rydberg Laboratory, School of Buisness, Engineering and Science, Halmstad University, Halmstad, Sweden
| | - Sylvia Lee
- Office of Research and Development, U.S. Environmental Protection Agency, Washington, District of Columbia, USA
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Shi R, Xu S, Qi Z, Zhu Q, Huang H, Weber F. Influence of suspended mariculture on vertical distribution profiles of bacteria in sediment from Daya Bay, Southern China. MARINE POLLUTION BULLETIN 2019; 146:816-826. [PMID: 31426223 DOI: 10.1016/j.marpolbul.2019.07.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Mariculture is known to contribute to oxygen depletion, pH decline and accumulation of nutrients and organic matter in sediments. However, studies on the bacterial vertical distribution of mariculture area are very limited. The bacterial abundance in the non-culture site (3.8 ± 0.8 × 109 copies g-1) was significantly higher than that in the three mariculture sites (1.2 ± 0.2 × 109 copies g-1), and bacterial diversity in the non-culture site was significantly higher than that in fish cage-TF (p < 0.05). The vertical distribution profiles of bacteria in non-culture and oyster culture sites were similar but very different from that of fish cage-TF. In addition, significant downward trends in bacterial abundance and diversity were observed as sediment depth increased (p < 0.05), and the most relevant environmental factors were moisture content, total nitrogen, total organic carbon and carbon/nitrogen. The dominant bacterial phyla in sediment were Proteobacteria, Chloroflexi and Bacteroidetes.
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Affiliation(s)
- Rongjun Shi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Shumin Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Zhanhui Qi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China.
| | - Qingzhi Zhu
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Felix Weber
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
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Ape F, Manini E, Quero GM, Luna GM, Sarà G, Vecchio P, Brignoli P, Ansferri S, Mirto S. Biostimulation of in situ microbial degradation processes in organically-enriched sediments mitigates the impact of aquaculture. CHEMOSPHERE 2019; 226:715-725. [PMID: 30959456 DOI: 10.1016/j.chemosphere.2019.03.178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/12/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Fish farm deposition, resulting in organic matter accumulation on bottom sediments, has been identified as among the main phenomena causing negative environmental impacts in aquaculture. An in situ bioremediation treatment was carried out in order to reduce the organic matter accumulation in the fish farm sediments by promoting the natural microbial biodegradation processes. To assess the effect of the treatment, the concentration of organic matter in the sediment and its microbial degradation, as well as the response of the benthic prokaryotic community, were investigated. The results showed a significant effect of the treatment in stimulating microbial degradation rates, and the consequent decrease in the concentration of biochemical components beneath the cages during the treatment. During the bioremediation process, the prokaryotic community in the fish farm sediment responded to the overall improvement of the sediment conditions by showing the decrease of certain anaerobic taxa (e.g. Clostridiales, Acidaminobacteraceae and Caldilinaceae). This suggested that the bioactivator was effective in promoting a shift from an anaerobic to an aerobic metabolism in the prokaryotic community. However, the larger importance of Lachnospiraceae (members of the gut and faecal microbiota of the farmed fishes) in treated compared to non-treated sediments suggested that the bioactivator was not efficient in reducing the accumulation of faecal bacteria from the farmed fishes. Our results indicate that bioremediation is a promising tool to mitigate the aquaculture impact in fish farm sediments, and that further research needs to be oriented to identifying more successful interventions able to specifically target also fish-faeces related microbes.
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Affiliation(s)
- Francesca Ape
- Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Via G. da Verrazzano, 17, 91014, Castellammare del Golfo, TP, Italy
| | - Elena Manini
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM-CNR), Via Largo Fiera della Pesca, 1 - 60122 Ancona, Italy
| | - Grazia Marina Quero
- Stazione Zoologica Anton Dohrn, Integrative Marine Ecology Department, 80121, Napoli, Italy
| | - Gian Marco Luna
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM-CNR), Via Largo Fiera della Pesca, 1 - 60122 Ancona, Italy
| | - Gianluca Sarà
- Dipartimento di Scienze della Terra e del Mare, University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy
| | - Paolo Vecchio
- Eurovix S.p.A. - V.le E. Mattei 17, 24060, Entratico (Bergamo), Italy
| | | | - Sante Ansferri
- Eurovix S.p.A. - V.le E. Mattei 17, 24060, Entratico (Bergamo), Italy
| | - Simone Mirto
- Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino (IAS-CNR), Via G. da Verrazzano, 17, 91014, Castellammare del Golfo, TP, Italy.
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