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Pathak A, Marquez M, Stothard P, Chukwujindu C, Su JQ, Zhou Y, Zhou XY, Jagoe CH, Chauhan A. A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential. iScience 2024; 27:110193. [PMID: 38984199 PMCID: PMC11231605 DOI: 10.1016/j.isci.2024.110193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/09/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Mario Marquez
- Texas Sea Grant College Program, 4115 TAMU Eller O&M 306, Texas A&M University, College Station, TX 77843, USA
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, General Services Bldg, Edmonton, AB 2-31 T6G 2H1, Canada
| | - Christian Chukwujindu
- Material & Energy Technology Department, Projects Development Institute, Emene Industrial Layout, Enugu-Nigeria 400104
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Yuan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Charles H. Jagoe
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
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Siriwardana H, Samarasekara RSM, Anthony D, Vithanage M. Measurements and analysis of nitrogen and phosphorus in oceans: Practice, frontiers, and insights. Heliyon 2024; 10:e28182. [PMID: 38560146 PMCID: PMC10979167 DOI: 10.1016/j.heliyon.2024.e28182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Nitrogen and phosphorus concentrations in oceans have been extensively studied, and advancements in associated disciplines have rapidly progressed, enabling the exploration of novel and previously challenging questions. A keyword analysis was conducted using the Scopus database to examine chronological trends and hotspots, offering comprehensive insights into the evolution of marine nitrogen and phosphorus research. For this purpose, author keyword networks were developed for the periods before 1990, 1990 to 2000, 2001 to 2011, and 2012 to 2022. Furthermore, analytical techniques employed in the recent decade to determine nitrogen and phosphorus concentrations in seawater were assessed for their applicability and limitations through a critical review of more than 50 journal articles. Taxonomy and nitrogen biogeochemistry were the prominent research interests for the first two periods, respectively, while stable isotopic tracking of nitrogen and phosphorus processes emerged as the dominant research focus for the last two decades. The integration of macroeconomic factors in research development and the chronological rise of interdisciplinary research were identified. Conventional analytical techniques such as spectrophotometry, colorimetry, fluorometry, and elemental analysis were noted, along with emerging techniques like remote sensing and microfluidic sensors.
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Affiliation(s)
- Hasitha Siriwardana
- Faculty of Engineering, University of Sri Jayewardenepura, 41, Lumbini Avenue, Ratmalana 10390, Sri Lanka
| | - R S M Samarasekara
- Faculty of Engineering, University of Sri Jayewardenepura, 41, Lumbini Avenue, Ratmalana 10390, Sri Lanka
| | - Damsara Anthony
- Faculty of Engineering, University of Sri Jayewardenepura, 41, Lumbini Avenue, Ratmalana 10390, Sri Lanka
- Department of Civil Engineering, Faculty of Engineering, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Meththika Vithanage
- Ecosphere Resilience Research Center (ERRC), Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
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Isokpehi RD, Kim Y, Krejci SE, Trivedi VD. Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential. Microorganisms 2024; 12:791. [PMID: 38674735 PMCID: PMC11052009 DOI: 10.3390/microorganisms12040791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.
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Affiliation(s)
| | - Yungkul Kim
- Oyster Microbiome Project, College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (S.E.K.); (V.D.T.)
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Filippini G, Bugnot AB, Ferguson A, Gribben PE, Palmer J, Erickson K, Dafforn KA. The influence of oyster reefs and surrounding sediments on nitrogen removal - An in-situ study along the East coast of Australia. ENVIRONMENTAL RESEARCH 2023; 237:116947. [PMID: 37611788 DOI: 10.1016/j.envres.2023.116947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/02/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Oyster reefs play a crucial role in the removal of nitrogen (N) from aquatic systems by facilitating nutrient regeneration and denitrification, both in their tissues and shells and surrounding sediments. However, we still have a limited understanding about the contribution of each component of the reefs (e.g. oysters vs sediments) to N processes, and whether rates are dependent on site-specific characteristics. To address these knowledge gaps, we conducted an experiment across six oyster reefs along 1080 km of the Eastern Australian coast with different sediment characteristics. By using in-situ clear and dark incubation chambers, we assessed how benthic metabolism, nutrient and dinitrogen gas (N2) fluxes varied among the following treatments: 'oysters', 'sediments', and 'sediments + oysters' that were used to represent components of the whole reef habitat (i.e. reef matrix vs surrounding sediments vs the interaction among them, respectively), and sites. We found that during dark conditions and at siltier sites, N2 effluxes from oysters can be up to 23 times higher than sediments, while N2 effluxes from chambers with both sediments and oysters were similar to sediment treatments, and lower than oyster treatments. These results can be explained by sediment processes including nutrient assimilation by benthic microalgae and/or lower nutrient diffusion into interstitial space. Additionally, oyster treatments showed an uptake of nitrate (NO3-) that was likely converted into N2, whereas sediment treatments showed an overall release of NO3-. In dark conditions, ammonium (NH4+) fluxes remained consistent across treatments and sites, indicating that any exports from oyster excretion (in those treatments including oysters) were either counterbalanced by or comparable to exports from sediments. This study provides evidence that the crucial contribution of oyster reefs to N removal is dependent on interactions between reef components and environmental factors.
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Affiliation(s)
- Giulia Filippini
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
| | - Ana B Bugnot
- CSIRO Environment, St. Lucia, QLD, 4067, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Angus Ferguson
- Department of Planning, Industry and Environment, Lidcombe, NSW, 2141, Australia
| | - Paul E Gribben
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia; Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia
| | - Julia Palmer
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Katherine Erickson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Katherine A Dafforn
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2109, Australia; Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia
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5
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Stevens JTE, Ray NE, Al-Haj AN, Fulweiler RW, Chowdhury PR. Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566866. [PMID: 38014072 PMCID: PMC10680616 DOI: 10.1101/2023.11.13.566866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas. Importance Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.
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Akter S, Wos-Oxley ML, Catalano SR, Hassan MM, Li X, Qin JG, Oxley AP. Host Species and Environment Shape the Gut Microbiota of Cohabiting Marine Bivalves. MICROBIAL ECOLOGY 2023; 86:1755-1772. [PMID: 36811710 PMCID: PMC10497454 DOI: 10.1007/s00248-023-02192-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Pacific oysters (Crassostrea gigas) and Mediterranean mussels (Mytilus galloprovincialis) are commercially important marine bivalves that frequently coexist and have overlapping feeding ecologies. Like other invertebrates, their gut microbiota is thought to play an important role in supporting their health and nutrition. Yet, little is known regarding the role of the host and environment in driving these communities. Here, bacterial assemblages were surveyed from seawater and gut aspirates of farmed C. gigas and co-occurring wild M. galloprovincialis in summer and winter using Illumina 16S rRNA gene sequencing. Unlike seawater, which was dominated by Pseudomonadata, bivalve samples largely consisted of Mycoplasmatota (Mollicutes) and accounted for >50% of the total OTU abundance. Despite large numbers of common (core) bacterial taxa, bivalve-specific species (OTUs) were also evident and predominantly associated with Mycoplasmataceae (notably Mycoplasma). An increase in diversity (though with varied taxonomic evenness) was observed in winter for both bivalves and was associated with changes in the abundance of core and bivalve-specific taxa, including several representing host-associated and environmental (free-living or particle-diet associated) organisms. Our findings highlight the contribution of the environment and the host in defining the composition of the gut microbiota in cohabiting, intergeneric bivalve populations.
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Affiliation(s)
- Shirin Akter
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | - Sarah R Catalano
- Aquatic Sciences Centre, South Australian Research and Development Institute, West Beach, SA, Australia
| | - Md Mahbubul Hassan
- Aquaculture Research and Development, Department of Primary Industries and Regional Development, Hillarys, WA, Australia
| | - Xiaoxu Li
- Aquatic Sciences Centre, South Australian Research and Development Institute, West Beach, SA, Australia
| | - Jian G Qin
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Andrew Pa Oxley
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
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Morris N, Alldred M, Zarnoch C, Alter SE. Estuarine Sediment Microbiomes from a Chronosequence of Restored Urban Salt Marshes. MICROBIAL ECOLOGY 2023; 85:916-930. [PMID: 36826588 DOI: 10.1007/s00248-023-02193-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/09/2023] [Indexed: 05/04/2023]
Abstract
Salt marshes play an important role in the global nutrient cycle. The sediments in these systems harbor diverse and complex bacterial communities possessing metabolic capacities that provide ecosystem services such as nutrient cycling and removal. On the East Coast of the USA, salt marshes have been experiencing degradation due to anthropogenic stressors. Salt marsh islands within Jamaica Bay, New York City (USA), are surrounded by a large highly urbanized watershed and have declined in area. Restoration efforts have been enacted to reduce further loss, but little is known about how microbial communities develop following restoration activities, or how processes such as nitrogen cycling are impacted. Sediment samples were collected at two sampling depths from five salt marsh islands to characterize the bacterial communities found in marsh sediment including a post-restoration chronosequence of 3-12 years. We used 16s rRNA amplicon sequencing to define alpha and beta diversity, taxonomic composition, and predicted metabolic profile of each sediment sample. We found significant differences in alpha diversity between sampling depths, and significant differences in beta diversity, taxonomic composition, and predicted metabolic capacity among the five sampling locations. The youngest restored site and the degraded natural sampling site exhibited the most distinct communities among the five sites. Our findings suggest that while the salt marsh islands are located in close proximity to each other, they harbor distinct bacterial communities that can be correlated with post-restoration age, marsh health, and other environmental factors such as availability of organic carbon. IMPORTANCE: Salt marshes play a critical role in the global nutrient cycle due to sediment bacteria and their metabolic capacities. Many East Coast salt marshes have experienced significant degradation over recent decades, thought largely to be due to anthropogenic stressors such as nitrogen loading, urban development, and sea-level rise. Salt marsh islands in Jamaica Bay (Queens/Brooklyn NY) are exposed to high water column nitrogen due to wastewater effluent. Several receding marsh islands have been subjected to restoration efforts to mitigate this loss. Little is known about the effect marsh restoration has on bacterial communities, their metabolic capacity, or how they develop post-restoration. Here, we describe the bacterial communities found in marsh islands including a post-restoration chronosequence of 3-12 years and one degraded marsh island that remains unrestored. We found distinct communities at marsh sites, despite their geographic proximity. Differences in diversity and community composition were consistent with changes in organic carbon availability that occur during marsh development, and may result in differences in ecosystem function among sites.
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Affiliation(s)
- Nathan Morris
- The Graduate Center City University of New York, New York, NY, USA
- York College City University of New York, Jamaica, NY, USA
| | - Mary Alldred
- Center for Earth and Environmental Science State University of New York (SUNY), Plattsburgh, NY, USA
| | - Chester Zarnoch
- The Graduate Center City University of New York, New York, NY, USA
- Baruch College City University of New York, New York, NY, USA
| | - S Elizabeth Alter
- The Graduate Center City University of New York, New York, NY, USA.
- California State University-Monterey Bay, Seaside, CA, USA.
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Yang J, Sooksa-nguan T, Kannan B, Cano-Alfanar S, Liu H, Kent A, Shanklin J, Altpeter F, Howe A. Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:56. [PMID: 36998044 PMCID: PMC10064762 DOI: 10.1186/s13068-023-02302-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/12/2023] [Indexed: 04/01/2023]
Abstract
Oilcane is a metabolically engineered sugarcane (Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI1 transgene. The WRI1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.
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Affiliation(s)
- Jihoon Yang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Ames, IA USA
| | - Thanwalee Sooksa-nguan
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Ames, IA USA
| | - Baskaran Kannan
- Present Address: Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL USA
| | - Sofia Cano-Alfanar
- Present Address: Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL USA
| | - Hui Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY USA
| | - Angela Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY USA
| | - Fredy Altpeter
- Present Address: Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Ames, IA USA
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Donelan SC, Ogburn MB, Breitburg D. Legacy of past exposure to hypoxia and warming regulates an ecosystem service provided by oysters. GLOBAL CHANGE BIOLOGY 2023; 29:1328-1339. [PMID: 36541067 DOI: 10.1111/gcb.16571] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 05/26/2023]
Abstract
Climate change is having substantial impacts on organism fitness and ability to deliver critical ecosystem services, but these effects are often examined only in response to current environments. Past exposure to stress can also affect individuals via carryover effects, and whether these effects scale from individuals to influence ecosystem function and services is unknown. We explored within-generation carryover effects of two coastal climate change stressors-hypoxia and warming-on oyster (Crassostrea virginica) growth and nitrogen bioassimilation, an important ecosystem service. Oysters were exposed to a factorial combination of two temperature and two diel-cycling dissolved oxygen treatments at 3-months-old and again 1 year later. Carryover effects of hypoxia and warming influenced oyster growth and nitrogen storage in complex and context-dependent ways. When operating, carryover effects of single stressors generally reduced oyster nitrogen bioassimilation and relative investment in tissue versus shell growth, particularly in warm environments, while early life exposure to multiple stressors generally allowed oysters to perform as well as control oysters. When extrapolated to the reef scale, carryover effects decreased nitrogen stored by modeled oyster reefs in most conditions, with reductions as large as 41%, a substantial decline in a critical ecosystem service. In some scenarios, however, carryover effects increased nitrogen storage by modeled oyster reefs, again highlighting the complexity of these effects. Hence, even brief exposure to climate change stressors early in life may have persistent effects on an ecosystem service 1 year later. Our results show for the first time that within-generation carryover effects on individual phenotypes can impact processes at the ecosystem scale and may therefore be an overlooked factor determining ecosystem service delivery in response to anthropogenic change.
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Affiliation(s)
- Sarah C Donelan
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Matthew B Ogburn
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Denise Breitburg
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
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10
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Filippini G, Dafforn KA, Bugnot AB. Shellfish as a bioremediation tool: A review and meta-analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120614. [PMID: 36356885 DOI: 10.1016/j.envpol.2022.120614] [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: 05/26/2022] [Revised: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Over the last century, human activities have increased the amount of nutrients inputs to terrestrial and aquatic ecosystems. These activities have altered nitrogen (N) and phosphorus (P) cycling, causing substantial changes in ecosystem function such as provision of clean air and water. Strategies that reduce and remove excess nutrients are urgently needed to remediate impacted systems. Reef-forming shellfish (oysters and mussels) can play a crucial role in nutrient cycling, particularly in N removal from aquatic systems by providing substrate for microbial colonisation and enhancing microbial denitrification in the surrounding sediments. However, the potential for shellfish to enhance nutrient cycling (and denitrification) will likely vary spatially and in response to several environmental factors. Here, we used 1) a qualitative analysis to review nutrient processes occurring on shellfish; and 2) a meta-analysis to evaluate the influence of shellfish on benthic metabolism and nutrient cycling in surrounding sediments, and how that is influenced by environmental factors such as grain size, seasonality, water body type, and tidal position. Overall, we found that shellfish increased oxygen consumption, with consequent release of ammonia (NH4+) and phosphate (PO43-) from shellfish and their surrounding sediments. These parameters did not depend on grain size, water body type and tidal height, but the release of PO43- was variable between seasons, being highest during summer and autumn. Shellfish presence also enhanced denitrification measured as dinitrogen gas (N2) efflux on both reefs and sediments. Denitrification was highest in lagoons; in sandy sediments; and during the warmest season (summer). Thus, our findings highlight that environmental context can mediate the effects of shellfish reefs on sediment function. This information is important for managers seeking to use these animals as an effective bioremediation tool.
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Affiliation(s)
- Giulia Filippini
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
| | - Katherine A Dafforn
- School of Natural Sciences, Macquarie University, North Ryde, NSW, 2109, Australia; Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia
| | - Ana B Bugnot
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia; Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, 4001, Australia
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Comparison of the Gill Microbiome of Retail Oysters from Two Geographical Locations Exhibited Distinct Microbial Signatures: A Pilot Study for Potential Future Applications for Monitoring Authenticity of Their Origins. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol3010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The oyster industry is a significant component of United States aquaculture and is vulnerable to various food frauds. In addition to species substitution, mislabeling of oyster geographical origin is performed for economic gains. The geographical origin misrepresentations are performed to claim a famed region of origin known for its unique flavor profile. DNA barcoding is the gold standard method for identifying seafood species but has limited resolution to the species level. This pilot study was conducted to characterize and compare the oyster gill microbiome as an alternative approach for tracking oysters’ origin. Commercially available raw east coast oysters (Crassostrea virginica) from two distinct geographical locations were purchased. Genomic DNA isolated from the gills was processed for microbiome analysis. The data revealed distinct microbiome signatures among the two sample sets. Oysters from Louisiana showed the presence of eighteen unique bacterial genera, whereas Maryland oysters showed a higher abundance of twelve genera. Findings from this study demonstrate the applicability of microbiome analysis as an emerging alternative approach for identifying geographical origin misrepresentations.
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Wyness AJ, Roush D, McQuaid CD. Global distribution and diversity of marine euendolithic cyanobacteria. JOURNAL OF PHYCOLOGY 2022; 58:746-759. [PMID: 36199189 PMCID: PMC10092097 DOI: 10.1111/jpy.13288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Euendolithic, or true-boring, cyanobacteria actively erode carbonate-containing substrata in a wide range of environments and pose significant risks to calcareous marine fauna. Their boring activities cause structural damage and increase susceptibility to disease and are projected to only intensify with global climate change. Most research has, however, focused on tropical coral systems, and limited information exists on the global distribution, diversity, and substratum specificity of euendoliths. This metastudy aimed to collate existing 16S rRNA gene surveys along with novel data from the south coast of South Africa to investigate the global distribution and genetic diversity of endoliths to identify a "core endolithic cyanobacterial microbiome" and assess global diversification of euendolithic cyanobacteria. The cyanobacterial families Phormidesmiaceae, Nodosilineaceae, Nostocaceae, and Xenococcaceae were the most prevalent, found in >92% of categories surveyed. All four known euendolith clusters were detected in both intertidal and subtidal habitats, in the North Atlantic, Mediterranean, and South Pacific oceans, across temperate latitudes, and within rock, travertine tiles, coral, shell, and coralline algae substrata. Analysis of the genetic variation within clusters revealed many organisms to be unique to substratum type and location, suggesting high diversity and niche specificity. Euendoliths are known to have important effects on their hosts. This is particularly important when hosts are globally significant ecological engineers or habitat-forming species. The findings of this study indicate high ubiquity and diversity of euendolithic cyanobacteria, suggesting high adaptability, which may lead to increased community and ecosystem-level effects with changing climatic conditions favoring the biochemical mechanisms of cyanobacterial bioerosion.
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Affiliation(s)
- Adam J. Wyness
- Coastal Research GroupDepartment of Zoology and EntomologyRhodes UniversityMakhanda (Grahamstown)South Africa6139
- School of Biology and Environmental SciencesUniversity of MpumalangaMbombelaSouth Africa1200
| | - Daniel Roush
- Center for Fundamental and Applied MicrobiomicsBiodesign InstituteArizona State UniversityTempeArizona85287USA
| | - Christopher D. McQuaid
- Coastal Research GroupDepartment of Zoology and EntomologyRhodes UniversityMakhanda (Grahamstown)South Africa6139
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Read-Daily B, Ben Maamar S, Sabba F, Green S, Nerenberg R. Effect of nitrous oxide (N 2O) on the structure and function of nitrogen-oxide reducing microbial communities. CHEMOSPHERE 2022; 307:135819. [PMID: 35977570 DOI: 10.1016/j.chemosphere.2022.135819] [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: 05/13/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas that can be produced by nitrifying and denitrifying bacteria. Yet the effects of N2O on microbial communities is not well understood. We used batch tests to explore the effects of N2O on mixed denitrifying communities. Batch tests were carried out with acetate as the electron donor and with the following electron acceptors: nitrate (NO3-), nitrite (NO2-), N2O, NO3- + N2O, and NO2- + N2O. Activated sludge from a municipal wastewater treatment plant was used as the inoculum. The bacteria grew readily with N2O as the sole acceptor. When N2O was provided along with NO3- or NO2-, it was used concurrently and resulted in higher growth rates than the same acceptors without added N2O. The microbial communities resulting from N2O addition were significantly different at the genus level from those with just NO3- or NO2-. Tests with N2O as the sole added acceptor revealed a reduced diversity. Analysis of inferred gene content using PICRUSt2 indicated a greater abundance of genera with a complete denitrification pathway when growing on N2O or NO2-, relative to all other tests. This suggests that specific N2O reduction rates are high, and that N2O alone selects for a low-diversity, fully denitrifying community. When N2O is present with NO2- or NO3-, the microbial communities were more diverse and did not select exclusively for full denitrifiers. N2O alone appears to select for a "generalist" community with full denitrification pathways and lower diversity. In terms of denitrification genes, the combination of acceptors with N2O appeared to increase the number of microbes carrying nirK, while fully denitrifying bacteria appear more likely to carry nirS. Lastly, all the taxa in NO2- and N2O samples were predicted to harbor nosZ. This suggests the potential for reduced N2O emissions in denitrifying systems.
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Affiliation(s)
- B Read-Daily
- Department of Engineering and Physics, Elizabethtown College, Elizabethtown, PA, 17022, USA; Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - S Ben Maamar
- Samuel J. Wood Library, Weill Cornell Medicine, New York, NY, 10065, USA
| | - F Sabba
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA; Black & Veatch, KS, USA
| | - S Green
- Rush Medical College, Chicago, IL, 60612, USA
| | - R Nerenberg
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
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Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound. Microbiol Spectr 2022; 10:e0198221. [PMID: 35536036 PMCID: PMC9241838 DOI: 10.1128/spectrum.01982-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Olympia oyster (Ostrea lurida) of the Puget Sound suffered a dramatic population crash, but restoration efforts hope to revive this native species. One overlooked variable in the process of assessing ecosystem health is association of bacteria with marine organisms and the environments they occupy. Oyster microbiomes are known to differ significantly between species, tissue type, and the habitat in which they are found. The goals of this study were to determine the impact of field site and habitat on the oyster microbiome and to identify core oyster-associated bacteria in the Puget Sound. Olympia oysters from one parental family were deployed at four sites in the Puget Sound both inside and outside of eelgrass (Zostera marina) beds. Using 16S rRNA gene amplicon sequencing of the oyster gut, shell, and surrounding seawater and sediment, we demonstrate that gut-associated bacteria are distinct from the surrounding environment and vary by field site. Furthermore, regional differences in the gut microbiota are associated with the survival rates of oysters at each site after 2 months of field exposure. However, habitat type had no influence on microbiome diversity. Further work is needed to identify the specific bacterial dynamics that are associated with oyster physiology and survival rates. IMPORTANCE This is the first exploration of the microbial colonizers of the Olympia oyster, a native oyster species to the West Coast, which is a focus of restoration efforts. The patterns of differential microbial colonization by location reveal microscale characteristics of potential restoration sites which are not typically considered. These microbial dynamics can provide a more holistic perspective on the factors that may influence oyster performance.
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Intrahabitat Differences in Bacterial Communities Associated with Corbicula fluminea in the Large Shallow Eutrophic Lake Taihu. Appl Environ Microbiol 2022; 88:e0232821. [PMID: 35285714 DOI: 10.1128/aem.02328-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Asian clam Corbicula fluminea is a keystone zoobenthos in freshwater ecosystems. However, its associated microbiome is not well understood. We investigated the bacterial communities of this clam and its surrounding environment, including sediment and water simultaneously, in a large lake by means of 16S rRNA gene sequencing. Approximately two-thirds of the bacterial operational taxonomic units (OTUs) associated with clams were observed in the surrounding environment and mostly from particle-associated samples. The associated bacterial communities were site specific and more similar to environmental bacteria from the same site than those at other sites, suggesting a local environmental influence on host bacteria. However, the significant differences in bacterial diversities and compositions between the clam and the environment also indicated strong host selection pressure on bacteria from the surrounding environment. Bacteria affiliated with Firmicutes, Spirochaetes, Tenericutes, Bacteroidetes, Epsilonbacteraeota, Patescibacteria, and Fusobacteria were found to be significantly enriched in the clams in comparison to their local environment. Oligotyping analyses of the core-associated bacterial OTUs also demonstrated that most of the core OTUs had lower relative abundances and occurrence frequencies in environmental samples. The core bacterial OTUs were found to play an important role in maintaining the stability of the bacterial community network. These core bacteria included the two most abundant taxa Romboutsia and Paraclostridium with the potential function of fermenting polysaccharides for assisting host clams in food digestion. Overall, we demonstrate that clam-associated bacteria were spatially dynamic and site specific, which were mainly structured both by local environments and host selection. IMPORTANCE The Asian clam Corbicula fluminea is an important benthic clam in freshwater ecosystems due to its high population densities and high filtering efficiency for particulate organic matter. While the associated microbiota is believed to be vital for host living, our knowledge about the compositions, sources, and potential functions is still lacking. We found that C. fluminea offers a unique ecological niche for specific lake bacteria. We also observed high intrahabitat variation in the associated bacterial communities. Such variations were driven mainly by local environments, followed by host selection pressure. While the local microbes served as a source of the clam-associated bacteria, host selection resulted in enrichments of bacterial taxa with the potential for assisting the host in organic matter digestion. These results significantly advance our current understanding of the origins and ecological roles of the microbiota associated with a keynote clam in freshwater ecosystems.
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Armstrong G, Rahman G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R. Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. FRONTIERS IN BIOINFORMATICS 2022; 2:821861. [PMID: 36304280 PMCID: PMC9580878 DOI: 10.3389/fbinf.2022.821861] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 01/05/2023] Open
Abstract
Dimensionality reduction techniques are a key component of most microbiome studies, providing both the ability to tractably visualize complex microbiome datasets and the starting point for additional, more formal, statistical analyses. In this review, we discuss the motivation for applying dimensionality reduction techniques, the special characteristics of microbiome data such as sparsity and compositionality that make this difficult, the different categories of strategies that are available for dimensionality reduction, and examples from the literature of how they have been successfully applied (together with pitfalls to avoid). We conclude by describing the need for further development in the field, in particular combining the power of phylogenetic analysis with the ability to handle sparsity, compositionality, and non-normality, as well as discussing current techniques that should be applied more widely in future analyses.
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Affiliation(s)
- George Armstrong
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Gal Mishne
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- *Correspondence: Rob Knight,
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Rose JM, Gosnell JS, Bricker S, Brush MJ, Colden A, Harris L, Karplus E, Laferriere A, Merrill NH, Murphy TB, Reitsma J, Shockley J, Stephenson K, Theuerkauf S, Ward D, Fulweiler RW. Opportunities and Challenges for Including Oyster-Mediated Denitrification in Nitrogen Management Plans. ESTUARIES AND COASTS : JOURNAL OF THE ESTUARINE RESEARCH FEDERATION 2021; 44:2041-2055. [PMID: 35340553 PMCID: PMC8942081 DOI: 10.1007/s12237-021-00936-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 02/10/2021] [Accepted: 03/25/2021] [Indexed: 06/14/2023]
Abstract
Nitrogen pollution is one of the primary threats to coastal water quality globally, and governmental regulations and marine policy are increasingly requiring nitrogen remediation in management programs. Traditional mitigation strategies (e.g., advanced wastewater treatment) are not always enough to meet reduction goals. Novel opportunities for additional nitrogen reduction are needed to develop a portfolio of long-term solutions. Increasingly, in situ nitrogen reduction practices are providing a complementary management approach to the traditional source control and treatment, including recognition of potential contributions of coastal bivalve shellfish. While policy interest in bivalves has focused primarily on nitrogen removal via biomass harvest, bivalves can also contribute to nitrogen removal by enhancing denitrification (the microbial driven process of bioavailable nitrogen transformation to di-nitrogen gas). Recent evidence suggests that nitrogen removed via enhanced denitrification may eclipse nitrogen removal through biomass harvest alone. With a few exceptions, bivalve-enhanced denitrification has yet to be incorporated into water quality policy. Here, we focus on oysters in considering how this issue may be addressed. We discuss policy options to support expansion of oyster-mediated denitrification, describe the practical considerations for incorporation into nitrogen management, and summarize the current state of the field in accounting for denitrification in oyster habitats. When considered against alternative nitrogen control strategies, we argue that enhanced denitrification associated with oysters should be included in a full suite of nitrogen removal strategies, but with the recognition that denitrification associated with oyster habitats will not alone solve our excess nitrogen loading problem.
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Affiliation(s)
- Julie M. Rose
- NOAA Fisheries, NEFSC Milford Laboratory, 212 Rogers Ave, Milford, CT 06460, USA
| | - J. Stephen Gosnell
- Department of Natural Sciences, Baruch College and the PhD Program in Biology, The Graduate Center of the City University of New York, 17 Lexington Avenue, New York, NY 10010, USA
| | - Suzanne Bricker
- NOAA NCCOS Oxford Laboratory, 904 South Morris Street, Oxford, MD 21654, USA
| | - Mark J. Brush
- Virginia Institute of Marine Science, William & Mary, 1370 Greate Road, Gloucester Point, VA 23062, USA
| | - Allison Colden
- Chesapeake Bay Foundation, 6 Herndon Avenue, Annapolis, MD 21403, USA
| | - Lora Harris
- University of Maryland Center for Environmental Science, 146 Williams Street, Solomons, MD 20688, USA
| | - Eric Karplus
- Science Wares, Inc., 87 Hamlin Ave, Falmouth, MA 02540, USA
| | - Alix Laferriere
- The Nature Conservancy, New Hampshire Chapter, 112 Bay Road, Newmarket, NH 03857, USA
| | - Nathaniel H. Merrill
- Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island, USA
| | - Tammy B. Murphy
- NOAA Fisheries, Northeast Fisheries Science Center, 166 Water Street, Woods Hole, MA 02543, USA
| | - Joshua Reitsma
- Cape Cod Cooperative Extension, County of Barnstable, P.O. Box 367, Barnstable, MA 02630, USA
| | - Johnny Shockley
- Blue Oyster Environmental, LLC, 541 Poplar Street, Cambridge, MD 21613, USA
| | - Kurt Stephenson
- Department of Agricultural and Applied Economics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Seth Theuerkauf
- The Nature Conservancy Provide Food and Water Sustainably Team, 4245 Fairfax Drive, Suite 100, Arlington, VA 22203, USA
- Present address: Office of Aquaculture, NOAA Fisheries, SSMC3, 1315 East West Highway, Silver Spring, MD 20910, USA
| | - Dan Ward
- Ward Aquafarms, 51 N Falmouth Hwy, North Falmouth, MA 02556, USA
| | - Robinson W. Fulweiler
- Department of Biology and Department of Earth and Environment, Boston University, 5 Cummington Mall, Room 101, Boston, MA 02215, USA
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Ayvazian S, Mulvaney K, Zarnoch C, Palta M, Reichert-Nguyen J, McNally S, Pilaro M, Jones A, Terry C, Fulweiler RW. Beyond Bioextraction: The Role of Oyster-Mediated Denitrification in Nutrient Management. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14457-14465. [PMID: 34672569 PMCID: PMC8966756 DOI: 10.1021/acs.est.1c01901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recently, interest has grown in using oyster-mediated denitrification resulting from aquaculture and restoration as mechanisms for reactive nitrogen (N) removal. To date, short-term N removal through bioextraction has received the most management interest, but there is a growing body of research that has shown oysters can also mediate the long-term removal of N through denitrification (the microbial conversion of reactive N to relatively inert dinitrogen (N2) gas). Oyster suspension feeding and ammonium release via waste and deposition of organic matter to the sediments can stimulate nitrification-denitrification near oyster reefs and aquaculture sites. Oysters also harbor a diverse microbial community in their tissue and shell promoting denitrification and thus enhanced N removal. Additionally, surface areas on oyster reefs provide a habitat for other filter-feeding macrofaunal communities that can further enhance denitrification. Denitrification is a complex biogeochemical process that can be difficult to convey to stakeholders. These complexities have limited consideration and inclusion of oyster-mediated denitrification within nutrient management. Although oyster-mediated denitrification will not be a standalone solution to excess N loading, it may provide an additional management tool that can leverage oyster aquaculture and habitat restoration as a N mitigation strategy. Here, we provide an overview of the biogeochemical processes involved in oyster-mediated denitrification and summarize how it could be incorporated into nutrient management efforts by various stakeholders.
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Affiliation(s)
- Suzanne Ayvazian
- Office of Research and Development, Center for Environmental Management and Modeling, Atlantic Coastal Environmental Sciences Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882, United States
| | - Kate Mulvaney
- Office of Research and Development, Center for Environmental Management and Modeling, Atlantic Coastal Environmental Sciences Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882, United States
| | - Chester Zarnoch
- Department of Natural Science, Baruch College, and Ph.D. Program in Biology, Graduate Center, City University of New York, New York City, New York 10016, United States
| | - Monica Palta
- Department of Environmental Studies and Science, Pace University, New York City, New York 10016, United States
| | - Julie Reichert-Nguyen
- NOAA Fisheries, U.S. Department of Commerce, Annapolis, Maryland 21401, United States
- The Oyster Recovery Partnership, Annapolis, Maryland 21401, United States
| | - Sean McNally
- School for the Environment, University of Massachusetts, Boston, Massachusetts 02125, United States
| | - Margaret Pilaro
- Pacific Coast Shellfish Growers Association, Olympia, Washington 98506, United States
| | - Aaron Jones
- School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Chip Terry
- Blue Trace, Castine, Maine 04421, United States
| | - Robinson W Fulweiler
- Department of Earth and Environment, Boston University, Boston, Massachusetts 02215, United States
- Department of Biology, Boston University, Boston, Massachusetts 02215, United States
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King WL, Kaestli M, Siboni N, Padovan A, Christian K, Mills D, Seymour J, Gibb K. Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues. Front Microbiol 2021; 12:723649. [PMID: 34434182 PMCID: PMC8381468 DOI: 10.3389/fmicb.2021.723649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 12/25/2022] Open
Abstract
Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These results suggest that Vibrio species are shared among different pearl oyster tissues. In particular, the similarity between the haemolymph, inside shell and solid tissues, suggests that the haemolymph and inside shell environment is a source of microbial spillover into the oyster tissues, and a potentially useful tool for non-destructive routine disease testing and early warning surveillance. These data provide important foundational information for future studies identifying the factors that drive microbial assembly in a valuable aquaculture species.
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Affiliation(s)
- William L King
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Anna Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Keith Christian
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - David Mills
- Genecology Research Centre, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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20
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Brasell KA, Howarth J, Pearman JK, Fitzsimons SJ, Zaiko A, Pochon X, Vandergoes MJ, Simon K, Wood SA. Lake microbial communities are not resistant or resilient to repeated large-scale natural pulse disturbances. Mol Ecol 2021; 30:5137-5150. [PMID: 34379827 DOI: 10.1111/mec.16110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022]
Abstract
Opportunities to study community level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well resolved sediment pulses, triggered by earthquakes. These paleo-records provide a means to study repeated pulse disturbance and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1,100 years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, c. 50 yrs) phases directly after the earthquakes and more stable (interseismic, c. 250 yr) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrates communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase likely represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.
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Affiliation(s)
- Katie A Brasell
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - Kevin Simon
- University of Auckland, Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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21
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Yeh H, Skubel SA, Patel H, Cai Shi D, Bushek D, Chikindas ML. From Farm to Fingers: an Exploration of Probiotics for Oysters, from Production to Human Consumption. Probiotics Antimicrob Proteins 2021; 12:351-364. [PMID: 32056150 DOI: 10.1007/s12602-019-09629-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oysters hold a unique place within the field of aquaculture as one of the only organisms that is regularly shipped live to be consumed whole and raw. The microbiota of oysters is capable of adapting to a wide range of environmental conditions within their dynamic estuarine environments; however, human aquaculture practices can challenge the resilience of this microbial community. Several discrete stages in oyster cultivation and market processing can cause disruption to the oyster microbiota, thus increasing the possibility of proliferation by pathogens and spoilage bacteria. These same pressure points offer the opportunity for the application of probiotics to help decrease disease occurrence in stocks, improve product yields, minimize the risk of shellfish poisoning, and increase product shelf life. This review provides a summary of the current knowledge on oyster microbiota, the impact of aquaculture upon this community, and the current status of oyster probiotic development. In response to this biotechnological gap, the authors highlight opportunities of highest potential impact within the aquaculture pipeline and propose a strategy for oyster-specific probiotic candidate development.
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Affiliation(s)
- Heidi Yeh
- Haskin Shellfish Research Laboratory, Rutgers State University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
| | - Sarah A Skubel
- Department of Plant Biology, Rutgers State University, New Brunswick, NJ, 08904, USA
| | - Harna Patel
- Department of Plant Biology, Rutgers State University, New Brunswick, NJ, 08904, USA
| | - Denia Cai Shi
- Department of Plant Biology, Rutgers State University, New Brunswick, NJ, 08904, USA
| | - David Bushek
- Haskin Shellfish Research Laboratory, Rutgers State University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Michael L Chikindas
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ, 08904, USA.,Don State Technical University, Rostov-on-Don, 344002, Russia
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22
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Microbiome Analysis Reveals Diversity and Function of Mollicutes Associated with the Eastern Oyster, Crassostrea virginica. mSphere 2021; 6:6/3/e00227-21. [PMID: 33980678 PMCID: PMC8125052 DOI: 10.1128/msphere.00227-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Despite their biological and ecological significance, a mechanistic characterization of microbiome function is frequently missing from many nonmodel marine invertebrates. As an initial step toward filling this gap for the eastern oyster, Crassostrea virginica, this study provides an integrated taxonomic and functional analysis of the oyster microbiome using samples from a coastal salt pond in August 2017. Marine invertebrate microbiomes play important roles in diverse host and ecological processes. However, a mechanistic understanding of host-microbe interactions is currently available for a small number of model organisms. Here, an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica, was performed using 16S rRNA gene-based amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. Relatively high variability of the microbiome was observed across individual oysters and among different tissue types. Specifically, a significantly higher alpha diversity was observed in the inner shell than in the gut, gill, mantle, and pallial fluid samples, and a distinct microbiome composition was revealed in the gut compared to other tissues examined in this study. Targeted metagenomic sequencing of the gut microbiota led to further characterization of a dominant bacterial taxon, the class Mollicutes, which was captured by the reconstruction of a metagenome-assembled genome (MAG). Genome-scale metabolic reconstruction of the oyster Mollicutes MAG revealed a reduced set of metabolic functions and a high reliance on the uptake of host-derived nutrients. A chitin degradation and an arginine deiminase pathway were unique to the MAG compared to closely related genomes of Mollicutes isolates, indicating distinct mechanisms of carbon and energy acquisition by the oyster-associated Mollicutes. A systematic reanalysis of public eastern oyster-derived microbiome data revealed a high prevalence of the Mollicutes among adult oyster guts and a significantly lower relative abundance of the Mollicutes in oyster larvae and adult oyster biodeposits. IMPORTANCE Despite their biological and ecological significance, a mechanistic characterization of microbiome function is frequently missing from many nonmodel marine invertebrates. As an initial step toward filling this gap for the eastern oyster, Crassostrea virginica, this study provides an integrated taxonomic and functional analysis of the oyster microbiome using samples from a coastal salt pond in August 2017. The study identified high variability of the microbiome across tissue types and among individual oysters, with some dominant taxa showing higher relative abundance in specific tissues. A high prevalence of Mollicutes in the adult oyster gut was revealed by comparative analysis of the gut, biodeposit, and larva microbiomes. Phylogenomic analysis and metabolic reconstruction suggested the oyster-associated Mollicutes is closely related but functionally distinct from Mollicutes isolated from other marine invertebrates. To the best of our knowledge, this study represents the first metagenomics-derived functional inference of Mollicutes in the eastern oyster microbiome.
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23
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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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24
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Pathak A, Stothard P, Chauhan A. Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster ( Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column. Microorganisms 2021; 9:490. [PMID: 33673397 PMCID: PMC7996774 DOI: 10.3390/microorganisms9030490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 01/10/2023] Open
Abstract
The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because of their immense metabolic and ecological potential. To obtain a comprehensive understanding on this aspect, we previously reported on the isolation and preliminary genomic characterization of three Pseudomonas species isolated from minced oyster tissue (P. alcaligenes strain OT69); oyster mantle fluid (P. stutzeri strain MF28) and the water collected from top of the oyster reef (P. aeruginosa strain WC55), respectively. In this comparative genomic analysis study conducted on these three targeted pseudomonads, native to the eastern oyster and its surrounding environment, provided further insights into their unique functional traits, conserved gene pools between the selected pseudomonads, as well as genes that render unique characteristics in context to metabolic traits recruited during their evolutionary history via horizontal gene transfer events as well as phage-mediated incorporation of genes. Moreover, the strains also supported extensively developed resistomes, which suggests that environmental microorganisms native to relatively pristine environments, such as Apalachicola Bay, Florida, have also recruited an arsenal of antibiotic resistant gene determinants, thus posing an emerging public health concern.
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Affiliation(s)
- Ashish Pathak
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA;
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada;
| | - Ashvini Chauhan
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA;
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25
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Marzocchi U, Bonaglia S, Zaiko A, Quero GM, Vybernaite-Lubiene I, Politi T, Samuiloviene A, Zilius M, Bartoli M, Cardini U. Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments. Front Microbiol 2021; 11:610269. [PMID: 33542710 PMCID: PMC7851879 DOI: 10.3389/fmicb.2020.610269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Bivalves are ubiquitous filter-feeders able to alter ecosystems functions. Their impact on nitrogen (N) cycling is commonly related to their filter-feeding activity, biodeposition, and excretion. A so far understudied impact is linked to the metabolism of the associated microbiome that together with the host constitute the mussel's holobiont. Here we investigated how colonies of the invasive zebra mussel (Dreissena polymorpha) alter benthic N cycling in the shallow water sediment of the largest European lagoon (the Curonian Lagoon). A set of incubations was conducted to quantify the holobiont's impact and to quantitatively compare it with the indirect influence of the mussel on sedimentary N transformations. Zebra mussels primarily enhanced the recycling of N to the water column by releasing mineralized algal biomass in the form of ammonium and by stimulating dissimilatory nitrate reduction to ammonium (DNRA). Notably, however, not only denitrification and DNRA, but also dinitrogen (N2) fixation was measured in association with the holobiont. The diazotrophic community of the holobiont diverged substantially from that of the water column, suggesting a unique niche for N2 fixation associated with the mussels. At the densities reported in the lagoon, mussel-associated N2 fixation may account for a substantial (and so far, overlooked) source of bioavailable N. Our findings contribute to improve our understanding on the ecosystem-level impact of zebra mussel, and potentially, of its ability to adapt to and colonize oligotrophic environments.
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Affiliation(s)
- Ugo Marzocchi
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Center for Water Technology (WATEC), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anastasija Zaiko
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Grazia M. Quero
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Institute for Biological Resources and Marine Biotechnologies, National Research Council of Italy, Ancona, Italy
| | | | - Tobia Politi
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | | | - Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Chemistry, Life science and Environmental Sustainability, Parma University, Parma, Italy
| | - Ulisse Cardini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
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26
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Stevick RJ, Post AF, Gómez-Chiarri M. Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary. Anim Microbiome 2021; 3:5. [PMID: 33499983 PMCID: PMC7934548 DOI: 10.1186/s42523-020-00066-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 11/29/2020] [Indexed: 01/04/2023] Open
Abstract
Background Oysters in coastal environments are subject to fluctuating environmental conditions that may impact the ecosystem services they provide. Oyster-associated microbiomes are responsible for some of these services, particularly nutrient cycling in benthic habitats. The effects of climate change on host-associated microbiome composition are well-known, but functional changes and how they may impact host physiology and ecosystem functioning are poorly characterized. We investigated how environmental parameters affect oyster-associated microbial community structure and function along a trophic gradient in Narragansett Bay, Rhode Island, USA. Adult eastern oyster, Crassostrea virginica, gut and seawater samples were collected at 5 sites along this estuarine nutrient gradient in August 2017. Samples were analyzed by 16S rRNA gene sequencing to characterize bacterial community structures and metatranscriptomes were sequenced to determine oyster gut microbiome responses to local environments. Results There were significant differences in bacterial community structure between the eastern oyster gut and water samples, suggesting selection of certain taxa by the oyster host. Increasing salinity, pH, and dissolved oxygen, and decreasing nitrate, nitrite and phosphate concentrations were observed along the North to South gradient. Transcriptionally active bacterial taxa were similar for the different sites, but expression of oyster-associated microbial genes involved in nutrient (nitrogen and phosphorus) cycling varied throughout the Bay, reflecting the local nutrient regimes and prevailing environmental conditions. Conclusions The observed shifts in microbial community composition and function inform how estuarine conditions affect host-associated microbiomes and their ecosystem services. As the effects of estuarine acidification are expected to increase due to the combined effects of eutrophication, coastal pollution, and climate change, it is important to determine relationships between host health, microbial community structure, and environmental conditions in benthic communities. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-020-00066-0.
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Affiliation(s)
- Rebecca J Stevick
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Anton F Post
- Division of Research, Florida Atlantic University, Boca Raton, FL, USA
| | - Marta Gómez-Chiarri
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, RI, USA.
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27
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Jiang H, Lan W, Li T, Xu Z, Liu W, Pan K. Isotopic Composition Reveals the Impact of Oyster Aquaculture on Pelagic Nitrogen Cycling in a Subtropical Estuary. WATER RESEARCH 2020; 187:116431. [PMID: 33007671 DOI: 10.1016/j.watres.2020.116431] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
To offset estuarine eutrophication, interest is increasing in restoring oyster reefs and expanding oyster aquaculture. However, ecosystem-scale evidence is lacking on oyster assemblages' impacts on estuarine pelagic nitrogen (N) cycling. Using a multiple-isotope approach and isotope-mixing model, we examined the sources, transformations, and influence of intensive oyster aquaculture on N pollution in a subtropical estuary. The salinity-dependent NO3- and NH4+ concentrations and their correlations with isotopic signals (δ15N-NO3-, δ18O-NO3-, δ15N-NH4+) indicated the nutrient spatial distribution in low-salinity areas was largely regulated by mixing between freshwater and seawater. However, the intensive oyster aquaculture greatly increased nitrification in the estuary. In high-salinity areas where oyster assemblages were absent, the assimilation of NO3- by phytoplankton became dominant and sharply increased the δ15N-NO3- and δ18O-NO3-. Soil organic nitrogen and fertilizer, domestic sewage, and wastewater treatment plants were the major NO3- sources in the estuary, while internal nitrification contributed 20.6% to the NO3- pool. Oyster biodeposits comprised up to one-third of the particulate organic matter in the water column, and as much as 47.3% of the NH4+ pool could be from the oysters. Our study shows that oysters significantly contribute to the pelagic nutrient pools and N transformations, adding an important dimension to our understanding of oyster assemblages' impacts on estuarine N cycling.
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Affiliation(s)
- Hao Jiang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenlu Lan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai 536000, China; Marine Environmental Monitoring Center of Guangxi, Beihai 536000, China
| | - Tianshen Li
- Marine Environmental Monitoring Center of Guangxi, Beihai 536000, China
| | - Zhifang Xu
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Wenjing Liu
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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28
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Dutta A, Smith B, Goldman T, Walker L, Streets M, Eden B, Dirmeier R, Bowman JS. Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring. Front Microbiol 2020; 11:585943. [PMID: 33343524 PMCID: PMC7744764 DOI: 10.3389/fmicb.2020.585943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023] Open
Abstract
Oil souring occurs when H2S is generated in oil reservoirs. This not only leads to operational risks and health hazards but also increases the cost of refining crude oil. Sulfate-reducing microorganisms are considered to be the main source of the H2S that leads to oil souring. Substrate competition between nitrate-reducing and sulfate-reducing microorganisms makes biosouring mitigation via the addition of nitrate salts a viable strategy. This study explores the shift in microbial community across different phases of biosouring and mitigation. Anaerobic sand-filled columns wetted with seawater and/or oil were used to initiate the processes of sulfidogenesis, followed by mitigation with nitrate, rebound sulfidogenesis, and rebound control phases (via nitrate and low salinity treatment). Shifts in microbial community structure and function were observed across different phases of seawater and oil setups. Marine bacterial taxa (Marinobacter, Marinobacterium, Thalassolituus, Alteromonas, and Cycloclasticus) were found to be the initial responders to the application of nitrate during mitigation of sulfidogenesis in both seawater- and oil- wetted columns. Autotrophic groups (Sulfurimonas and Desulfatibacillum) were found to be higher in seawater-wetted columns compared to oil-wetted columns, suggesting the potential for autotrophic volatile fatty acid (VFA) production in oil-field aquifers when seawater is introduced. Results indicate that fermentative (such as Bacteroidetes) and oil-degrading bacteria (such as Desulfobacula toluolica) play an important role in generating electron donors in the system, which may sustain biosouring and nitrate reduction. Persistence of certain microorganisms (Desulfobacula) across different phases was observed, which may be due to a shift in metabolic lifestyle of the microorganisms across phases, or zonation based on nutrient availability in the columns. Overall results suggest mitigation strategies for biosouring can be improved by monitoring VFA concentrations and microbial community dynamics in the oil reservoirs during secondary recovery of oil.
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Affiliation(s)
- Avishek Dutta
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Ben Smith
- BP Upstream Technology, London, United Kingdom
| | | | - Leanne Walker
- Rawwater Engineering Company Ltd., Culcheth, United Kingdom
| | | | - Bob Eden
- Rawwater Engineering Company Ltd., Culcheth, United Kingdom
| | | | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
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29
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Yang C, Ho YN, Inoue C, Chien MF. Long-term effectiveness of microbe-assisted arsenic phytoremediation by Pteris vittata in field trials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140137. [PMID: 32927575 DOI: 10.1016/j.scitotenv.2020.140137] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Phytoremediation is a promising inexpensive method of detoxifying arsenic (As) contaminated soils using plants and associated soil microorganisms. The potential of Pteris vittata to hyperaccumulate As contamination has been investigated widely. Since As(V) is efficiently taken up by P. vittata than As(III), As speciation by associated rhizobacteria could offer enormous possibility to enhance As phytoremediation. Specifically, increased rhizobacteria mediated As(III) to As(V) conversion appeared to be a crucial step in As mobilization and translocation. In this study, Pseudomonasvancouverensis strain m318 with the potential to improve As phytoremediation was inoculated to P. vittata in a field trial for three years to evaluate its long-term efficacy and stability for enhancing As phytoextraction. The biomass, As concentration, and As accumulation of ferns showed to be increased by inoculation treatment. Although this trend occasionally declined which may be accounted to lower As concentration in soil and amount of precipitation during experiments, the potential of inoculation was observed in increased enrichment coefficients. Further, the arsenite oxidase (aioA-like) genes in the rhizosphere were detected to evaluate the influence of inoculation on As phytoremediation. The findings of this study suggested the potential application of rhizosphere regulation to improve phytoremediation technologies for As contaminated soils. However, the conditions which set the efficacy of this method could be further optimized.
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Affiliation(s)
- Chongyang Yang
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan
| | - Ying-Ning Ho
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan
| | - Mei-Fang Chien
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan.
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30
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Zilius M, Bonaglia S, Broman E, Chiozzini VG, Samuiloviene A, Nascimento FJA, Cardini U, Bartoli M. N 2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont. Sci Rep 2020; 10:13966. [PMID: 32811860 PMCID: PMC7435186 DOI: 10.1038/s41598-020-70834-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.
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Affiliation(s)
- Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | | | | | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Ulisse Cardini
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Napoli, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Italy
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31
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The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica. Sci Rep 2020; 10:11088. [PMID: 32632188 PMCID: PMC7338443 DOI: 10.1038/s41598-020-67851-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Long-standing evidence supports the importance of maintaining healthy populations of microbiota for the survival, homeostasis, and complete development of marine mollusks. However, the long-term ecological effects of agricultural runoff on these populations remains largely unknown. Atrazine (6-Chloro-n-ethyl-n'-(1-methylethyl)-triazine-2,4-diamine), a prevalent herbicide in the United States, is often used along tributaries of the Chesapeake Bay where oyster breeding programs are concentrated. To investigate any potential effects atrazine maybe having on mollusk-prokaryote interactions, we used 16S rRNA gene amplicons to evaluate how microbial compositions shift in response to exposure of environmentally relevant concentrations of atrazine previously found within the Chesapeake Bay. The dominant bacterial genera found within all groups included those belonging to Pseudoalteromonas, Burkholderia, Bacteroides, Lactobacillis, Acetobacter, Allobaculum, Ruminococcus, and Nocardia. Our results support previously published findings of a possible core microbial community in Crassostrea virginica. We also report a novel finding: oysters exposed to atrazine concentrations as low as 3 µg/L saw a significant loss of a key mutualistic microbial species and a subsequent colonization of a pathogenic bacteria Nocardia. We conclude that exposure to atrazine in the Chesapeake Bay may be contributing to a significant shift in the microbiomes of juvenile oysters that reduces fitness and impedes natural and artificial repopulation of the oyster species within the Bay.
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32
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Yang C, Ho YN, Makita R, Inoue C, Chien MF. A multifunctional rhizobacterial strain with wide application in different ferns facilitates arsenic phytoremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:134504. [PMID: 31831229 DOI: 10.1016/j.scitotenv.2019.134504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Pteris vittata and Pteris multifida are widely studied As hyperaccumulators that absorb As mainly via roots. Hence, rhizobacteria exhibit promising potential in phytoextraction owing to their immense microbial diversity and interactions with plants. Pseudomonas vancouverensis strain m318 that contains aioA-like genes was screened from P. multifida's rhizosphere through the high As resistance (minimum inhibitory concentrations (MICs) against As(III): 16 mM; MICs against As(V): 320 mM), rapid As oxidation (98% oxidation by bacterial cultures (OD600nm = 1) from 200 μL of 0.1 mM As(III) within 24 h), predominant secretion of IAA (12.45 mg L-1) and siderophores (siderophore unit: 88%). Strain m318 showed significant chemotactic response and high colonization efficiency to P. vittata roots, which suggested its wide host affinity. Interestingly, inoculation with strain m318 enhanced the proportion of aioA-like genes in the rhizosphere. And in field trials, inoculation with strain m318 increased As accumulation in P. vittata by 48-146% and in P. multifida by 42-233%. Post-transplantation inoculations also increased As accumulation in both ferns. The abilities of the isolated multifunctional strain m318 and the increase in the rhizosphere microbial aioA-like genes are thus speculated to be involved in As transformation in the rhizospheres and roots of P. vittata and P. multifida.
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Affiliation(s)
- Chongyang Yang
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan
| | - Ying-Ning Ho
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan; Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan
| | - Ryota Makita
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan
| | - Mei-Fang Chien
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai 980-8579, Japan.
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Yang C, Ho YN, Makita R, Inoue C, Chien MF. Cupriavidus basilensis strain r507, a toxic arsenic phytoextraction facilitator, potentiates the arsenic accumulation by Pteris vittata. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 190:110075. [PMID: 31881405 DOI: 10.1016/j.ecoenv.2019.110075] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 12/07/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
As a toxic and carcinogenic metalloid, arsenic has posed serious threat to human health. Phytoremediation has emerged as a promising approach to circumvent this problem. Arsenic uptake by Pteris vittata is largely determined by arsenic speciation and mainly occurs via roots; thus, rhizospheric microbial activities may play a key role in arsenic accumulation. The aim of this study was to investigate the potential of arsenic resistant rhizobacteria to enhance arsenic phytoextraction. A total of 49 cultivable rhizobacteria were isolated from the arsenic hyperaccumulating fern, Pteris vittata, and subjected to an initial analysis to identify potentially useful traits for arsenic phytoextraction, such as arsenic resistance and the presence of aioA(aroA)-like (arsenite oxidase-like) gene. Isolated strain r507, named as Cupriavidus basilensis strain r507, was a selected candidate for its outstanding arsenic tolerance, rapid arsenite oxidation ability, and strong colonization to P. vittata. Strain r507 was used in co-cultivation trials with P. vittata in the field for six months. Results showed that the inoculation with strain r507 potentiated As accumulation of P. vittata up to 171%. Molecular analysis confirmed that the inoculation increased the abundance of aioA-like genes in the rhizosphere, which might have facilitated arsenite oxidation and absorption. The findings of this study suggested the feasibility of co-cultivating hyperaccumulators with facilitator bacteria for practical arsenic phytoremediation.
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Affiliation(s)
- Chongyang Yang
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai, 980-8579, Japan
| | - Ying-Ning Ho
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai, 980-8579, Japan; Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Ryota Makita
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai, 980-8579, Japan
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai, 980-8579, Japan
| | - Mei-Fang Chien
- Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, 6-6-20 Aoba, Sendai, 980-8579, Japan.
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Bozcal E, Dagdeviren M. Bacterial metagenome analysis of Mytilus galloprovincialis collected from Istanbul and Izmir coastal stations of Turkey. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:186. [PMID: 32072329 DOI: 10.1007/s10661-020-8129-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Mytilus galloprovincialis is a marine mollusk belonging to the Bivalvia class. It has been distributed largely in Turkish shores and worldwide aquatic environments. Besides being known as an environmental pollution indicator, it is highly consumed as a food and has a high economic value. Due to their nutritional mechanisms by filtering water, they are affected by pollution in seawater and mussels can host-microbial diversity of environmental origin as well as pathogenic bacteria. Therefore, in this study, bacterial species found in Mediterranean mussels collected from the coastal stations of Istanbul [Rumeli Kavagi (RK), Kucukcekmece (KC)], and Izmir [(Foca (MF), Urla (MU)] were investigated and compared with microbiological and metagenomic analyses. According to microbiological analysis results, 34 mussel-associated Enterobacteriaceae and Vibrionaceae family members were identified. As a result of the culture-independent metagenomic analysis, taxonomic groups for each station were identified and compared based on Operational Taxonomic Unit data. For all stations, the most abundant bacterial genera were the unclassified bacterial genera. The total number of mussel-related total richness identified in all groups was 4889 (RK = 1605; KC = 1930; MF = 1508; and MU = 1125). According to the metagenomic data obtained in this study, different relative amounts of Lachnospiraceae and Bacteroidetes taxa groups were reported for all stations. The pathogenic bacterial genera identified by metagenomic analyses which may be significant for the public health are Arcobacter, Clostridium, Aeromonas, Vibrio, Escherichia_Shigella, Klebsiella, Campylobacter, Helicobacter, Pseudomonas, Morganella, Serratia, Corynebacterium, Enterococcus, Staphylococcus, Yersinia, Mycoplasma, Brucellaceae_unclassified, Pantoea, and Proteus.
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Affiliation(s)
- Elif Bozcal
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
| | - Melih Dagdeviren
- Department of Biology, Faculty of Science, Ege University, Bornova, 35040, Izmir, Turkey
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Avşar C, Aras ES. Quantification of denitrifier genes population size and its relationship with environmental factors. Arch Microbiol 2020; 202:1181-1192. [PMID: 32076734 DOI: 10.1007/s00203-020-01826-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 108, 2.25 × 107, 2.9 × 105, 4.0 × 106 and 1.75 × 107 copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N2O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.
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Affiliation(s)
- Cumhur Avşar
- Department of Biology, Faculty of Arts and Sciences, Sinop University, Sinop, Turkey.
| | - E Sümer Aras
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
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Zarnoch CB, Hossain N, Fusco E, Alldred M, Hoellein TJ, Perdikaris S. Size and density of upside-down jellyfish, Cassiopea sp., and their impact on benthic fluxes in a Caribbean lagoon. MARINE ENVIRONMENTAL RESEARCH 2020; 154:104845. [PMID: 32056699 DOI: 10.1016/j.marenvres.2019.104845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/12/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Anthropogenic disturbances may be increasing jellyfish populations globally. Epibenthic jellyfish are ideal organisms for studying this phenomenon due to their sessile lifestyle, broad geographic distribution, and prevalence in near-shore coastal environments. There are few studies, however, that have documented epibenthic jellyfish abundance and measured their impact on ecological processes in tropical ecosystems. In this study, the density and size of the upside-down jellyfish (Cassiopea spp.) were measured in Codrington Lagoon, Barbuda. A sediment core incubation study, with and without Cassiopea, also was performed to determine their impact on benthic oxygen and nutrient fluxes. Densities of Cassiopea were 24-168 m-2, among the highest reported values in the literature. Under illuminated conditions, Cassiopea increased oxygen production >300% compared to sediment alone, and they changed sediments from net heterotrophy to net autotrophy. Cassiopea increased benthic ammonium uptake, but reduced nitrate uptake, suggesting they can significantly alter nitrogen cycling. Future studies should quantify the abundance of Cassiopea and measure their impacts on ecosystem processes, in order to further determine how anthropogenic-related changes may be altering the function of tropical coastal ecosystems.
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Affiliation(s)
- Chester B Zarnoch
- Department of Natural Sciences, Baruch College and Graduate Center CUNY, New York, NY, 11510, USA.
| | - Noshin Hossain
- Department of Natural Sciences, Baruch College and Graduate Center CUNY, New York, NY, 11510, USA
| | - Erika Fusco
- Department of Natural Sciences, Baruch College and Graduate Center CUNY, New York, NY, 11510, USA
| | - Mary Alldred
- Center for Earth and Environmental Science, SUNY Plattsburgh, Plattsburgh, NY, 12901, USA
| | - Timothy J Hoellein
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Sophia Perdikaris
- Department of Anthropology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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Tamber S, Montgomery A, Eloranta K, Buenaventura E. Enumeration and Survival of Salmonella enterica in Live Oyster Shellstock Harvested from Canadian Waters. J Food Prot 2020; 83:6-12. [PMID: 31799879 DOI: 10.4315/0362-028x.jfp-19-318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Since 2015, 11 recalls of live oyster shellstock have been issued in Canada due to the presence of Salmonella enterica. Six of those recalls took place in 2018. To understand this increase, fundamental information is needed on the relationship between S. enterica and oysters. The aims of this study were to address important data gaps concerning the levels of Salmonella in naturally contaminated oysters and the ability of this pathogen to survive in live oyster shellstock. Enumeration data were evaluated for five oyster and clam samples collected from the east coast of Canada from 2015 to 2018. The reported levels were <0.0015 to 0.064 most probable number per g of oyster tissue. The S. enterica isolates recovered from these animals belonged to serovars Typhimurium, Infantis, Enteritidis, and I 4,5:i:-. Filter feeding by the oysters was exploited to assess the Salmonella accumulation that would occur following a natural contamination event. Detectable levels of the pathogen were observed after 30 min of exposure and began to plateau at 60 min. A survival study in live oyster shellstock indicated that after 4 days of storage at ambient temperatures, the Salmonella level declined slightly from 4.3 to 3.7 log CFU/g. These data indicate that the levels of Salmonella found in naturally contaminated oysters are low and are not expected to increase between the point of harvest and the point of consumption. The changing ecology of shellfish environments requires continued monitoring and testing to safeguard public health. The data presented here will be useful for the evaluation and design of sampling plans and risk management approaches for the control of Salmonella in live oyster shellstock.
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Affiliation(s)
- Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada K1A 0K9
| | - Alex Montgomery
- Science Branch, Canadian Food Inspection Agency, 3155 Willingdon Green, Burnaby, British Columbia, Canada V5G 4P2
| | - Katie Eloranta
- Science Branch, Canadian Food Inspection Agency, 3155 Willingdon Green, Burnaby, British Columbia, Canada V5G 4P2
| | - Enrico Buenaventura
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada K1A 0K9
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Gut Microbiomes of the Eastern Oyster ( Crassostrea virginica) and the Blue Mussel ( Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities. mSphere 2019; 4:4/6/e00730-19. [PMID: 31826972 PMCID: PMC6908423 DOI: 10.1128/msphere.00730-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment. Gut microbial community structure was evaluated for two species of bivalve molluscs, the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis) collected from Long Island Sound, Connecticut, over the course of a year. These bivalves utilize a shared feeding mechanism, which may result in similar gut microbial communities. Their particle diet, marine aggregates, and surrounding environment, aggregate-free seawater (AFSW), were also collected for comparison. Due to the suspension-feeding activities of bivalves, the potential for aggregate- and AFSW-associated microbiota to influence their microbial communities may be significant. Both taxonomic and functional diversity of the samples were assessed. 16S rRNA gene amplicon sequencing indicated that oysters and mussels maintained similar, but not identical, gut microbiomes, with some temporal variation. Throughout the year, bivalve species had gut microbial community compositions that were more similar to one another than to aggregates. Within a month, bivalves shared on average a quarter of their total operational taxonomic units (OTUs) with each other and a 10th of their total OTUs with aggregates. During months with warm water temperatures, individuals within each of the four sample types had similar alpha diversity, but again, temporal variation was observed. On a functional level, bivalve gut microbial communities exhibited variation attributed to host species and season. Unlike oysters, mussel gut bacterial communities maintained high richness and evenness values throughout the year, even when values for the particle diet and AFSW were reduced. Overall, a core gut bivalve microbiome was present, and it was partially influenced by the marine aggregate microbial community. IMPORTANCE This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.
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Ray NE, Maguire TJ, Al-Haj AN, Henning MC, Fulweiler RW. Low Greenhouse Gas Emissions from Oyster Aquaculture. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:9118-9127. [PMID: 31295406 DOI: 10.1021/acs.est.9b02965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Production of animal protein is associated with high greenhouse gas (GHG) emissions. Globally, oyster aquaculture is increasing as a way to meet growing demands for protein, yet its associated GHG-emissions are largely unknown. We quantified oyster aquaculture GHG-emissions from the three main constituents of GHG-release associated with terrestrial livestock production: fermentation in the animal gut, manure management, and fodder production. We found that oysters release no methane (CH4) and only negligible amounts of nitrous oxide (0.00012 ± 0.00004 μmol N2O gDW-1 hr-1) and carbon dioxide (3.556 ± 0.471 μmol CO2 gDW-1 hr-1). Further, sediment fluxes of N2O and CH4 were unchanged in the presence of oyster aquaculture, regardless of the length of time it had been in place. Sediment CO2 release was slightly stimulated between 4 and 6 years of aquaculture presence and then returned to baseline levels but was not significantly different between aquaculture and a control site when all ages of culture were pooled. There is no GHG-release from oyster fodder production. Considering the main drivers of GHG-release in terrestrial livestock systems, oyster aquaculture has less than 0.5% of the GHG-cost of beef, small ruminants, pork, and poultry in terms of CO2-equivalents per kg protein, suggesting that shellfish aquaculture may provide a a low GHG alternative for future animal protein production compared to land based sources. We estimate that if 10% of the protein from beef consumption in the United States was replaced with protein from oysters, the GHG savings would be equivalent to 10.8 million fewer cars on the road.
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Affiliation(s)
- Nicholas E Ray
- Department of Biology , Boston University , 5 Cummington Mall , Boston , Massachusetts 02215 , United States
| | - Timothy J Maguire
- Department of Biology , Boston University , 5 Cummington Mall , Boston , Massachusetts 02215 , United States
- Great Lakes Institute for Environmental Research , University of Windsor , Windsor , ON N9B 3P4 , Canada
| | - Alia N Al-Haj
- Department of Earth and Environment , Boston University , 685 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
| | - Maria C Henning
- Department of Earth and Environment , Boston University , 685 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
| | - Robinson W Fulweiler
- Department of Biology , Boston University , 5 Cummington Mall , Boston , Massachusetts 02215 , United States
- Department of Earth and Environment , Boston University , 685 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
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Pathirana E, McPherson A, Whittington R, Hick P. The role of tissue type, sampling and nucleic acid purification methodology on the inferred composition of Pacific oyster (Crassostrea gigas) microbiome. J Appl Microbiol 2019; 127:429-444. [PMID: 31102430 DOI: 10.1111/jam.14326] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/05/2019] [Accepted: 05/13/2019] [Indexed: 01/02/2023]
Abstract
AIMS This study evaluated methods to sample and extract nucleic acids from Pacific oysters to accurately determine the microbiome associated with different tissues. METHODS AND RESULTS Samples were collected from haemolymph, gill, gut and adductor muscle, using swabs and homogenates of solid tissues. Nucleic acids were extracted from fresh and frozen samples using three different commercial kits. The bacterial DNA yield varied between methods (P < 0·05) and each tissue harboured a unique microbiota, except for gill and muscle. Higher bacterial DNA yields were obtained by swabbing compared to tissue homogenates and from fresh tissues compared to frozen tissues, without impacting the bacterial community composition estimated by 16S rRNA gene (V1-V3 region) sequencing. Despite the higher bacterial DNA yields with QIAamp® DNA Microbiome Kit, the E.Z.N.A.® Mollusc DNA Kit identified twice as many operational taxonomic units (OTUs) and eliminated PCR inhibition from gut tissues. CONCLUSIONS Sampling and nucleic acid purification substantially affected the quantity and diversity of bacteria identified in Pacific oyster microbiome studies and a fit-for-purpose strategy is recommended. SIGNIFICANCE AND IMPACT OF THE STUDY Accurate identification of Pacific oyster microbial diversity is instrumental for understanding the polymicrobial aetiology of Pacific oyster mortality diseases which greatly impact oyster production.
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Affiliation(s)
- E Pathirana
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW, Australia
| | - A McPherson
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW, Australia
| | - R Whittington
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW, Australia
| | - P Hick
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW, Australia
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Neu AT, Allen EE, Roy K. Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:434-447. [PMID: 30834681 DOI: 10.1111/1758-2229.12743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/02/2019] [Indexed: 06/09/2023]
Abstract
Marine biogeographic boundaries act as barriers to dispersal for many animal species, thereby creating distinctive faunas on either side. However, how such boundaries affect the distributions of microbial taxa remains poorly known. To test whether biogeographic boundaries influence the diversity and composition of host-associated microbiota, we analysed the microbiomes of three species of common intertidal gastropods at two sites separated by the biogeographic boundary at Point Conception (PtC), CA, using 16S rRNA gene sequencing. Our results show that each host species shows microbiome compositional specificity, even across PtC, and that alpha diversity does not change significantly across this boundary for any of the gastropod hosts. However, for two of the host species, beta diversity differs significantly across PtC, indicating that there may be multiple levels of organization of the marine gastropod microbiome. Overall, our results suggest that while biogeographic boundaries do not constrain the distribution of a core set of microbes associated with each host species, they can play a role in structuring the transient portion of the microbiome.
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Affiliation(s)
- Alexander T Neu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
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Fernández Robledo JA, Yadavalli R, Allam B, Pales Espinosa E, Gerdol M, Greco S, Stevick RJ, Gómez-Chiarri M, Zhang Y, Heil CA, Tracy AN, Bishop-Bailey D, Metzger MJ. From the raw bar to the bench: Bivalves as models for human health. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:260-282. [PMID: 30503358 PMCID: PMC6511260 DOI: 10.1016/j.dci.2018.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/09/2018] [Accepted: 11/24/2018] [Indexed: 05/05/2023]
Abstract
Bivalves, from raw oysters to steamed clams, are popular choices among seafood lovers and once limited to the coastal areas. The rapid growth of the aquaculture industry and improvement in the preservation and transport of seafood have enabled them to be readily available anywhere in the world. Over the years, oysters, mussels, scallops, and clams have been the focus of research for improving the production, managing resources, and investigating basic biological and ecological questions. During this decade, an impressive amount of information using high-throughput genomic, transcriptomic and proteomic technologies has been produced in various classes of the Mollusca group, and it is anticipated that basic and applied research will significantly benefit from this resource. One aspect that is also taking momentum is the use of bivalves as a model system for human health. In this review, we highlight some of the aspects of the biology of bivalves that have direct implications in human health including the shell formation, stem cells and cell differentiation, the ability to fight opportunistic and specific pathogens in the absence of adaptive immunity, as source of alternative drugs, mucosal immunity and, microbiome turnover, toxicology, and cancer research. There is still a long way to go; however, the next time you order a dozen oysters at your favorite raw bar, think about a tasty model organism that will not only please your palate but also help unlock multiple aspects of molluscan biology and improve human health.
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Affiliation(s)
| | | | - Bassem Allam
- Stony Brook University, School of Marine and Atmospheric Sciences, Stony Brook, NY, 11794, USA
| | | | - Marco Gerdol
- University of Trieste, Department of Life Sciences, 34127, Trieste, Italy
| | - Samuele Greco
- University of Trieste, Department of Life Sciences, 34127, Trieste, Italy
| | - Rebecca J Stevick
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, 02882, USA
| | - Marta Gómez-Chiarri
- University of Rhode Island, Department of Fisheries, Animal and Veterinary Science, Kingston, RI, 02881, USA
| | - Ying Zhang
- University of Rhode Island, Department of Cell and Molecular Biology, Kingston, RI, 02881, USA
| | - Cynthia A Heil
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Adrienne N Tracy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA; Colby College, Waterville, 4,000 Mayflower Hill Dr, ME, 04901, USA
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Genome Analysis of the Marine Bacterium Labrenzia sp. Strain 011, a Potential Protective Agent of Mollusks. DATA 2019. [DOI: 10.3390/data4010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The marine bacterium Labrenzia sp. strain 011 was isolated from the coastal sediment of Kronsgaard, Germany. The Labrenzia species are suggested to be protective agents of mollusks. Labrenzia sp. strain 011 produces specialized metabolites, which showed activity against a range of microorganisms, thereunder strong inhibitory effects against Pseudoroseovarius crassostreae DSM 16,950 (genus Roseovarius), the causative agent of oyster disease. The genome of Labrenzia sp. strain 011 was sequenced and assembled into 65 contigs, has a size of 5.1 Mbp, and a G+C content of 61.6%. A comparative genome analysis defined Labrenzia sp. strain 011 as a distinct new species within the genus Labrenzia, whereby 44% of the genome was contributed to the Labrenzia core genome. The genomic data provided here is expected to contribute to a deeper understanding of the mollusk-protective role of Labrenzia spp.
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Murphy AE, Kolkmeyer R, Song B, Anderson IC, Bowen J. Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves. MICROBIAL ECOLOGY 2019; 77:343-357. [PMID: 30612185 DOI: 10.1007/s00248-018-01312-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.
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Affiliation(s)
- Anna E Murphy
- Marine Science Center, Northeastern University, Nahant, MA, 01908, USA.
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA.
| | | | - Bongkuen Song
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Iris C Anderson
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Jennifer Bowen
- Marine Science Center, Northeastern University, Nahant, MA, 01908, USA
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Jackson M, Owens MS, Cornwell JC, Kellogg ML. Comparison of methods for determining biogeochemical fluxes from a restored oyster reef. PLoS One 2018; 13:e0209799. [PMID: 30586465 PMCID: PMC6306202 DOI: 10.1371/journal.pone.0209799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/11/2018] [Indexed: 11/24/2022] Open
Abstract
Oyster reef restoration can significantly increase benthic denitrification rates. Methods applied to measure nutrient fluxes and denitrification from oyster reefs in previous studies include incubations of sediment cores collected adjacent to oyster clumps, benthic chambers filled with intact reef segments that have undergone in situ equilibration and ex situ incubation, and cores with single oysters. However, fluxes of nutrients vary by orders of magnitude among oyster reefs and methods. This study compares two methods of measuring nutrient and metabolic fluxes on restored oyster reefs: incubations including intact segments of oyster reef and incubations containing oyster clumps without underlying sediments. Fluxes of oxygen (O2), dissolved inorganic carbon (DIC), ammonium (NH4+), combined nitrate and nitrite (NO2/3-), di-nitrogen (N2), and soluble reactive phosphorus (SRP) were determined in June and August in Harris Creek, a tributary of the Chesapeake Bay, Maryland, USA. Regression of fluxes measured from clumps alone against those measured from intact reef segments showed significant positive relationships for O2, DIC, NH4+, and SRP (R2 = 0.920, 0.61, 0.26, and 0.52, respectively). Regression of clump fluxes against the oyster tissue biomass indicates significant positive relationships for O2 and NH4+, marginally significant and positive relationships for DIC and N2, and no significant relationship for NO2/3- or SRP. Although these results demonstrate that the incubation of oyster clumps without underlying sediments does not accurately represent biogeochemical fluxes measured from the whole oyster and sediment community, this work supports the need to understand the balance between the metabolism of oysters and local sediments to correctly estimate biogeochemical rates.
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Affiliation(s)
- Melanie Jackson
- University of Maryland Center for Environmental Science, Horn Point Laboratory, Cambridge, Maryland, United States of America
| | - Michael S Owens
- University of Maryland Center for Environmental Science, Horn Point Laboratory, Cambridge, Maryland, United States of America
| | - Jeffrey C Cornwell
- University of Maryland Center for Environmental Science, Horn Point Laboratory, Cambridge, Maryland, United States of America
| | - M Lisa Kellogg
- Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, United States of America
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Nakagawa T, Tsuchiya Y, Ueda S, Fukui M, Takahashi R. Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan. Microbes Environ 2018; 34:13-22. [PMID: 30504642 PMCID: PMC6440730 DOI: 10.1264/jsme2.me18103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.
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Affiliation(s)
| | | | - Shingo Ueda
- College of Bioresource Sciences, Nihon University
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University
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Amiri Moghaddam J, Dávila-Céspedes A, Kehraus S, Crüsemann M, Köse M, Müller CE, König GM. Cyclopropane-Containing Fatty Acids from the Marine Bacterium Labrenzia sp. 011 with Antimicrobial and GPR84 Activity. Mar Drugs 2018; 16:md16100369. [PMID: 30297608 PMCID: PMC6213206 DOI: 10.3390/md16100369] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 11/23/2022] Open
Abstract
Bacteria of the family Rhodobacteraceae are widespread in marine environments and known to colonize surfaces, such as those of e.g., oysters and shells. The marine bacterium Labrenzia sp. 011 is here investigated and it was found to produce two cyclopropane-containing medium-chain fatty acids (1, 2), which inhibit the growth of a range of bacteria and fungi, most effectively that of a causative agent of Roseovarius oyster disease (ROD), Pseudoroseovarius crassostreae DSM 16950. Additionally, compound 2 acts as a potent partial, β-arrestin-biased agonist at the medium-chain fatty acid-activated orphan G-protein coupled receptor GPR84, which is highly expressed on immune cells. The genome of Labrenzia sp. 011 was sequenced and bioinformatically compared with those of other Labrenzia spp. This analysis revealed several cyclopropane fatty acid synthases (CFAS) conserved in all Labrenzia strains analyzed and a putative gene cluster encoding for two distinct CFASs is proposed as the biosynthetic origin of 1 and 2.
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Affiliation(s)
| | | | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
| | - Meryem Köse
- Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Gabriele Maria König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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Semedo M, Song B, Sparrer T, Phillips RL. Antibiotic Effects on Microbial Communities Responsible for Denitrification and N 2O Production in Grassland Soils. Front Microbiol 2018; 9:2121. [PMID: 30254616 PMCID: PMC6141661 DOI: 10.3389/fmicb.2018.02121] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N2O) and dinitrogen (N2) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N2O and N2 production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N2O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference. Soil samples treated with tetracycline generated 12 times more N2O, but N2 production was reduced by 84% compared to the control. In parallel with greater N2O production, we observed an increase in the fungi:bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected. NosZ-II-carrying Bacillus spp. (Firmicutes) and Anaeromyxobacter spp. (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N2O sink in grassland soils. Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N2O production due to the inhibitory effects on nosZ-II-carrying communities.
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Affiliation(s)
- Miguel Semedo
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA, United States
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA, United States
| | - Tavis Sparrer
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA, United States
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