1
|
de Vogel FA, Goudriaan M, Zettler ER, Niemann H, Eich A, Weber M, Lott C, Amaral-Zettler LA. Biodegradable plastics in Mediterranean coastal environments feature contrasting microbial succession. Sci Total Environ 2024; 928:172288. [PMID: 38599394 DOI: 10.1016/j.scitotenv.2024.172288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/09/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
Plastic pollution of the ocean is a top environmental concern. Biodegradable plastics present a potential "solution" in combating the accumulation of plastic pollution, and their production is currently increasing. While these polymers will contribute to the future plastic marine debris budget, very little is known still about the behavior of biodegradable plastics in different natural environments. In this study, we molecularly profiled entire microbial communities on laboratory confirmed biodegradable polybutylene sebacate-co-terephthalate (PBSeT) and polyhydroxybutyrate (PHB) films, and non-biodegradable conventional low-density polyethylene (LDPE) films that were incubated in situ in three different coastal environments in the Mediterranean Sea. Samples from a pelagic, benthic, and eulittoral habitat were taken at five timepoints during an incubation period of 22 months. We assessed the presence of potential biodegrading bacterial and fungal taxa and contrasted them against previously published in situ disintegration data of these polymers. Scanning electron microscopy imaging complemented our molecular data. Putative plastic degraders occurred in all environments, but there was no obvious "core" of shared plastic-specific microbes. While communities varied between polymers, the habitat predominantly selected for the underlying communities. Observed disintegration patterns did not necessarily match community patterns of putative plastic degraders.
Collapse
Affiliation(s)
- Fons A de Vogel
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands
| | - Maaike Goudriaan
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands
| | - Erik R Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.115, 3508 TC Utrecht, the Netherlands; CAGE-Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, 9037 Tromsø, Norway
| | - Andreas Eich
- HYDRA Marine Sciences GmbH, D-77815 Bühl, Germany
| | - Miriam Weber
- HYDRA Marine Sciences GmbH, D-77815 Bühl, Germany
| | | | - Linda A Amaral-Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands; Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, the Netherlands.
| |
Collapse
|
2
|
Bos RP, Kaul D, Zettler ER, Hoffman JM, Dupont CL, Amaral-Zettler LA, Mincer TJ. Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients. Environ Microbiol 2023; 25:2761-2775. [PMID: 37132662 DOI: 10.1111/1462-2920.16391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/19/2023] [Indexed: 05/04/2023]
Abstract
Little is known about early plastic biofilm assemblage dynamics and successional changes over time. By incubating virgin microplastics along oceanic transects and comparing adhered microbial communities with those of naturally occurring plastic litter at the same locations, we constructed gene catalogues to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were reproducibly dominated by Alteromonadaceae and harboured significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, hydrocarbon degradation and motility. Comparative genomic analyses among the Alteromonadaceae metagenome assembled genomes (MAGs) highlighted the importance of the mannose-sensitive hemagglutinin (MSHA) operon, recognized as a key factor for intestinal colonization, for early colonization of hydrophobic plastic surfaces. Synteny alignments of MSHA also demonstrated positive selection for mshA alleles across all MAGs, suggesting that mshA provides a competitive advantage for surface colonization and nutrient acquisition. Large-scale genomic characteristics of early colonizers varied little, despite environmental variability. Mature plastic biofilms were composed of predominantly Rhodobacteraceae and displayed significantly higher proportions of carbohydrate hydrolysis enzymes and genes for photosynthesis and secondary metabolism. Our metagenomic analyses provide insight into early biofilm formation on plastics in the ocean and how early colonizers self-assemble, compared to mature, phylogenetically and metabolically diverse biofilms.
Collapse
Affiliation(s)
- Ryan P Bos
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, USA
| | - Drishti Kaul
- Environmental Sustainability, J. Craig Venter Institute, La Jolla, California, USA
| | - Erik R Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Jeffrey M Hoffman
- Environmental Sustainability, J. Craig Venter Institute, La Jolla, California, USA
| | - Christopher L Dupont
- Environmental Sustainability, J. Craig Venter Institute, La Jolla, California, USA
| | - Linda A Amaral-Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Tracy J Mincer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, USA
- Department of Biology, Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, USA
| |
Collapse
|
3
|
Mincer TJ, Bos RP, Zettler ER, Zhao S, Asbun AA, Orsi WD, Guzzetta VS, Amaral-Zettler LA. Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat. Water Res 2023; 242:120033. [PMID: 37244770 DOI: 10.1016/j.watres.2023.120033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/25/2023] [Accepted: 05/01/2023] [Indexed: 05/29/2023]
Abstract
We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic Ocean. Annotation and mapping of these 16 bacterial genome sequences to a PMD-derived Vibrio metagenome-assembled genome created for this study showcased vertebrate pathogen genes closely-related to cholera and non-cholera pathovars. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic, and lipophospholytic activities, consistent with pathogenic potential. Our study illustrates that open ocean vibrios represent a heretofore undescribed group of microbes, some representing potential new species, possessing an amalgam of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize.
Collapse
Affiliation(s)
- Tracy J Mincer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA; Department of Biology, Wilkes Honors College, Florida Atlantic University, Jupiter, FL, USA.
| | - Ryan P Bos
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Erik R Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Shiye Zhao
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushimacho, Yokosuka 237-0061, Japan
| | - Alejandro A Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology,Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | | | - Linda A Amaral-Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands; Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands; Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
| |
Collapse
|
4
|
Zhao S, Zettler ER, Bos RP, Lin P, Amaral-Zettler LA, Mincer TJ. Large quantities of small microplastics permeate the surface ocean to abyssal depths in the South Atlantic Gyre. Glob Chang Biol 2022; 28:2991-3006. [PMID: 35048454 DOI: 10.1111/gcb.16089] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/20/2021] [Accepted: 01/11/2022] [Indexed: 05/22/2023]
Abstract
Hundreds of studies have surveyed plastic debris in surface ocean gyre and convergence zones, however, comprehensive microplastics (MPs, ≤5 mm) assessments beneath these surface accumulation areas are lacking. Using in situ high-volume filtration, Manta net and MultiNet sampling, combined with micro-Fourier-transform-infrared imaging, we discovered a high abundance (up to 244.3 pieces per cubic meter [n m-3 ]) of small microplastics (SMPs, characteristically <100 μm) from the surface to near-sea floor waters of the remote South Atlantic Subtropical Gyre. Large horizontal and vertical variations in the abundances of SMP were observed, displaying inverse vertical trends in some cases. SMP abundances in pump samples were more than two orders of magnitude higher than large microplastics (LMPs, >300 μm) concurrently collected in MultiNet samples. Higher-density polymers (e.g., alkyd resins and polyamide) comprised >65% of the total pump sample count, highlighting a discrepancy between polymer compositions from previous ocean surface-based surveys, typically dominated by buoyant polymers such as polyethylene and polypropylene. Contrary to previous reports stating LMP preferentially accumulated at density gradients, SMP with presumably slower sinking rates are much less influenced by density gradients, thus resulting in a more even vertical distribution in the water column, and potentially longer residence times. Overall, our findings suggest that SMP is a critical and largely underexplored constituent of the oceanic plastic inventory. Additionally, our data support that weak current systems contribute to the formation of SMP hotspots at depth, implying a higher encounter rate for subsurface particle feeders. Our study unveils the prevalence of plastics in the entire water column, highlighting the urgency for more quantification of the deep-ocean MP, particularly the smaller size fraction, to better understand ecosystem exposure and to predict MP fate and impacts.
Collapse
Affiliation(s)
- Shiye Zhao
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, USA
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Erik R Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Ryan P Bos
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, USA
| | - Peigen Lin
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Linda A Amaral-Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Tracy J Mincer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, USA
- Department of Biology, Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, USA
| |
Collapse
|
5
|
Amaral-Zettler LA, Ballerini T, Zettler ER, Asbun AA, Adame A, Casotti R, Dumontet B, Donnarumma V, Engelmann JC, Frère L, Mansui J, Philippon M, Pietrelli L, Sighicelli M. Diversity and predicted inter- and intra-domain interactions in the Mediterranean Plastisphere. Environ Pollut 2021; 286:117439. [PMID: 34438479 DOI: 10.1016/j.envpol.2021.117439] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/21/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the biogeography, the presence and diversity of potentially harmful taxa harbored, and potential interactions between and within bacterial and eukaryotic domains of life on plastic debris in the Mediterranean. Using a combination of high-throughput DNA sequencing (HTS), Causal Network Analysis, and Scanning Electron Microscopy (SEM), we show regional differences and gradients in the Mediterranean microbial communities associated with marine litter, positive causal effects between microbes including between and within domains of life, and how these might impact the marine ecosystems surrounding them. Adjacent seas within the Mediterranean region showed a gradient in the microbial communities on plastic with non-overlapping endpoints (Adriatic and Ligurian Seas). The largest predicted inter-domain effects included positive effects of a novel red-algal Plastisphere member on its potential microbiome community. Freshwater and marine samples housed a diversity of fungi including some related to disease-causing microbes. Algal species related to those responsible for Harmful Blooms (HABs) were also observed on plastic pieces including members of genera not previously reported on Plastic Marine Debris (PMD).
Collapse
Affiliation(s)
- Linda A Amaral-Zettler
- NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB, Den Burg (Texel), The Netherlands; Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.
| | - Tosca Ballerini
- Association "Expédition MED" - Mer En Danger, 4, Allée des Avettes, 56230, Questembert, France; Thalassa - Marine Research and Science Communication, 40 Rue Francis Davso, 13001, Marseille, France
| | - Erik R Zettler
- NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB, Den Burg (Texel), The Netherlands
| | - Alejandro Abdala Asbun
- NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB, Den Burg (Texel), The Netherlands
| | - Alvaro Adame
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Raffaella Casotti
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Bruno Dumontet
- Association "Expédition MED" - Mer En Danger, 4, Allée des Avettes, 56230, Questembert, France
| | | | - Julia C Engelmann
- NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB, Den Burg (Texel), The Netherlands
| | - Laura Frère
- Association "Expédition MED" - Mer En Danger, 4, Allée des Avettes, 56230, Questembert, France
| | - Jeremy Mansui
- Association "Expédition MED" - Mer En Danger, 4, Allée des Avettes, 56230, Questembert, France
| | - Marion Philippon
- Association "Expédition MED" - Mer En Danger, 4, Allée des Avettes, 56230, Questembert, France
| | - Loris Pietrelli
- Chemistry Department - Sapienza University of Rome, P.le Aldo Moro 5, 00185, Roma, Italy
| | - Maria Sighicelli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) CR Casaccia, Via Anguillarese 301, 00123, Rome, Italy
| |
Collapse
|
6
|
Amaral-Zettler LA, Zettler ER, Mincer TJ, Klaassen MA, Gallager SM. Biofouling impacts on polyethylene density and sinking in coastal waters: A macro/micro tipping point? Water Res 2021; 201:117289. [PMID: 34102596 DOI: 10.1016/j.watres.2021.117289] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/06/2021] [Accepted: 05/22/2021] [Indexed: 05/21/2023]
Abstract
Biofouling causing an increase in plastic density and sinking is one of the hypotheses to account for the unexpectedly low amount of buoyant plastic debris encountered at the ocean surface. Field surveys show that polyethylene and polypropylene, the two most abundant buoyant plastics, both occur below the surface and in sediments, and experimental studies confirm that biofouling can cause both of these plastics to sink. However, studies quantifying the actual density of fouled plastics are rare, despite the fact that density will determine the transport and eventual fate of plastic in the ocean. Here we investigated the role of microbial biofilms in sinking of polyethylene microplastic and quantified the density changes natural biofouling communities cause in the coastal waters of the North Sea. Molecular data confirmed the variety of bacteria and eukaryotes (including animals and other multicellular organisms) colonizing the plastic over time. Fouling communities increased the density of plastic and caused sinking, and the plastic remained negatively buoyant even during the winter with lower growth rates. Relative surface area alone, however, did not predict whether a plastic piece sank. Due to patchy colonization, fragmentation of sinking pieces may result in smaller pieces regaining buoyancy and returning to the surface. Our results suggest that primarily multicellular organisms cause sinking of plastic pieces with surface area to volume ratios (SA:V) below 100 (generally pieces above a couple hundred micrometers in size), and that this is a "tipping point" at which microbial biofilms become the key players causing sinking of smaller pieces with higher SA:V ratios, including most fibers that are too small for larger (multicellular) organisms to colonize.
Collapse
Affiliation(s)
- Linda A Amaral-Zettler
- NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands; Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, The University of Amsterdam, 1090 GE Amsterdam, The Netherlands; The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Erik R Zettler
- NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands
| | - Tracy J Mincer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL 34946, USA
| | - Michiel A Klaassen
- NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands; Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, The University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | | |
Collapse
|
7
|
Abstract
The plastisphere, which comprises the microbial community on plastic debris, rivals that of the built environment in spanning multiple biomes on Earth. Although human-derived debris has been entering the ocean for thousands of years, microplastics now numerically dominate marine debris and are primarily colonized by microbial and other microscopic life. The realization that this novel substrate in the marine environment can facilitate microbial dispersal and affect all aquatic ecosystems has intensified interest in the microbial ecology and evolution of this biotope. Whether a 'core' plastisphere community exists that is specific to plastic is currently a topic of intense investigation. This Review provides an overview of the microbial ecology of the plastisphere in the context of its diversity and function, as well as suggesting areas for further research.
Collapse
Affiliation(s)
- Linda A Amaral-Zettler
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands. .,The University of Amsterdam, Amsterdam, The Netherlands.
| | - Erik R Zettler
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands
| | - Tracy J Mincer
- Wilkes Honors College and Harbor Branch Oceanographic Institute, Florida Atlantic University, Boca Raton, FL, USA
| |
Collapse
|
8
|
Schlundt C, Mark Welch JL, Knochel AM, Zettler ER, Amaral-Zettler LA. Spatial structure in the "Plastisphere": Molecular resources for imaging microscopic communities on plastic marine debris. Mol Ecol Resour 2019; 20:620-634. [PMID: 31782619 PMCID: PMC7318237 DOI: 10.1111/1755-0998.13119] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/21/2019] [Accepted: 11/05/2019] [Indexed: 12/01/2022]
Abstract
Plastic marine debris (PMD) affects spatial scales of life from microbes to whales. However, understanding interactions between plastic and microbes in the “Plastisphere”—the thin layer of life on the surface of PMD—has been technology‐limited. Research into microbe–microbe and microbe–substrate interactions requires knowledge of community phylogenetic composition but also tools to visualize spatial distributions of intact microbial biofilm communities. We developed a CLASI‐FISH (combinatorial labelling and spectral imaging – fluorescence in situ hybridization) method using confocal microscopy to study Plastisphere communities. We created a probe set consisting of three existing phylogenetic probes (targeting all Bacteria, Alpha‐, and Gammaproteobacteria) and four newly designed probes (targeting Bacteroidetes, Vibrionaceae, Rhodobacteraceae and Alteromonadaceae) labelled with a total of seven fluorophores and validated this probe set using pure cultures. Our nested probe set strategy increases confidence in taxonomic identification because targets are confirmed with two or more probes, reducing false positives. We simultaneously identified and visualized these taxa and their spatial distribution within the microbial biofilms on polyethylene samples in colonization time series experiments in coastal environments from three different biogeographical regions. Comparing the relative abundance of 16S rRNA gene amplicon sequencing data with cell‐count abundance data retrieved from the microscope images of the same samples showed a good agreement in bacterial composition. Microbial communities were heterogeneous, with direct spatial relationships between bacteria, cyanobacteria and eukaryotes such as diatoms but also micro‐metazoa. Our research provides a valuable resource to investigate biofilm development, succession and associations between specific microscopic taxa at micrometre scales.
Collapse
Affiliation(s)
- Cathleen Schlundt
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Jessica L Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Anna M Knochel
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Erik R Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Texel, The Netherlands
| | - Linda A Amaral-Zettler
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Texel, The Netherlands.,Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
9
|
Amaral-Zettler LA, Dragone NB, Schell J, Slikas B, Murphy LG, Morrall CE, Zettler ER. Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent "Golden Tides" in the Western Atlantic. Ecol Evol 2016; 7:516-525. [PMID: 28116048 PMCID: PMC5243773 DOI: 10.1002/ece3.2630] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022] Open
Abstract
Over the past 5 years, massive accumulations of holopelagic species of the brown macroalga Sargassum in coastal areas of the Caribbean have created “golden tides” that threaten local biodiversity and trigger economic losses associated with beach deterioration and impact on fisheries and tourism. In 2015, the first report identifying the cause of these extreme events implicated a rare form of the holopelagic species Sargassum natans (form VIII). However, since the first mention of S. natans VIII in the 1930s, based solely on morphological characters, no molecular data have confirmed this identification. We generated full‐length mitogenomes and partial chloroplast genomes of all representative holopelagic Sargassum species, S. fluitans III and S. natans I alongside the putatively rare S. natans VIII, to demonstrate small but consistent differences between S. natans I and VIII (7 bp differences out of the 34,727). Our comparative analyses also revealed that both S. natans I and S. natans VIII share a very close phylogenetic relationship with S. fluitans III (94‐ and 96‐bp differences of 34,727). We designed novel primers that amplified regions of the cox2 and cox3 marker genes with consistent polymorphic sites that enabled differentiation between the two S. natans forms (I and VIII) from each other and both from S. fluitans III in over 150 Sargassum samples including those from the 2014 golden tide event. Despite remarkable gene synteny and sequence conservation, the three Sargassum forms differ in morphology, ecology, and distribution patterns, warranting more extensive interrogation of holopelagic Sargassum genomes as a whole.
Collapse
Affiliation(s)
- Linda A Amaral-Zettler
- Marine Biological Laboratory Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole MA USA; Department of Earth, Environmental, and Planetary Sciences Brown University Providence RI USA
| | | | | | - Beth Slikas
- Marine Biological Laboratory Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole MA USA
| | - Leslie G Murphy
- Marine Biological Laboratory Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole MA USA
| | | | - Erik R Zettler
- Sea Education Association Woods Hole MA USA; Oekologia Environmental Research & Education Falmouth MA USA
| |
Collapse
|
10
|
Law KL, Morét-Ferguson SE, Goodwin DS, Zettler ER, Deforce E, Kukulka T, Proskurowski G. Distribution of surface plastic debris in the eastern Pacific Ocean from an 11-year data set. Environ Sci Technol 2014; 48:4732-8. [PMID: 24708264 DOI: 10.1021/es4053076] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We present an extensive survey of floating plastic debris in the eastern North and South Pacific Oceans from more than 2500 plankton net tows conducted between 2001 and 2012. From these data we defined an accumulation zone (25 to 41 °N, 130 to 180 °W) in the North Pacific subtropical gyre that closely corresponds to centers of accumulation resulting from the convergence of ocean surface currents predicted by several oceanographic numerical models. Maximum plastic concentrations from individual surface net tows exceeded 10(6) pieces km(-2), with concentrations decreasing with increasing distance from the predicted center of accumulation. Outside the North Pacific subtropical gyre the median plastic concentration was 0 pieces km(-2). We were unable to detect a robust temporal trend in the data set, perhaps because of confounded spatial and temporal variability. Large spatiotemporal variability in plastic concentration causes order of magnitude differences in summary statistics calculated over short time periods or in limited geographic areas. Utilizing all available plankton net data collected in the eastern Pacific Ocean (17.4 °S to 61.0 °N; 85.0 to 180.0 °W) since 1999, we estimated a minimum of 21,290 t of floating microplastic.
Collapse
Affiliation(s)
- Kara Lavender Law
- Sea Education Association, P.O. Box 6, Woods Hole, Massachusetts 02543, United States
| | | | | | | | | | | | | |
Collapse
|
11
|
Abstract
Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.
Collapse
Affiliation(s)
- Erik R Zettler
- Sea Education Association, P.O. Box 6, Woods Hole, Massachusetts 02543, United States
| | | | | |
Collapse
|
12
|
Hirai H, Takada H, Ogata Y, Yamashita R, Mizukawa K, Saha M, Kwan C, Moore C, Gray H, Laursen D, Zettler ER, Farrington JW, Reddy CM, Peacock EE, Ward MW. Organic micropollutants in marine plastics debris from the open ocean and remote and urban beaches. Mar Pollut Bull 2011; 62:1683-92. [PMID: 21719036 DOI: 10.1016/j.marpolbul.2011.06.004] [Citation(s) in RCA: 432] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/29/2011] [Accepted: 06/02/2011] [Indexed: 05/20/2023]
Abstract
To understand the spatial variation in concentrations and compositions of organic micropollutants in marine plastic debris and their sources, we analyzed plastic fragments (∼10 mm) from the open ocean and from remote and urban beaches. Polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), dichloro-diphenyl-trichloroethane and its metabolites (DDTs), polybrominated diphenyl ethers (PBDEs), alkylphenols and bisphenol A were detected in the fragments at concentrations from 1 to 10,000 ng/g. Concentrations showed large piece-to-piece variability. Hydrophobic organic compounds such as PCBs and PAHs were sorbed from seawater to the plastic fragments. PCBs are most probably derived from legacy pollution. PAHs showed a petrogenic signature, suggesting the sorption of PAHs from oil slicks. Nonylphenol, bisphenol A, and PBDEs came mainly from additives and were detected at high concentrations in some fragments both from remote and urban beaches and the open ocean.
Collapse
Affiliation(s)
- Hisashi Hirai
- Laboratory of Organic Geochemistry (LOG), Tokyo University of Agriculture and Technology, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Nuzzio DB, Zettler ER, Aguilera A, Amaral-Zettler LA. A direct in situ fingerprinting method for acid rock drainage using voltammetric techniques with a single renewable gold microelectrode. Sci Total Environ 2011; 409:1984-1989. [PMID: 21354595 DOI: 10.1016/j.scitotenv.2011.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Revised: 12/30/2010] [Accepted: 01/05/2011] [Indexed: 05/30/2023]
Abstract
Electrochemistry allows for rapid identification of multiple metals and other chemical complexes common in acid rock drainage (ARD) systems. Voltammetric scans using a single gold microelectrode of water samples from geochemically distinct areas of the Río Tinto (RT) in southwestern Spain were clearly recognizable in the field and in samples stored at room temperature for over 6 months. Major voltammetric peaks of iron(III) and copper(II) were identified on a single constantly renewable gold microelectrode. Confirmation of these peaks was performed by spiking with standard metal solutions in the laboratory. This voltammetric technique is a rapid, direct and inexpensive in situ method for identification of water sources and their chemical characteristics, as well as an economical way to monitor environmental changes and remediation efforts.
Collapse
Affiliation(s)
- Donald B Nuzzio
- Analytical Instrument Systems, Inc., P.O. Box 458, Flemington, NJ 08822-0458, USA
| | | | | | | |
Collapse
|
14
|
Amaral-Zettler LA, Zettler ER, Theroux SM, Palacios C, Aguilera A, Amils R. Microbial community structure across the tree of life in the extreme Río Tinto. ISME J 2010; 5:42-50. [PMID: 20631808 DOI: 10.1038/ismej.2010.101] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.
Collapse
Affiliation(s)
- Linda A Amaral-Zettler
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | | | | | | | | | | |
Collapse
|
15
|
Olson RJ, Chisholm SW, Zettler ER, Altabet MA, Dusenberry JA. Spatial and temporal distributions of prochlorophyte picoplankton in the North Atlantic Ocean. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0198-0149(90)90109-9] [Citation(s) in RCA: 190] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
16
|
Olson RJ, Zettler ER, Anderson OK. Discrimination of eukaryotic phytoplankton cell types from light scatter and autofluorescence properties measured by flow cytometry. Cytometry 1989; 10:636-43. [PMID: 2776580 DOI: 10.1002/cyto.990100520] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Flow cytometric methods for recognizing several groups of eukaryotic marine phytoplankton were tested using 26 laboratory cultures. Each culture was divided into three aliquots, and these samples were analyzed for 1) Coulter volume; 2) light scatter (magnitude and polarization properties of forward scattered light and magnitude of right-angle scattered light) and autofluorescence emission (phycoerythrin and chlorophyll); and 3) autofluorescence excitation (by 488 nm and 515 nm light). Three kinds of cells could be easily distinguished from others in the culture collection: 1) The two cryptophytes and the rhodophyte had high phycoerythrin/chlorophyll ratios; 2) the two coccolithophores depolarized forward scattered light; and 3) the two pennate diatoms scattered only a relatively small amount of light in the forward direction compared with that at right angles. Mean chlorophyll fluorescence excited by blue light relative to that excited by green light was highest in the four chlorophytes, but there was overlap between some of these and some other kinds of cells. Unresolved cell types included centric diatoms, dinoflagellates, and naked coccolithophores. Forward light scatter and Coulter volume were closely related (except for the pennate diatoms) over a range of about 0.01 to 30 pL (equivalent spherical diameter about 3 to 40 microns), according to a logarithmic function.
Collapse
Affiliation(s)
- R J Olson
- Biology Department, Woods Hole Oceanographic Institution, Massachusetts 02543
| | | | | |
Collapse
|
17
|
Chisholm SW, Olson RJ, Zettler ER, Goericke R, Waterbury JB, Welschmeyer NA. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 1988. [DOI: 10.1038/334340a0] [Citation(s) in RCA: 764] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|