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Balmonte JP, Giebel HA, Arnosti C, Simon M, Wietz M. Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean. Environ Microbiol 2024; 26:e16594. [PMID: 38418376 DOI: 10.1111/1462-2920.16594] [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: 05/04/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.
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Affiliation(s)
- John Paul Balmonte
- Department of Earth, Marine and Environmental Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, PA, USA
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Carol Arnosti
- Department of Earth, Marine and Environmental Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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2
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Brown S, Lloyd CC, Giljan G, Ghobrial S, Amann R, Arnosti C. Pulsed inputs of high molecular weight organic matter shift the mechanisms of substrate utilisation in marine bacterial communities. Environ Microbiol 2024; 26:e16580. [PMID: 38254313 DOI: 10.1111/1462-2920.16580] [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: 07/06/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024]
Abstract
Heterotrophic bacteria hydrolyze high molecular weight (HMW) organic matter extracellularly prior to uptake, resulting in diffusive loss of hydrolysis products. An alternative 'selfish' uptake mechanism that minimises this loss has recently been found to be common in the ocean. We investigated how HMW organic matter addition affects these two processing mechanisms in surface and bottom waters at three stations in the North Atlantic Ocean. A pulse of HMW organic matter increased cell numbers, as well as the rate and spectrum of extracellular enzymatic activities at both depths. The effects on selfish uptake were more differentiated: in Gulf Stream surface waters and productive surface waters south of Newfoundland, selfish uptake of structurally simple polysaccharides increased upon HMW organic matter addition. The number of selfish bacteria taking up structurally complex polysaccharides, however, was largely unchanged. In contrast, in the oligotrophic North Atlantic gyre, despite high external hydrolysis rates, the number of selfish bacteria was unchanged, irrespective of polysaccharide structure. In deep bottom waters (> 4000 m), structurally complex substrates were processed only by selfish bacteria. Mechanisms of substrate processing-and the extent to which hydrolysis products are released to the external environment-depend on substrate structural complexity and the resident bacterial community.
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Affiliation(s)
- Sarah Brown
- Environment, Ecology, and Energy Program, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - C Chad Lloyd
- Department of Earth, Marine and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Greta Giljan
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sherif Ghobrial
- Department of Earth, Marine and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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3
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Giljan G, Brown S, Lloyd CC, Ghobrial S, Amann R, Arnosti C. Selfish bacteria are active throughout the water column of the ocean. ISME Commun 2023; 3:11. [PMID: 36739317 PMCID: PMC9899235 DOI: 10.1038/s43705-023-00219-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 02/06/2023]
Abstract
Heterotrophic bacteria in the ocean invest carbon, nitrogen, and energy in extracellular enzymes to hydrolyze large substrates to smaller sizes suitable for uptake. Since hydrolysis products produced outside of a cell may be lost to diffusion, the return on this investment is uncertain. Selfish bacteria change the odds in their favor by binding, partially hydrolyzing, and transporting polysaccharides into the periplasmic space without loss of hydrolysis products. We expected selfish bacteria to be most common in the upper ocean, where phytoplankton produce abundant fresh organic matter, including complex polysaccharides. We, therefore, sampled water in the western North Atlantic Ocean at four depths from three stations differing in physiochemical conditions; these stations and depths also differed considerably in microbial community composition. To our surprise, we found that selfish bacteria are common throughout the water column of the ocean, including at depths greater than 5500 m. Selfish uptake as a strategy thus appears to be geographically-and phylogenetically-widespread. Since processing and uptake of polysaccharides require enzymes that are highly sensitive to substrate structure, the activities of these bacteria might not be reflected by measurements relying on uptake only of low molecular weight substrates. Moreover, even at the bottom of the ocean, the supply of structurally-intact polysaccharides, and therefore the return on enzymatic investment, must be sufficient to maintain these organisms.
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Affiliation(s)
- Greta Giljan
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sarah Brown
- Environment, Ecology, and Energy Program, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - C Chad Lloyd
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Sherif Ghobrial
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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4
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Lloyd CC, Brown S, Balmonte JP, Hoarfrost A, Ghobrial S, Arnosti C. Particles act as ‘specialty centers’ with expanded enzymatic function throughout the water column in the western North Atlantic. Front Microbiol 2022; 13:882333. [PMID: 36246226 PMCID: PMC9553992 DOI: 10.3389/fmicb.2022.882333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Heterotrophic bacteria initiate the degradation of high molecular weight organic matter by producing an array of extracellular enzymes to hydrolyze complex organic matter into sizes that can be taken up into the cell. These bacterial communities differ spatially and temporally in composition, and potentially also in their enzymatic complements. Previous research has shown that particle-associated bacteria can be considerably more active than bacteria in the surrounding bulk water, but most prior studies of particle-associated bacteria have been focused on the upper ocean - there are few measurements of enzymatic activities of particle-associated bacteria in the mesopelagic and bathypelagic ocean, although the bacterial communities in the deep are dependent upon degradation of particulate organic matter to fuel their metabolism. We used a broad suite of substrates to compare the glucosidase, peptidase, and polysaccharide hydrolase activities of particle-associated and unfiltered seawater microbial communities in epipelagic, mesopelagic, and bathypelagic waters across 11 stations in the western North Atlantic. We concurrently determined bacterial community composition of unfiltered seawater and of samples collected via gravity filtration (>3 μm). Overall, particle-associated bacterial communities showed a broader spectrum of enzyme activities compared with unfiltered seawater communities. These differences in enzymatic activities were greater at offshore than at coastal locations, and increased with increasing depth in the ocean. The greater differences in enzymatic function measured on particles with depth coincided with increasing differences in particle-associated community composition, suggesting that particles act as ‘specialty centers’ that are essential for degradation of organic matter even at bathypelagic depths.
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Affiliation(s)
- C. Chad Lloyd
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: C. Chad Lloyd,
| | - Sarah Brown
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - John Paul Balmonte
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biology, HADAL and Nordcee, University of Southern Denmark, Odense, Denmark
| | - Adrienne Hoarfrost
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Marine Sciences, University of Georgia, Athens, GA, United States
| | - Sherif Ghobrial
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Manna V, Zoccarato L, Banchi E, Arnosti C, Grossart H, Celussi M. Linking lifestyle and foraging strategies of marine bacteria: selfish behaviour of particle-attached bacteria in the northern Adriatic Sea. Environ Microbiol Rep 2022; 14:549-558. [PMID: 35362215 PMCID: PMC9546125 DOI: 10.1111/1758-2229.13059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/13/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Microbe-mediated enzymatic hydrolysis of organic matter entails the production of hydrolysate, the recovery of which may be more or less efficient. The selfish uptake mechanism, recently discovered, allows microbes to hydrolyze polysaccharides and take up large oligomers, which are then degraded in the periplasmic space. By minimizing the hydrolysate loss, selfish behaviour may be profitable for free-living cells dwelling in a patchy substrate landscape. However, selfish uptake seems to be tailored to algal-derived polysaccharides, abundant in organic particles, suggesting that particle-attached microbes may use this strategy. We tracked selfish polysaccharides uptake in surface microbial communities of the northeastern Mediterranean Sea, linking the occurrence of this processing mode with microbial lifestyle. Additionally, we set up fluorescently labelled polysaccharides incubations supplying phytodetritus to investigate a 'pioneer' scenario for particle-attached microbes. Under both conditions, selfish behaviour was almost exclusively carried out by particle-attached microbes, suggesting that this mechanism may represent an advantage in the race for particle exploitation. Our findings shed light on the selfish potential of particle-attached microbes, suggesting multifaceted foraging strategies exerted by particle colonizers.
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Affiliation(s)
- Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics – OGSDepartment of OceanographyTriesteItaly
| | - Luca Zoccarato
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB)Department of Experimental LimnologyZur alten Fischerhuette 2, D‐16775 StechlinGermany
| | - Elisa Banchi
- National Institute of Oceanography and Applied Geophysics – OGSDepartment of OceanographyTriesteItaly
| | - Carol Arnosti
- University of North Carolina – Chapel HillDepartment of Earth, Marine, and Environmental SciencesChapel HillNC27599USA
| | - Hans‐Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB)Department of Experimental LimnologyZur alten Fischerhuette 2, D‐16775 StechlinGermany
- Potsdam UniversityInstitute for Biochemistry and BiologyMaulbeeralle 2, D‐14469 PotsdamGermany
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics – OGSDepartment of OceanographyTriesteItaly
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Giljan G, Arnosti C, Kirstein IV, Amann R, Fuchs BM. Strong seasonal differences of bacterial polysaccharide utilization in the North Seas over an annual cycle. Environ Microbiol 2022; 24:2333-2347. [PMID: 35384240 DOI: 10.1111/1462-2920.15997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/26/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022]
Abstract
Marine heterotrophic bacteria contribute considerably to global carbon cycling, in part by utilizing phytoplankton-derived polysaccharides. The patterns and rates of two different polysaccharide utilization modes - extracellular hydrolysis and selfish uptake - have previously been found to change during spring phytoplankton bloom events. Here we investigated seasonal changes in bacterial utilization of three polysaccharides, laminarin, xylan, and chondroitin sulfate. Strong seasonal differences were apparent in mode and speed of polysaccharide utilization, as well as in bacterial community compositions. Compared to the winter month of February, during the spring bloom in May, polysaccharide utilization was detected earlier in the incubations and a higher portion of all bacteria took up laminarin selfishly. Highest polysaccharide utilization was measured in June and September, mediated by bacterial communities that were significantly different from spring assemblages. Extensive selfish laminarin uptake, for example, was detectible within a few hours in June, while extracellular hydrolysis of chondroitin was dominant in September. In addition to the well-known Bacteroidota and Gammaproteobacteria clades, the numerically minor verrucomicrobial clade Pedosphaeraceae could be identified as a rapid laminarin utilizer. In summary, polysaccharide utilization proved highly variable over the seasons, both in mode and speed, and also by the bacterial clades involved. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Greta Giljan
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Inga V Kirstein
- Alfred-Wegner-Institute Helmholtz-Center for Polar and Marine Research, Biological Station Helgoland, Helgoland, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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7
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Klassen L, Reintjes G, Tingley JP, Jones DR, Hehemann JH, Smith AD, Schwinghamer TD, Arnosti C, Jin L, Alexander TW, Amundsen C, Thomas D, Amann R, McAllister TA, Abbott DW. Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. Microbiome 2021; 9:23. [PMID: 33482928 PMCID: PMC7825182 DOI: 10.1186/s40168-020-00975-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/07/2020] [Indexed: 05/03/2023]
Abstract
Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as "medium grower" and "high grower." Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and "omics" approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem. Video abstract.
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Affiliation(s)
- Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Greta Reintjes
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
- Center for Marine Environmental Sciences, University of Bremen (MARUM), 28359, Bremen, Germany
| | - Adam D Smith
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Timothy D Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, 27599-3300, NC, USA
| | - Long Jin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Carolyn Amundsen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Dallas Thomas
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada.
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada.
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Arnosti C, Wietz M, Brinkhoff T, Hehemann JH, Probandt D, Zeugner L, Amann R. The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle. Ann Rev Mar Sci 2021; 13:81-108. [PMID: 32726567 DOI: 10.1146/annurev-marine-032020-012810] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Polysaccharides are major components of macroalgal and phytoplankton biomass and constitute a large fraction of the organic matter produced and degraded in the ocean. Until recently, however, our knowledge of marine polysaccharides was limited due to their great structural complexity, the correspondingly complicated enzymatic machinery used by microbial communities to degrade them, and a lack of readily applied means to isolate andcharacterize polysaccharides in detail. Advances in carbohydrate chemistry, bioinformatics, molecular ecology, and microbiology have led to new insights into the structures of polysaccharides, the means by which they are degraded by bacteria, and the ecology of polysaccharide production and decomposition. Here, we survey current knowledge, discuss recent advances, and present a new conceptual model linking polysaccharide structural complexity and abundance to microbially driven mechanisms of polysaccharide processing. We conclude by highlighting specific future research foci that will shed light on this central but poorly characterized component of the marine carbon cycle.
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Affiliation(s)
- C Arnosti
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - M Wietz
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - T Brinkhoff
- Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - J-H Hehemann
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences (MARUM), University of Bremen, and Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - D Probandt
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - L Zeugner
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - R Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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Reintjes G, Fuchs BM, Amann R, Arnosti C. Extensive Microbial Processing of Polysaccharides in the South Pacific Gyre via Selfish Uptake and Extracellular Hydrolysis. Front Microbiol 2020; 11:583158. [PMID: 33391202 PMCID: PMC7775370 DOI: 10.3389/fmicb.2020.583158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 07/14/2020] [Accepted: 11/25/2020] [Indexed: 11/13/2022] Open
Abstract
Primary productivity occurs throughout the deep euphotic zone of the oligotrophic South Pacific Gyre (SPG), fueled largely by the regeneration of nutrients and thus recycling of organic matter. We investigated the heterotrophic capabilities of the SPG's bacterial communities by examining their ability to process polysaccharides, an important component of marine organic matter. We focused on the initial step of organic matter degradation by measuring the activities of extracellular enzymes that hydrolyze six different polysaccharides to smaller sizes. This process can occur by two distinct mechanisms: "selfish uptake," in which initial hydrolysis is coupled to transport of large polysaccharide fragments into the periplasmic space of bacteria, with little to no loss of hydrolysis products to the external environment, and "external hydrolysis," in which low molecular weight (LMW) hydrolysis products are produced in the external environment. Given the oligotrophic nature of the SPG, we did not expect high enzymatic activity; however, we found that all six polysaccharides were hydrolyzed externally and taken up selfishly in the central SPG, observations that may be linked to a comparatively high abundance of diatoms at the depth and location sampled (75 m). At the edge of the gyre and close to the center of the gyre, four of six polysaccharides were externally hydrolyzed, and a lower fraction of the bacterial community showed selfish uptake. One polysaccharide (fucoidan) was selfishly taken up without measurable external hydrolysis at two stations. Additional incubations of central gyre water from depths of 1,250 and 2,800 m with laminarin (an abundant polysaccharide in the ocean) led to extreme growth of opportunistic bacteria (Alteromonas), as tracked by cell counts and next generation sequencing of the bacterial communities. These Alteromonas appear to concurrently selfishly take up laminarin and release LMW hydrolysis products. Overall, extracellular enzyme activities in the SPG were similar to activities in non-oligotrophic regions, and a considerable fraction of the community was capable of selfish uptake at all three stations. A diverse set of bacteria responded to and are potentially important for the recycling of organic matter in the SPG.
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Affiliation(s)
- Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Bernhard M. Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, United States
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10
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Hoarfrost A, Brown N, Brown CT, Arnosti C. Sequencing data discovery with MetaSeek. Bioinformatics 2020; 35:4857-4859. [PMID: 31225863 DOI: 10.1093/bioinformatics/btz499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 05/01/2019] [Accepted: 06/17/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Sequencing data resources have increased exponentially in recent years, as has interest in large-scale meta-analyses of integrated next-generation sequencing datasets. However, curation of integrated datasets that match a user's particular research priorities is currently a time-intensive and imprecise task. MetaSeek is a sequencing data discovery tool that enables users to flexibly search and filter on any metadata field to quickly find the sequencing datasets that meet their needs. MetaSeek automatically scrapes metadata from all publicly available datasets in the Sequence Read Archive, cleans and parses messy, user-provided metadata into a structured, standard-compliant database and predicts missing fields where possible. MetaSeek provides a web-based graphical user interface and interactive visualization dashboard, as well as a programmatic API to rapidly search, filter, visualize, save, share and download matching sequencing metadata. AVAILABILITY AND IMPLEMENTATION The MetaSeek online interface is available at https://www.metaseek.cloud/. The MetaSeek database can also be accessed via API to programmatically search, filter and download all metadata. MetaSeek source code, metadata scrapers and documents are available at https://github.com/MetaSeek-Sequencing-Data-Discovery/metaseek/.
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Affiliation(s)
- Adrienne Hoarfrost
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - C Titus Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Reintjes G, Fuchs BM, Scharfe M, Wiltshire KH, Amann R, Arnosti C. Short-term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom. Environ Microbiol 2020; 22:1884-1900. [PMID: 32128969 DOI: 10.1111/1462-2920.14971] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 11/28/2022]
Abstract
Spring phytoplankton blooms in temperate environments contribute disproportionately to global marine productivity. Bloom-derived organic matter, much of it occurring as polysaccharides, fuels biogeochemical cycles driven by interacting autotrophic and heterotrophic communities. We tracked changes in the mode of polysaccharide utilization by heterotrophic bacteria during the course of a diatom-dominated bloom in the German Bight, North Sea. Polysaccharides can be taken up in a 'selfish' mode, where initial hydrolysis is coupled to transport into the periplasm, such that little to no low-molecular weight (LMW) products are externally released to the environment. Alternatively, polysaccharides hydrolyzed by cell-surface attached or free extracellular enzymes (external hydrolysis) yield LMW products available to the wider bacterioplankton community. In the early bloom phase, selfish activity was accompanied by low extracellular hydrolysis rates of a few polysaccharides. As the bloom progressed, selfish uptake increased markedly, and external hydrolysis rates increased, but only for a limited range of substrates. The late bloom phase was characterized by high external hydrolysis rates of a broad range of polysaccharides and reduced selfish uptake of polysaccharides, except for laminarin. Substrate utilization mode is related both to substrate structural complexity and to the bloom-stage dependent composition of the heterotrophic bacterial community.
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Affiliation(s)
- Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | | | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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Hehemann JH, Reintjes G, Klassen L, Smith AD, Ndeh D, Arnosti C, Amann R, Abbott DW. Single cell fluorescence imaging of glycan uptake by intestinal bacteria. ISME J 2019; 13:1883-1889. [PMID: 30936421 PMCID: PMC6776043 DOI: 10.1038/s41396-019-0406-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 12/03/2018] [Accepted: 02/27/2019] [Indexed: 01/15/2023]
Abstract
Microbes in the intestines of mammals degrade dietary glycans for energy and growth. The pathways required for polysaccharide utilization are functionally diverse; moreover, they are unequally dispersed between bacterial genomes. Hence, assigning metabolic phenotypes to genotypes remains a challenge in microbiome research. Here we demonstrate that glycan uptake in gut bacteria can be visualized with fluorescent glycan conjugates (FGCs) using epifluorescence microscopy. Yeast α-mannan and rhamnogalacturonan-II, two structurally distinct glycans from the cell walls of yeast and plants, respectively, were fluorescently labeled and fed to Bacteroides thetaiotaomicron VPI-5482. Wild-type cells rapidly consumed the FGCs and became fluorescent; whereas, strains that had deleted pathways for glycan degradation and transport were non-fluorescent. Uptake of FGCs, therefore, is direct evidence of genetic function and provides a direct method to assess specific glycan metabolism in intestinal bacteria at the single cell level.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany. .,Center for Marine Environmental Sciences, University of Bremen (MARUM), 28359, Bremen, Germany.
| | - Greta Reintjes
- Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Adam D Smith
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Didier Ndeh
- Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Rudolf Amann
- Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada.
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Balmonte JP, Buckley A, Hoarfrost A, Ghobrial S, Ziervogel K, Teske A, Arnosti C. Community structural differences shape microbial responses to high molecular weight organic matter. Environ Microbiol 2018; 21:557-571. [PMID: 30452115 DOI: 10.1111/1462-2920.14485] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 11/26/2022]
Abstract
The extent to which differences in microbial community structure result in variations in organic matter (OM) degradation is not well understood. Here, we tested the hypothesis that distinct marine microbial communities from North Atlantic surface and bottom waters would exhibit varying compositional succession and functional shifts in response to the same pool of complex high molecular weight (HMW-OM). We also hypothesized that microbial communities would produce a broader spectrum of enzymes upon exposure to HMW-OM, indicating a greater potential to degrade these compounds than reflected by initial enzymatic activities. Our results show that community succession in amended mesocosms was congruent with cell growth, increased bacterial production and most notably, with substantial shifts in enzymatic activities. In all amended mesocosms, closely related taxa that were initially rare became dominant at time frames during which a broader spectrum of active enzymes were detected compared to initial timepoints, indicating a similar response among different communities. However, succession on the whole-community level, and the rates, spectra and progression of enzymatic activities, reveal robust differences among distinct communities from discrete water masses. These results underscore the crucial role of rare bacterial taxa in ocean carbon cycling and the importance of bacterial community structure for HMW-OM degradation.
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Affiliation(s)
- John Paul Balmonte
- Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrew Buckley
- Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Adrienne Hoarfrost
- Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sherif Ghobrial
- Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kai Ziervogel
- Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH, 03824, USA
| | - Andreas Teske
- Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Carol Arnosti
- Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Balmonte JP, Teske A, Arnosti C. Structure and function of high Arctic pelagic, particle‐associated and benthic bacterial communities. Environ Microbiol 2018; 20:2941-2954. [DOI: 10.1111/1462-2920.14304] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- John Paul Balmonte
- Department of Marine Sciences The University of North Carolina at Chapel Hill 3202 Venable Hall, Chapel Hill NC 27599 USA
| | - Andreas Teske
- Department of Marine Sciences The University of North Carolina at Chapel Hill 3202 Venable Hall, Chapel Hill NC 27599 USA
| | - Carol Arnosti
- Department of Marine Sciences The University of North Carolina at Chapel Hill 3202 Venable Hall, Chapel Hill NC 27599 USA
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15
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Bullock A, Ziervogel K, Ghobrial S, Smith S, McKee B, Arnosti C. A Multi-season Investigation of Microbial Extracellular Enzyme Activities in Two Temperate Coastal North Carolina Rivers: Evidence of Spatial but Not Seasonal Patterns. Front Microbiol 2018; 8:2589. [PMID: 29312262 PMCID: PMC5743733 DOI: 10.3389/fmicb.2017.02589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 08/12/2017] [Accepted: 12/12/2017] [Indexed: 01/17/2023] Open
Abstract
Riverine systems are important sites for the production, transport, and transformation of organic matter. Much of the organic matter processing is carried out by heterotrophic microbial communities, whose activities may be spatially and temporally variable. In an effort to capture and evaluate some of this variability, we sampled four sites-two upstream and two downstream-at each of two North Carolina rivers (the Neuse River and the Tar-Pamlico River) ca. twelve times over a time period of 20 months from 2010 to 2012. At all of the sites and dates, we measured the activities of extracellular enzymes used to hydrolyze polysaccharides and peptides, and thus to initiate heterotrophic carbon processing. We additionally measured bacterial abundance, bacterial production, phosphatase activities, and dissolved organic carbon (DOC) concentrations. Concurrent collection of physical data (stream flow, temperature, salinity, dissolved oxygen) enabled us to explore possible connections between physiochemical parameters and microbial activities throughout this time period. The two rivers, both of which drain into Pamlico Sound, differed somewhat in microbial activities and characteristics: the Tar-Pamlico River showed higher β-glucosidase and phosphatase activities, and frequently had higher peptidase activities at the lower reaches, than the Neuse River. The lower reaches of the Neuse River, however, had much higher DOC concentrations than any site in the Tar River. Both rivers showed activities of a broad range of polysaccharide hydrolases through all stations and seasons, suggesting that the microbial communities are well-equipped to access enzymatically a broad range of substrates. Considerable temporal and spatial variability in microbial activities was evident, variability that was not closely related to factors such as temperature and season. However, Hurricane Irene's passage through North Carolina coincided with higher concentrations of DOC at the downstream sampling sites of both rivers. This DOC maximum persisted into the month following the hurricane, when it continued to stimulate bacterial protein production and phosphatase activity in the Neuse River, but not in the Tar-Pamlico River. Microbial community activities are related to a complex array of factors, whose interactions vary considerably with time and space.
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Affiliation(s)
- Avery Bullock
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Kai Ziervogel
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Sherif Ghobrial
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Shannon Smith
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Brent McKee
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, United States
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16
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Reintjes G, Arnosti C, Fuchs BM, Amann R. An alternative polysaccharide uptake mechanism of marine bacteria. ISME J 2017; 11:1640-1650. [PMID: 28323277 PMCID: PMC5520146 DOI: 10.1038/ismej.2017.26] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/06/2016] [Accepted: 01/22/2017] [Indexed: 12/29/2022]
Abstract
Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered-using super-resolution structured illumination microscopy-that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS). Fluorescence in situ hybridisation identified these organisms as members of the bacterial phyla Bacteroidetes and Planctomycetes and the gammaproteobacterial genus Catenovulum. Simultaneous membrane staining with nile red indicated that the FLA-PS labelling occurred in the cell but not in the cytoplasm. The dynamics of FLA-PS staining was further investigated in pure culture experiments using Gramella forsetii, a marine member of Bacteroidetes. The staining patterns observed in environmental samples and pure culture tests are consistent with a 'selfish' uptake mechanisms of larger oligosaccharides (>600 Da), as demonstrated for gut Bacteroidetes. Ecologically, this alternative polysaccharide uptake mechanism secures substantial quantities of substrate in the periplasmic space, where further processing can occur without diffusive loss. Such a mechanism challenges the paradigm that hydrolysis of HMW substrates inevitably yields low-molecular-weight fragments that are available to the surrounding community and demonstrates the importance of an alternative mechanism of polysaccharide uptake in marine bacteria.
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Affiliation(s)
- Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Balmonte JP, Arnosti C, Underwood S, McKee BA, Teske A. Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia. Front Microbiol 2016; 7:1441. [PMID: 27695444 PMCID: PMC5023673 DOI: 10.3389/fmicb.2016.01441] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 04/29/2016] [Accepted: 08/30/2016] [Indexed: 12/16/2022] Open
Abstract
Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance.
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Affiliation(s)
- John Paul Balmonte
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Carol Arnosti
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Sarah Underwood
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Brent A McKee
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Andreas Teske
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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18
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Neumann AM, Balmonte JP, Berger M, Giebel HA, Arnosti C, Voget S, Simon M, Brinkhoff T, Wietz M. Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes. Environ Microbiol 2015; 17:3857-68. [PMID: 25847866 DOI: 10.1111/1462-2920.12862] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/29/2015] [Indexed: 10/23/2022]
Abstract
The marine bacterium Alteromonas macleodii is a copiotrophic r-strategist, but little is known about its potential to degrade polysaccharides. Here, we studied the degradation of alginate and other algal polysaccharides by A. macleodii strain 83-1 in comparison to other A. macleodii strains. Cell densities of strain 83-1 with alginate as sole carbon source were comparable to those with glucose, but the exponential phase was delayed. The genome of 83-1 was found to harbour an alginolytic system comprising five alginate lyases, whose expression was induced by alginate. The alginolytic system contains additional CAZymes, including two TonB-dependent receptors, and is part of a 24 kb genomic island unique to the A. macleodii 'surface clade' ecotype. In contrast, strains of the 'deep clade' ecotype contain only a single alginate lyase in a separate 7 kb island. This difference was reflected in an eightfold greater efficiency of surface clade strains to grow on alginate. Strain 83-1 furthermore hydrolysed laminarin, pullulan and xylan, and corresponding polysaccharide utilization loci were detected in the genome. Alteromonas macleodii alginate lyases were predominantly detected in Atlantic Ocean metagenomes. The demonstrated hydrolytic capacities are likely of ecological relevance and represent another level of adaptation among A. macleodii ecotypes.
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Affiliation(s)
- Anna M Neumann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - John P Balmonte
- Department of Marine Sciences, University of North Carolina, 3117 Venable Hall, Chapel Hill, NC, USA
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, 3117 Venable Hall, Chapel Hill, NC, USA
| | - Sonja Voget
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, 37077, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
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Steen AD, Arnosti C. Picky, hungry eaters in the cold: persistent substrate selectivity among polar pelagic microbial communities. Front Microbiol 2014; 5:527. [PMID: 25339946 PMCID: PMC4189390 DOI: 10.3389/fmicb.2014.00527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 01/20/2014] [Accepted: 09/22/2014] [Indexed: 11/13/2022] Open
Abstract
Polar pelagic microbial communities access a narrower range of polysaccharide substrates than communities at lower latitudes. For example, the glucose-containing polysaccharide pullulan is typically not hydrolyzed in fjord waters of Svalbard, even though pullulan is rapidly hydrolyzed in sediments from Svalbard fjords, other polysaccharides are hydrolyzed rapidly in Svalbard waters, and pullulan is hydrolyzed rapidly in temperate waters. The purpose of this study was to investigate potential factors preventing hydrolysis of pullulan in Svalbard fjord waters. To this end, in two separate years, water from Isfjorden, Svalbard, was amended with different carbon sources and/or additional nutrients in order to determine whether increasing the concentration of these potentially-limiting factors would lead to measurable enzymatic activity. Addition of nitrate, phosphate, glucose, or amino acids did not yield detectable pullulan hydrolysis. The only treatment that led to detectable pullulan hydrolysis was extended incubation after the addition of maltotriose (a subunit of pullulan, and potential inducer of pullulanase). In these fjords, the ability to enzymatically access pullulan is likely confined to numerically minor members of the pelagic microbial community. These results are consistent with the hypothesis that pelagic microbial communities at high latitudes exhibit streamlined functionality, focused on a narrower range of substrates, than their temperate counterparts.
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Affiliation(s)
- Andrew D Steen
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA ; Department of Earth and Planetary Sciences, University of Tennessee Knoxville, TN, USA
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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D'Ambrosio L, Ziervogel K, MacGregor B, Teske A, Arnosti C. Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison. ISME J 2014; 8:2167-79. [PMID: 24763371 DOI: 10.1038/ismej.2014.67] [Citation(s) in RCA: 65] [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] [Received: 08/01/2013] [Revised: 03/19/2014] [Accepted: 03/23/2014] [Indexed: 11/09/2022]
Abstract
We compared the function and composition of free-living and particle-associated microbial communities at an inshore site in coastal North Carolina and across a depth profile on the Blake Ridge (offshore). Hydrolysis rates of six different polysaccharide substrates were compared for particle-associated (>3 μm) and free-living (<3 to 0.2 μm) microbial communities. The 16S rRNA- and rDNA-based clone libraries were produced from the same filters used to measure hydrolysis rates. Particle-associated and free-living communities resembled one another; they also showed similar enzymatic hydrolysis rates and substrate preferences. All six polysaccharides were hydrolyzed inshore. Offshore, only a subset was hydrolyzed in surface water and at depths of 146 and 505 m; just three polysaccharides were hydrolyzed at 505 m. The spectrum of bacterial taxa changed more subtly between inshore and offshore surface waters, but changed greatly with depth offshore. None of the OTUs occurred at all sites: 27 out of the 28 major OTUs defined in this study were found either exclusively in a surface or in a mid-depth/bottom water sample. This distinction was evident with both 16S rRNA and rDNA analyses. At the offshore site, despite the low community overlap, bacterial communities maintained a degree of functional redundancy on the whole bacterial community level with respect to hydrolysis of high-molecular-weight substrates.
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Affiliation(s)
- Lindsay D'Ambrosio
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kai Ziervogel
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Barbara MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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21
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Arnosti C, Steen AD. Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities. Front Microbiol 2013; 4:318. [PMID: 24198812 PMCID: PMC3813923 DOI: 10.3389/fmicb.2013.00318] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 09/05/2013] [Accepted: 10/10/2013] [Indexed: 11/22/2022] Open
Abstract
The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburg Fjord), and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in “downstream” aspects of microbial metabolism (metabolism of monomers and biomass production). Only four of six polysaccharide substrates were hydrolyzed in Smeerenburg Fjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO2. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments.
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Affiliation(s)
- Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill NC, USA
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Arnosti C, Fuchs BM, Amann R, Passow U. Contrasting extracellular enzyme activities of particle-associated bacteria from distinct provinces of the North Atlantic Ocean. Front Microbiol 2012; 3:425. [PMID: 23248623 PMCID: PMC3521168 DOI: 10.3389/fmicb.2012.00425] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [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: 07/29/2012] [Accepted: 11/27/2012] [Indexed: 12/31/2022] Open
Abstract
Microbial communities play a key role in the marine carbon cycle, processing much of phytoplankton-derived organic matter. The composition of these communities varies by depth, season, and location in the ocean; the functional consequences of these compositional variations for the carbon cycle are only beginning to be explored. We measured the abilities of microbial communities in the large-particle fraction (retained by a 10-μm pore-size cartridge filter) to enzymatically hydrolyze high molecular weight substrates, and therefore initiate carbon remineralization in four distinct oceanic provinces: the boreal polar (BPLR), the Arctic oceanic (ARCT), the North Atlantic drift (NADR), and the North Atlantic subtropical (NAST) provinces. Since we expected the large-particle fraction to include phytoplankton cells, we measured the hydrolysis of polysaccharide substrates (laminarin, fucoidan, xylan, and chondroitin sulfate) expected to be associated with phytoplankton. Hydrolysis rates and patterns clustered into two groups, the BPLR/ARCT and the NADR/NAST. All four substrates were hydrolyzed by the BPLR/ARCT communities; hydrolysis rates of individual substrate varied by factors of ca. 1–4. In contrast, chondroitin was not hydrolyzed in the NADR/NAST, and hydrolytic activity was dominated by laminarinase. Fluorescence in situ hybridization of the large-particle fraction post-incubation showed a substantial contribution (15–26%) of CF319a-positive cells (Bacteroidetes) to total DAPI-stainable cells. Concurrent studies of microbial community composition and of fosmids from these same stations also demonstrated similarities between BPLR and ARCT stations, which were distinct from the NADR/NAST stations. Together, these data support a picture of compositionally as well as functionally distinct communities across these oceanic provinces.
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Affiliation(s)
- Carol Arnosti
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PSG, Reitenga KG, Xie G, Poulton NJ, Gomez ML, Masland DED, Thompson B, Bellows WK, Ziervogel K, Lo CC, Ahmed S, Gleasner CD, Detter CJ, Stepanauskas R. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS One 2012; 7:e35314. [PMID: 22536372 PMCID: PMC3335022 DOI: 10.1371/journal.pone.0035314] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 03/13/2012] [Indexed: 11/19/2022] Open
Abstract
Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation.
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Affiliation(s)
- Manuel Martinez-Garcia
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - David M. Brazel
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
- Colby College, Waterville, Main, United States of America
| | - Brandon K. Swan
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Patrick S. G. Chain
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Krista G. Reitenga
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Gary Xie
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Nicole J. Poulton
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Monica Lluesma Gomez
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Dashiell E. D. Masland
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Brian Thompson
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Wendy K. Bellows
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Kai Ziervogel
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Chien-Chi Lo
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Sanaa Ahmed
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Cheryl D. Gleasner
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Chris J. Detter
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
- * E-mail:
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Ziervogel K, McKay L, Rhodes B, Osburn CL, Dickson-Brown J, Arnosti C, Teske A. Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site. PLoS One 2012; 7:e34816. [PMID: 22509359 PMCID: PMC3324544 DOI: 10.1371/journal.pone.0034816] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 03/06/2012] [Indexed: 11/24/2022] Open
Abstract
The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.
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Affiliation(s)
- Kai Ziervogel
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
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25
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Abstract
Extracellular enzymes initiate microbial remineralization of organic matter by hydrolyzing substrates to sizes sufficiently small to be transported across cell membranes. As much of marine primary productivity is processed by heterotrophic microbes, the substrate specificities of extracellular enzymes, the rates at which they function in seawater and sediments, and factors controlling their production, distribution, and active lifetimes, are central to carbon cycling in marine systems. In this review, these topics are considered from biochemical, microbial/molecular biological, and geochemical perspectives. Our understanding of the capabilities and limitations of heterotrophic microbial communities has been greatly advanced in recent years, in part through genetic and genomic approaches. New methods to measure enzyme activities in the field are needed to keep pace with these advances and to pursue intriguing evidence that patterns of enzyme activities in different environments are linked to differences in microbial community composition that may profoundly affect the marine carbon cycle.
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Affiliation(s)
- Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599-3300, USA.
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Hubert C, Arnosti C, Brüchert V, Loy A, Vandieken V, Jørgensen BB. Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperature. Environ Microbiol 2010; 12:1089-104. [PMID: 20192966 DOI: 10.1111/j.1462-2920.2010.02161.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50 degrees C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0 degrees C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50 degrees C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50 degrees C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50 degrees C. Incubations with four different fluorescently labelled polysaccharides at 4 degrees C and 50 degrees C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere.
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Affiliation(s)
- Casey Hubert
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Hubert C, Loy A, Nickel M, Arnosti C, Baranyi C, Brüchert V, Ferdelman T, Finster K, Christensen FM, Rosa de Rezende J, Vandieken V, Jørgensen BB. A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 2009; 325:1541-4. [PMID: 19762643 DOI: 10.1126/science.1174012] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 10(8) spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50 degrees C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.
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Affiliation(s)
- Casey Hubert
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
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Steen AD, Gururaj P, Ma J, Blough NV, Arnosti C. Fluorescence anisotropy as a means to determine extracellular polysaccharide hydrolase activity in environmental samples. Anal Biochem 2008; 383:340-2. [PMID: 18835237 DOI: 10.1016/j.ab.2008.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 09/03/2008] [Indexed: 11/29/2022]
Abstract
Current approaches to measure the activities of microbial extracellular enzymes in aquatic environments are hampered by slow throughput or by differences between the structure of simple substrate proxies and macromolecules. Here we show that measurements of fluorescence anisotropy can be used to determine the hydrolysis rate of two fluorescently labeled polysaccharides, laminarin and xylan, in environmental samples. A simple analysis shows that the anisotropy of these fluorescently labeled polysaccharides can be approximated using a modification of the Perrin equation.
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Affiliation(s)
- Andrew D Steen
- Department of Marine Sciences, University of North Carolina at Chapel Hill, 340 Chapman Hall, CB#3300 Chapel Hill, NC 27599, USA.
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29
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Arnosti C. Functional differences between Arctic seawater and sedimentary microbial communities: contrasts in microbial hydrolysis of complex substrates. FEMS Microbiol Ecol 2008; 66:343-51. [PMID: 18778275 DOI: 10.1111/j.1574-6941.2008.00587.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The activities and structural specificities of extracellular enzymes that initiate microbial remineralization of high-molecular-weight (MW) organic matter were investigated in surface waters and sediments of an Arctic fjord of Svalbard. Hydrolysis rates of a suite of fluorescently labeled macromolecular substrates, including seven commercially available polysaccharides and three high-carbohydrate-content plankton extracts ranged from rapid to not detectable, and differed markedly between seawater and sediments. Order (fastest to slowest) of hydrolysis in surface water was laminarin, Spirulina extract, xylan>chondroitin, alginic acid, Wakame extract>arabinogalactan, fucoidan>Isochrysis extract>>>pullulan, while in sediments the order was pullulan, laminarin, alginic acid, Wakame extract>chondroitin, xylan>arabinogalactan, Isochrysis extract>Spirulina extract>fucoidan. These differences cannot be explained by simple scaling factors such as differences in microbial cell numbers between seawater and sediments. Other investigations have shown that microbial community composition of Svalbard sediments and of polar bacterioplankton samples differ markedly. These results demonstrate that sedimentary and seawater microbial communities also differ fundamentally in their abilities to access specific high-MW substrates. Substrate bioavailability depends on the capabilities of a microbial community, as well as the chemical and structural features of the substrate itself.
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Affiliation(s)
- Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA.
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30
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Boudreau BP, Arnosti C, Jørgensen BB, Canfield DE. Comment on "Physical Model for the Decay and Preservation of Marine Organic Carbon". Science 2008; 319:1616; author reply 1616. [DOI: 10.1126/science.1148589] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Bernard P. Boudreau
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599–3300, USA
- Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany
- Nordic Center for Earth Evolution and Institute of Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Carol Arnosti
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599–3300, USA
- Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany
- Nordic Center for Earth Evolution and Institute of Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Bo Barker Jørgensen
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599–3300, USA
- Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany
- Nordic Center for Earth Evolution and Institute of Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Donald E. Canfield
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599–3300, USA
- Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany
- Nordic Center for Earth Evolution and Institute of Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Ziervogel K, Arnosti C. Polysaccharide hydrolysis in aggregates and free enzyme activity in aggregate-free seawater from the north-eastern Gulf of Mexico. Environ Microbiol 2007; 10:289-99. [PMID: 18093165 DOI: 10.1111/j.1462-2920.2007.01451.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Marine snow aggregates represent hotspots of carbon remineralization in the ocean. Various aspects of bacterial dynamics have been investigated on marine snow. To date, extracellular enzymatic activities in aggregates have been measured using small substrate proxies that do not adequately reflect the complexity of biomacromolecules such as polysaccharides, proteins and lipids. To address this issue, we used six structurally distinct, fluorescently labelled polysaccharides to measure enzymatic hydrolysis on aggregates formed with a roller table and in aggregate-free (ambient) seawater from two near-coast sites, north-eastern Gulf of Mexico. A single polysaccharide was incubated in aggregates and ambient seawater. Changes in polysaccharide molecular weight were monitored over time to measure the course of enzymatic hydrolysis. All six polysaccharides were hydrolysed in aggregates, indicating a broad range of enzyme activities in aggregate-associated bacteria. Four substrates were also hydrolysed in ambient waters. Epifluorescence microscopy revealed that nearly all of the bacteria present in original waters were incorporated into aggregates. Therefore hydrolytic activities in ambient waters were presumably due to enzymes spatially disconnected from cells and aggregates. Our results show substantial enzymatic activity in cell/aggregate-free seawater, suggesting a significant role of free enzymes in hydrolytic activity in waters from the north-eastern Gulf of Mexico.
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Affiliation(s)
- Kai Ziervogel
- University of North Carolina-Chapel Hill, Department of Marine Sciences, Chapel Hill, NC 27599, USA.
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Abstract
As organic matter produced in the euphotic zone of the ocean sinks through the mesopelagic zone, its composition changes from one that is easily characterized by standard chromatographic techniques to one that is not. The material not identified at the molecular level is called "uncharacterized". Several processes account for this transformation of organic matter: aggregation/disaggregation of particles resulting in incorporation of older and more degraded material; recombination of organic compounds into geomacromolecules; and selective preservation of specific biomacromolecules. Furthermore, microbial activities may introduce new cell wall or other biomass material that is not easily characterized, or they may produce such material as a metabolic product. In addition, black carbon produced by combustion processes may compose a fraction of the uncharacterized organic matter, as it is not analyzed in standard biochemical techniques. Despite these poorly-defined compositional changes that hinder chemical identification, the vast majority of organic matter in sinking particles remains accessible to and is ultimately remineralized by marine microbes.
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Affiliation(s)
- Cindy Lee
- Marine Sciences Research Center, Stony Brook University, NY 11794-5000, USA.
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Arnosti C. Fluorescent derivatization of polysaccharides and carbohydrate-containing biopolymers for measurement of enzyme activities in complex media. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 793:181-91. [PMID: 12880865 DOI: 10.1016/s1570-0232(03)00375-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Fluorescence derivatization provides a means of tracing the dynamics of polysaccharides even in the presence of high concentrations of other organic compounds or salts. A method of labeling polysaccharides with fluoresceinamine was extended to polysaccharides of a wide range of chemical composition, and alternative means of preparation were established for polysaccharides not initially amenable to column chromatography. The polysaccharides were activated with cyanogen bromide, coupled to fluoresceinamine, and separated from unreacted fluorophore via gel filtration chromatography or dialysis. Since the resulting derivatized polysaccharides proved to be stable to further physical and chemical manipulation, methods were also developed for re-activation and labeling with a second fluorophore, as well as for tethering the labeled polysaccharides to agarose beads. As an example of the application of this approach, five distinct fluorescently-labeled polysaccharides (pullulan, laminarin, xylan, chondroitin sulfate, and alginic acid) were used to investigate the activities and structural specificities of extracellular enzymes produced in situ by marine microbial communities, providing a means of measuring specifically the activities of endo-acting extracellular enzymes and avoiding use of low molecular mass substrate proxies. These labeled polysaccharides could be used to explore the dynamics of polysaccharides in other types of complex media, as well as to investigate the activities and specificities of endo-acting enzymes in other systems.
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Affiliation(s)
- C Arnosti
- Department of Marine Sciences, 12-7 Venable Hall CB #3300, University of North Carolina, Chapel Hill, NC 27599-3300, USA.
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Weiner R, Seagren E, Arnosti C, Quintero E. Bacterial survival in biofilms: probes for exopolysaccharide and its hydrolysis, and measurements of intra- and interphase mass fluxes. Methods Enzymol 1999; 310:403-26. [PMID: 10547808 DOI: 10.1016/s0076-6879(99)10032-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- R Weiner
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park 20742-0001, USA
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Arnosti C, Repeta DJ. Extracellular enzyme activity in anaerobic bacterial cultures: evidence of pullulanase activity among mesophilic marine bacteria. Appl Environ Microbiol 1994; 60:840-6. [PMID: 8161177 PMCID: PMC201400 DOI: 10.1128/aem.60.3.840-846.1994] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The extracellular enzymatic activity of a mixed culture of anaerobic marine bacteria enriched on pullulan [alpha(1,6)-linked maltotriose units] was directly assessed with a combination of gel permeation chromatography (GPC) and nuclear magnetic resonance spectroscopy (NMR). Hydrolysis products of pullulan were separated by GPC into three fractions with molecular weights of > or = 10,000, approximately 5,000, and < or = 1,200. NMR spectra of these fractions demonstrated that pullulan was rapidly and specifically hydrolyzed at alpha(1,6) linkages by pullulanase enzymes, most likely type II pullulanase. Although isolated pullulanase enzymes have been shown to hydrolyze pullulan completely to maltotriose (S. H. Brown, H. R. Costantino, and R. M. Kelly, Appl. Environ. Microbiol. 56:1985-1991, 1990; M. Klingeberg, H. Hippe, and G. Antranikian, FEMS Microbiol. Lett. 69:145-152, 1990; R. Koch, P. Zablowski, A. Spreinat, and G. Antranikian, FEMS Microbiol. Lett. 71:21-26, 1990), the smallest carbohydrate detected in the bacterial cultures consisted of two maltotriose units linked through one alpha(1,6) linkage. Either the final hydrolysis step was closely linked to substrate uptake, or specialized porins similar to maltoporin might permit direct transport of large oligosaccharides into the bacterial cell. This is the first report of pullulanase activity among mesophilic marine bacteria. The combination of GPC and NMR could easily be used to assess other types of extracellular enzyme activity in bacterial cultures.
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Affiliation(s)
- C Arnosti
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Massachusetts 02543
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