1
|
Cummings S, Ardor Bellucci LM, Seabrook S, Raineault NA, McPhail KL, Thurber AR. Variations and gradients between methane seep and off-seep microbial communities in a submarine canyon system in the Northeast Pacific. PeerJ 2023; 11:e15119. [PMID: 37009161 PMCID: PMC10064993 DOI: 10.7717/peerj.15119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46-47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.
Collapse
Affiliation(s)
- Susie Cummings
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States of America
| | - Lila M. Ardor Bellucci
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States of America
| | - Sarah Seabrook
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | | | - Kerry L. McPhail
- College of Pharmacy, Oregon State University, Corvallis, OR, United States of America
| | - Andrew R. Thurber
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States of America
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States of America
| |
Collapse
|
2
|
Moreira VA, Cravo-Laureau C, de Carvalho ACB, Baldy A, Bidone ED, Sabadini-Santos E, Duran R. Microbial indicators along a metallic contamination gradient in tropical coastal sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130244. [PMID: 36327839 DOI: 10.1016/j.jhazmat.2022.130244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/03/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.
Collapse
Affiliation(s)
- Vanessa Almeida Moreira
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Angelo Cezar Borges de Carvalho
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Alice Baldy
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Edison Dausacker Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
| |
Collapse
|
3
|
Liau P, Kim C, Saxton MA, Malkin SY. Microbial succession in a marine sediment: Inferring interspecific microbial interactions with marine cable bacteria. Environ Microbiol 2022; 24:6348-6364. [PMID: 36178156 PMCID: PMC10092204 DOI: 10.1111/1462-2920.16230] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/27/2022] [Indexed: 01/12/2023]
Abstract
Cable bacteria are long, filamentous, multicellular bacteria that grow in marine sediments and couple sulfide oxidation to oxygen reduction over centimetre-scale distances via long-distance electron transport. Cable bacteria can strongly modify biogeochemical cycling and may affect microbial community networks. Here we examine interspecific interactions with marine cable bacteria (Ca. Electrothrix) by monitoring the succession of 16S rRNA amplicons (DNA and RNA) and cell abundance across depth and time, contrasting sediments with and without cable bacteria growth. In the oxic zone, cable bacteria activity was positively associated with abundant predatory bacteria (Bdellovibrionota, Myxococcota, Bradymonadales), indicating putative predation on cathodic cells. At suboxic depths, cable bacteria activity was positively associated with sulfate-reducing and magnetotactic bacteria, consistent with cable bacteria functioning as ecosystem engineers that modify their local biogeochemical environment, benefitting certain microbes. Cable bacteria activity was negatively associated with chemoautotrophic sulfur-oxidizing Gammaproteobacteria (Thiogranum, Sedimenticola) at oxic depths, suggesting competition, and positively correlated with these taxa at suboxic depths, suggesting syntrophy and/or facilitation. These observations are consistent with chemoautotrophic sulfur oxidizers benefitting from an oxidizing potential imparted by cable bacteria at suboxic depths, possibly by using cable bacteria as acceptors for electrons or electron equivalents, but by an as yet enigmatic mechanism.
Collapse
Affiliation(s)
- Pinky Liau
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Carol Kim
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Matthew A Saxton
- Department of Biological Sciences, Miami University, Middletown, Ohio, USA
| | - Sairah Y Malkin
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| |
Collapse
|
4
|
Zhang C, Atashgahi S, Bosma TNP, Peng P, Smidt H. Organohalide respiration potential in marine sediments from Aarhus Bay. FEMS Microbiol Ecol 2022; 98:fiac073. [PMID: 35689665 PMCID: PMC9303371 DOI: 10.1093/femsec/fiac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/09/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
Collapse
Affiliation(s)
- Chen Zhang
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom N P Bosma
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109-2125, United States
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|
5
|
Walker AM, Leigh MB, Mincks SL. Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope. Front Microbiol 2021; 12:581124. [PMID: 33584606 PMCID: PMC7876419 DOI: 10.3389/fmicb.2021.581124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.
Collapse
Affiliation(s)
- Alexis M Walker
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Sarah L Mincks
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
| |
Collapse
|
6
|
Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, Matthews S, Li C, Fowler M, Morrison NM, MacDonald A, Groves RA, Lewis IA, Wang SH, Mayumi D, Greening C, Hubert CRJ. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nat Commun 2020; 11:5825. [PMID: 33203858 PMCID: PMC7673041 DOI: 10.1038/s41467-020-19648-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/06/2020] [Indexed: 11/08/2022] Open
Abstract
At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.
Collapse
Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Jayne E Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - D Calvin Campbell
- Geological Survey of Canada-Atlantic, Dartmouth, NS, B3B 1A6, Canada
| | - Jamie Webb
- Applied Petroleum Technology (Canada), Calgary, AB, T2N 1Z6, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Oyeboade Adebayo
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Stuart Matthews
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Martin Fowler
- Applied Petroleum Technology (Canada), Calgary, AB, T2N 1Z6, Canada
| | - Natasha M Morrison
- Nova Scotia Department of Energy and Mines, Halifax, NS, B2Y 4A2, Canada
| | - Adam MacDonald
- Nova Scotia Department of Energy and Mines, Halifax, NS, B2Y 4A2, Canada
| | - Ryan A Groves
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Scott H Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| |
Collapse
|
7
|
Marietou A, Lund MB, Marshall IP, Schreiber L, Jørgensen BB. Complete genome sequence of Desulfobacter hydrogenophilus AcRS1. Mar Genomics 2020. [DOI: 10.1016/j.margen.2019.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|