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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential. mBio 2024; 15:e0291823. [PMID: 38380943 PMCID: PMC10936187 DOI: 10.1128/mbio.02918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Humphries NE, Fuller DW, Schaefer KM, Sims DW. Highly active fish in low oxygen environments: vertical movements and behavioural responses of bigeye and yellowfin tunas to oxygen minimum zones in the eastern Pacific Ocean. Mar Biol 2024; 171:55. [PMID: 38226137 PMCID: PMC10787700 DOI: 10.1007/s00227-023-04366-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 11/24/2023] [Indexed: 01/17/2024]
Abstract
Oxygen minimum zones in the open ocean are predicted to significantly increase in volume over the coming decades as a result of anthropogenic climatic warming. The resulting reduction in dissolved oxygen (DO) in the pelagic realm is likely to have detrimental impacts on water-breathing organisms, particularly those with higher metabolic rates, such as billfish, tunas, and sharks. However, little is known about how free-living fish respond to low DO environments, and therefore, the effect increasing OMZs will have cannot be predicted reliably. Here, we compare the responses of two active predators (bigeye tuna Thunnus obesus and yellowfin tuna Thunnus albacares) to DO at depth throughout the eastern Pacific Ocean. Using time-series data from 267 tagged tunas (59,910 days) and 3D maps of modelled DO, we find that yellowfin tuna respond to low DO at depth by spending more time in shallower, more oxygenated waters. By contrast, bigeye tuna, which forage at deeper depths well below the thermocline, show fewer changes in their use of the water column. However, we find that bigeye tuna increased the frequency of brief upward vertical excursions they performed by four times when DO at depth was lower, but with no concomitant significant difference in temperature, suggesting that this behaviour is driven in part by the need to re-oxygenate following time spent in hypoxic waters. These findings suggest that increasing OMZs will impact the behaviour of these commercially important species, and it is therefore likely that other water-breathing predators with higher metabolic rates will face similar pressures. A more comprehensive understanding of the effect of shoaling OMZs on pelagic fish vertical habitat use, which may increase their vulnerability to surface fisheries, will be important to obtain if these effects are to be mitigated by future management actions. Supplementary Information The online version contains supplementary material available at 10.1007/s00227-023-04366-2.
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Affiliation(s)
- Nicolas E. Humphries
- The Laboratory, Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB UK
| | - Daniel W. Fuller
- Inter-American Tropical Tuna Commission, La Jolla, San Diego, CA USA
| | - Kurt M. Schaefer
- Inter-American Tropical Tuna Commission, La Jolla, San Diego, CA USA
| | - David W. Sims
- The Laboratory, Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB UK
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Waterfront Campus, Southampton, SO14 3ZH UK
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Ye W, Ma X, Liu C, Ye R, Priyadarshani WNC, Jayathilake R, Weerakoon A, Wimalasiri U, Dissanayake PAKN, Pathirana G, Iroshanie RGA, Zhu Y, Li Z, Wang B, Shou L, Ran L, Zhou F, Chen J, Du P. Vertical variation of bacterial production and potential role in oxygen loss in the southern Bay of Bengal. Front Microbiol 2023; 14:1250575. [PMID: 38029132 PMCID: PMC10663246 DOI: 10.3389/fmicb.2023.1250575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Marine environments wherein long-term microbial oxygen consumption exceeds oxygen replenishment can be associated with oxygen minimum zones (OMZ). The Bay of Bengal OMZ (BOB-OMZ) is one of the most intense OMZs globally. To assess the contribution of bacterial oxygen consumption to oxygen loss in BOB-OMZ, we measured bacterial production (BP), temperature, salinity, and dissolved oxygen (DO) in the whole water column. We then compared the estimated bacterial oxygen demand (BOD) with diapycnal oxygen supply (DOS) at depths of 50-200 m in the southern BOB in January 2020. The average BP was 3.53 ± 3.15 μmol C m-3 h-1 in the upper 200 m of four stations, which was lower than those reported in other tropical waters. The vertical distribution of BP differed between the open ocean and nearshore areas. In the open ocean, temperature and DO were the most important predictors for BP in the whole water column. In the nearshore areas, when DO increased sharply from the suboxic state, extremely high BP occurred at 200 m. The average estimated BOD/DOS could reach up to 153% at depths of 50-200 m, indicating advection and anticyclonic eddies probably are important DO replenishment pathways in the BOB.
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Affiliation(s)
- Wenqi Ye
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Xiao Ma
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, MNR, Hangzhou, China
| | - Chenggang Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Ruijie Ye
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, MNR, Hangzhou, China
| | - W. N. C. Priyadarshani
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - Ruchi Jayathilake
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - Ashoka Weerakoon
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - Udeshika Wimalasiri
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency (NARA), Colombo, Sri Lanka
| | - P. A. K. N. Dissanayake
- Department of Oceanography and Marine Geology, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka
| | - Gayan Pathirana
- Department of Oceanography and Marine Geology, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka
| | - R. G. A. Iroshanie
- Department of Oceanography and Marine Geology, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka
| | - Yuanli Zhu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Zhongqiao Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Bin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Lu Shou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Lihua Ran
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Feng Zhou
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, MNR, Hangzhou, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources (MNR), Hangzhou, China
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Rangamaran VR, Sankara Subramanian SH, Balachandran KRS, Gopal D. Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications. Microb Ecol 2023; 85:357-371. [PMID: 35195736 DOI: 10.1007/s00248-021-01952-z] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.
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Affiliation(s)
- Vijaya Raghavan Rangamaran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India.
| | - Sai H Sankara Subramanian
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - Karpaga Raja Sundari Balachandran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - Dharani Gopal
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India.
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Piscoya E, von Dassow P, Aldunate M, Vargas CA. Physical-chemical factors influencing the vertical distribution of phototrophic pico-nanoplankton in the Oxygen Minimum Zone ( OMZ) off Northern Chile: The relative influence of low pH/low O 2 conditions. Mar Environ Res 2022; 180:105710. [PMID: 35932510 DOI: 10.1016/j.marenvres.2022.105710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
The vertical distribution of phytoplankton is of fundamental importance in the structure, dynamic, and biogeochemical pathways in marine ecosystems. Nevertheless, what are the main factors determining this distribution remains as an open question. Here, we evaluated the relative influence of environmental factors that might control the coexistence and vertical distribution of pico-nanoplankton associated with the OMZ off northern Chile. Our results showed that in the upper layer Synechococcus-like cells were numerically important at all sampling stations. Pico-nano eukaryotes and phototrophic nanoflagellates (PNF) also showed high abundances in the upper layer decreasing in abundance down to the upper oxycline, while only Prochlorococcus showed high abundances under oxycline and within the oxygen-depleted layer. Statistical analyses evidenced that temperature, oxygen, and carbonate chemistry parameters (pH and dissolved inorganic carbon, DIC) influenced significantly the vertical distribution of phototrophic pico-nanoplankton. Additionally, we experimentally-evaluated the combined effect of low pH/low O2 conditions on a nanophytoplankton species, the haptophyte Imantonia sp. Under control conditions (pH = 8.1; O2 = 287.5 μM, light = 169.6 μEm-2s-1), Imantonia sp. in vivo fluorescence increased over fifty times, inducing supersaturated O2 conditions (900 μM) and an increasing pH (8.5), whereas upon an experimental treatment mimicking OMZ conditions (pH = 7.5; O2 = 55.6 μM; light = 169.6 μEm-2s-1), in vivo fluorescence declined dramatically, suggesting that Imantonia sp. did not survive. Although preliminary, our study provides evidence about the role of low pH/low O2 conditions on the vertical distribution of nanophytoplankton, which deserve future attention through both fieldwork and more extended experimental experiences.
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Affiliation(s)
- Edson Piscoya
- Graduate Program in Oceanography, Department of Oceanography, Universidad de Concepción, Casilla 160-C, Concepcion, Chile; Millennium Institute of Oceanography (IMO), Concepción, Chile; Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Department of Aquatic Systems, Faculty of Environmental Sciences, Universidad de Concepción, Concepcion, Chile
| | - Peter von Dassow
- Millennium Institute of Oceanography (IMO), Concepción, Chile; Department of Ecology, P. Universidad Católica de Chile, Alameda 340, Santiago, Chile; Research Fellow, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Montserrat Aldunate
- Millennium Institute of Oceanography (IMO), Concepción, Chile; Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Department of Aquatic Systems, Faculty of Environmental Sciences, Universidad de Concepción, Concepcion, Chile
| | - Cristian A Vargas
- Millennium Institute of Oceanography (IMO), Concepción, Chile; Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Department of Aquatic Systems, Faculty of Environmental Sciences, Universidad de Concepción, Concepcion, Chile; Coastal Socio-ecological Millennium Institute (SECOS), P. Universidad Católica de Chile, Chile.
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Muñoz P, Hevia-Hormazabal V, Araya K, Maldonado A, Salamanca M. Metal enrichment evolution in marine sediments influenced by oxygen-deficient waters in a mineral loading zone, Atacama, Chile (27° S). Mar Environ Res 2022; 177:105619. [PMID: 35405422 DOI: 10.1016/j.marenvres.2022.105619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 03/01/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
This study examines metal concentrations in sediments under the influence of the oxygen minimum zone of the SE-Pacific and the anthropogenic impact following industrialization in Caldera Bay (27° S), which is one of the main ore-loading ports in operation from 1849. 210Pb and the CRS dating method were employed to estimate the age in two sediment cores sectioned at 1 cm. Metal concentrations from selected samples suggested clear impacts of industrial activities after ∼1860 on Cu, and moderate impacts on Fe, Pb, and Zn. Further, authigenic enrichment of nutrient type and redox-sensitive elements (Ni, Cd, Mo, and V) in ancient times was observed. This enrichment was related to low oxygen at the bottom and high productivity. As this condition varies over time, it could result in erroneous estimations of preindustrial values. Overall, we highlight the impact of natural processes on metal distribution in marine sediments during environmental assessments and regulations.
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Affiliation(s)
- Práxedes Muñoz
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo-La Serena, Chile.
| | - Valentina Hevia-Hormazabal
- Programa de Doctorado en Biología y Ecología Aplicada, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile
| | - Karen Araya
- Laboratoire Géosciences Montpellier (GM), Université de Montpellier, 34095, Montpellier, Cedex 05, France
| | - Antonio Maldonado
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo-La Serena, Chile; Instituto de Investigación Multidisciplinario en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Marco Salamanca
- Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
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Ruiz-Perez CA, Bertagnolli AD, Tsementzi D, Woyke T, Stewart FJ, Konstantinidis KT. Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Syst Appl Microbiol 2021; 44:126185. [PMID: 33676264 DOI: 10.1016/j.syapm.2021.126185] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/29/2022]
Abstract
The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades.
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Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, One Cyclotron Road, Mail Stop 91R0183, Berkeley, CA 94720, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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Shah V, Zhao X, Lundeen RA, Ingalls AE, Nicastro D, Morris RM. Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation. mBio 2019; 10:e00216-19. [PMID: 31064824 DOI: 10.1128/mBio.00216-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Identifying shifts in microbial metabolism across redox gradients will improve efforts to model marine oxygen minimum zone (OMZ) ecosystems. Here, we show that aerobic morphology and metabolism increase cell size, sulfur storage capacity, and carbon fixation rates in “Ca. Thioglobus autotrophicus,” a chemosynthetic bacterium from the SUP05 clade that crosses oxic-anoxic boundaries. Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic bacteria survive across oxygen and sulfur gradients and how their mode of survival impacts the environment. Here, we use growth experiments, proteomics, and cryo-electron tomography to show that a SUP05 isolate, “Candidatus Thioglobus autotrophicus,” is amorphous in shape and several times larger and stores considerably more intracellular sulfur when it respires oxygen. We also show that these cells can use diverse sources of reduced organic and inorganic sulfur at submicromolar concentrations. Enhanced cell size, carbon content, and metabolic activity of the aerobic phenotype are likely facilitated by a stabilizing surface-layer (S-layer) and an uncharacterized form of FtsZ-less cell division that supports morphological plasticity. The additional sulfur storage provides an energy source that allows cells to continue metabolic activity when exogenous sulfur sources are not available. This metabolic flexibility leads to the production of more organic carbon in the ocean than is estimated based solely on their anaerobic phenotype.
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Bristow LA, Dalsgaard T, Tiano L, Mills DB, Bertagnolli AD, Wright JJ, Hallam SJ, Ulloa O, Canfield DE, Revsbech NP, Thamdrup B. Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters. Proc Natl Acad Sci U S A 2016; 113:10601-6. [PMID: 27601665 DOI: 10.1073/pnas.1600359113] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (<10 nmol⋅L(-1)) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O2 levels between 5 nmol⋅L(-1) and 20 μmol⋅L(-1) Rates of both processes were detectable in the low nanomolar range (5-33 nmol⋅L(-1) O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L(-1) O2 for ammonium oxidation and 778 ± 168 nmol⋅L(-1) O2 for nitrite oxidation assuming one-component Michaelis-Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis-Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.
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Décima M, Landry MR, Stukel MR, Lopez-Lopez L, Krause JW. Mesozooplankton biomass and grazing in the Costa Rica Dome: amplifying variability through the plankton food web. J Plankton Res 2016; 38:317-330. [PMID: 27275033 PMCID: PMC4889985 DOI: 10.1093/plankt/fbv091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/24/2015] [Indexed: 05/25/2023]
Abstract
We investigated standing stocks and grazing rates of mesozooplankton assemblages in the Costa Rica Dome (CRD), an open-ocean upwelling ecosystem in the eastern tropical Pacific. While phytoplankton biomass in the CRD is dominated by picophytoplankton (<2-µm cells) with especially high concentrations of Synechococcus spp., we found high mesozooplankton biomass (∼5 g dry weight m-2) and grazing impact (12-50% integrated water column chlorophyll a), indicative of efficient food web transfer from primary producers to higher levels. In contrast to the relative uniformity in water-column chlorophyll a and mesozooplankton biomass, variability in herbivory was substantial, with lower rates in the central dome region and higher rates in areas offset from the dome center. While grazing rates were unrelated to total phytoplankton, correlations with cyanobacteria (negative) and biogenic SiO2 production (positive) suggest that partitioning of primary production among phytoplankton sizes contributes to the variability observed in mesozooplankton metrics. We propose that advection of upwelled waters away from the dome center is accompanied by changes in mesozooplankton composition and grazing rates, reflecting small changes within the primary producers. Small changes within the phytoplankton community resulting in large changes in the mesozooplankton suggest that the variability in lower trophic level dynamics was effectively amplified through the food web.
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Affiliation(s)
- Moira Décima
- Scripps Institution of Oceanography, 9500 Gilman Dr., LA Jolla, CA 92093-0227, USA; Present Address: National Institute of Water and Atmospheric Research (NIWA), 301 Evans Bay Parade, Hataitai 6021, Wellington, New Zealand
| | - Michael R Landry
- Scripps Institution of Oceanography , 9500 Gilman Dr., LA Jolla, CA 92093-0227 , USA
| | - Michael R Stukel
- Department of Earth, Ocean, and Atmospheri Science , Florida State University , Tallahasee, FL 32306 , USA
| | - Lucia Lopez-Lopez
- Ieo Centro Oceanografico De Santander , Promontorio San Martin S/N, 39004 Santander-Cantabria , Spain
| | - Jeffrey W Krause
- Dauphin Island Sea Lab , 101 Bienville Blvd, Dauphin Island, AL 36528 , USA
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Enge AJ, Wukovits J, Wanek W, Watzka M, Witte UFM, Hunter WR, Heinz P. Carbon and Nitrogen Uptake of Calcareous Benthic Foraminifera along a Depth-Related Oxygen Gradient in the OMZ of the Arabian Sea. Front Microbiol 2016; 7:71. [PMID: 26903959 PMCID: PMC4749719 DOI: 10.3389/fmicb.2016.00071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 10/31/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Abstract
Foraminifera are an important faunal element of the benthos in oxygen-depleted settings such as Oxygen Minimum Zones (OMZs) where they can play a relevant role in the processing of phytodetritus. We investigated the uptake of phytodetritus (labeled with (13)C and (15)N) by calcareous foraminifera in the 0-1 cm sediment horizon under different oxygen concentrations within the OMZ in the eastern Arabian Sea. The in situ tracer experiments were carried out along a depth transect on the Indian margin over a period of 4 to 10 days. The uptake of phytodetrital carbon within 4 days by all investigated species shows that phytodetritus is a relevant food source for foraminifera in OMZ sediments. The decrease of total carbon uptake from 540 to 1100 m suggests a higher demand for carbon by species in the low-oxygen core region of the OMZ or less food competition with macrofauna. Especially Uvigerinids showed high uptake of phytodetrital carbon at the lowest oxygenated site. Variation in the ratio of phytodetrital carbon to nitrogen between species and sites indicates that foraminiferal carbon and nitrogen use can be decoupled and different nutritional demands are found between species. Lower ratio of phytodetrital carbon and nitrogen at 540 m could hint for greater demand or storage of food-based nitrogen, ingestion, or hosting of bacteria under almost anoxic conditions. Shifts in the foraminiferal assemblage structure (controlled by oxygen or food availability) and in the presence of other benthic organisms are likely to account for observed changes in the processing of phytodetritus in the different OMZ habitats. Foraminifera dominate the short-term processing of phytodetritus in the OMZ core but are less important in the lower OMZ boundary region of the Indian margin as biological interactions and species distribution of foraminifera change with depth and oxygen levels.
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Affiliation(s)
| | - Julia Wukovits
- Department of Palaeontology, University of Vienna Vienna, Austria
| | - Wolfgang Wanek
- Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Margarete Watzka
- Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | | | - William R Hunter
- School of Biological Sciences, Queen's University Belfast Belfast, UK
| | - Petra Heinz
- Department of Palaeontology, University of Vienna Vienna, Austria
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Azhar MA, Canfield DE, Fennel K, Thamdrup B, Bjerrum CJ. A model-based insight into the coupling of nitrogen and sulfur cycles in a coastal upwelling system. J Geophys Res Biogeosci 2014; 119. [PMID: 26213661 PMCID: PMC4508913 DOI: 10.1002/2012jg002271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The biogeochemical cycling in oxygen-minimum zones (OMZs) is dominated by the interactions of microbial nitrogen transformations and, as recently observed in the Chilean upwelling system, also through the energetically less favorable remineralization of sulfate reduction. The latter process is masked, however, by rapid sulfide oxidation, most likely through nitrate reduction. Thus, the cryptic sulfur cycle links with the nitrogen cycle in OMZ settings. Here, we model the physical-chemical water column structure and the observed process rates as driven by formation and sinking of organic detritus, to quantify the nitrogen and sulfur cycles in the Chilean OMZ. A new biogeochemical submodule was developed and coupled to the Regional Ocean Model System (ROMS). The model results generally agree with the observed distribution of reactive species and the measured process rates. Modeled heterotrophic nitrate reduction and sulfate reduction are responsible for 47% and 36%, respectively, of organic remineralization in a 150 m deep zone below mixed layer. Anammox contributes to 61% of the fixed nitrogen lost to N2 gas, while the rest of the loss is through canonical denitrification as a combination of organic matter oxidation by nitrite reduction and sulfide-driven denitrification. Mineralization coupled to heterotrophic nitrate reduction supplies ∼48% of the ammonium required by anammox. Due to active sulfate reduction, model results suggest that sulfide-driven denitrification contributes to 36% of the nitrogen loss as N2 gas. Our model results highlight the importance of considering the coupled nitrogen and sulfur cycle in examining open-ocean anoxic processes under present, past, and future conditions.
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Affiliation(s)
- Muchamad Al Azhar
- Nordic Center for Earth Evolution (NordCEE) and Department of Geosciences and Natural Resource Management, University of CopenhagenKøbenhavn K, Denmark
- Correspondence to: M. A. Azhar,
| | - Donald E Canfield
- Nordic Center for Earth Evolution (NordCEE) and Institute of Biology, University of Southern DenmarkOdense M, Denmark
| | - Katja Fennel
- Department of Oceanography, Dalhousie UniversityHalifax, Nova Scotia, Canada
| | - Bo Thamdrup
- Nordic Center for Earth Evolution (NordCEE) and Institute of Biology, University of Southern DenmarkOdense M, Denmark
| | - Christian J Bjerrum
- Nordic Center for Earth Evolution (NordCEE) and Department of Geosciences and Natural Resource Management, University of CopenhagenKøbenhavn K, Denmark
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Orsi W, Charvet S, Vd'ačný P, Bernhard JM, Edgcomb VP. Prevalence of partnerships between bacteria and ciliates in oxygen-depleted marine water columns. Front Microbiol 2012; 3:341. [PMID: 23049527 PMCID: PMC3446810 DOI: 10.3389/fmicb.2012.00341] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [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: 06/29/2012] [Accepted: 09/04/2012] [Indexed: 11/30/2022] Open
Abstract
Symbioses between Bacteria, Archaea, and Eukarya in deep-sea marine environments represent a means for eukaryotes to exploit otherwise inhospitable habitats. Such symbioses are abundant in many low-oxygen benthic marine environments, where the majority of microbial eukaryotes contain prokaryotic symbionts. Here, we present evidence suggesting that in certain oxygen-depleted marine water-column habitats, the majority of microbial eukaryotes are also associated with prokaryotic cells. Ciliates (protists) associated with bacteria were found to be the dominant eukaryotic morphotype in the haloclines of two different deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea. These findings are compared to associations between ciliates and bacteria documented from the permanently anoxic waters of the Cariaco Basin (Caribbean Sea). The dominance of ciliates exhibiting epibiotic bacteria across three different oxygen-depleted marine water column habitats suggests that such partnerships confer a fitness advantage for ciliates in these environments.
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Affiliation(s)
- William Orsi
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution Woods Hole, MA, USA
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