The Physiology and Biogeochemistry of SUP05

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Robert M. Morris ◽  
Rachel L. Spietz
Keyword(s):  
Hydrothermal Vents ◽  
Heterotrophic Bacteria ◽  
Primary Source ◽  
Annual Review ◽  
Publication Date ◽  
Community Studies ◽  
Oxygen Minimum Zones ◽  
Anoxic Waters ◽  
Total Bacterial Community ◽  
Oxygen Minimum

The SUP05 clade of gammaproteobacteria (Thioglobaceae) comprises both primary producers and primary consumers of organic carbon in the oceans. Host-associated autotrophs are a principal source of carbon and other nutrients for deep-sea eukaryotes at hydrothermal vents, and their free-living relatives are a primary source of organic matter in seawater at vents and in marine oxygen minimum zones. Similar to other abundant marine heterotrophs, such as SAR11 and Roseobacter, heterotrophic Thioglobaceae use the dilute pool of osmolytes produced by phytoplankton for growth, including methylated amines and sulfonates. Heterotrophic members are common throughout the ocean, and autotrophic members are abundant at hydrothermal vents and in anoxic waters; combined, they can account for more than 50% of the total bacterial community. Studies of both cultured and uncultured representatives from this diverse family are providing novel insights into the shifting biogeochemical roles of autotrophic and heterotrophic bacteria that cross oxic–anoxic boundary layers in the ocean. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Organic Matter Supply and Utilization in Oxygen Minimum Zones

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Anja Engel ◽  
Rainer Kiko ◽  
Marcus Dengler
Keyword(s):  
Organic Matter ◽  
Collaborative Research ◽  
Research Priorities ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
Low Oxygen ◽  
Oxygen Minimum Zones ◽  
New Findings ◽  
Oxygen Minimum

Organic matter (OM) plays a significant role in the formation of oxygen minimum zones (OMZs) and associated biogeochemical cycling. OM supply processes to the OMZ include physical transport, particle formation, and sinking as well as active transport by migrating zooplankton and nekton. In addition to the availability of oxygen and other electron acceptors, the remineralization rate of OM is controlled by its biochemical quality. Enhanced microbial respiration of OM can induce anoxic microzones in an otherwise oxygenated water column. Reduced OM degradation under low-oxygen conditions, on the other hand, may increase the CO2 storage time in the ocean. Understanding the interdependencies between OM and oxygen cycling is of high relevance for an ocean facing deoxygenation as a consequence of global warming. In this review, we describe OM fluxes into and cycling within two large OMZs associated with eastern boundary upwelling systems that differ greatly in the extent of oxygen loss: the highly oxygen-depleted OMZ in the tropical South Pacific and the moderately hypoxic OMZ in the tropical North Atlantic. We summarize new findings from a large German collaborative research project, Collaborative Research Center 754 (SFB 754), and identify knowledge gaps and future research priorities. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
E. Maggie Sogin ◽  
Manuel Kleiner ◽  
Christian Borowski ◽  
Harald R. Gruber-Vodicka ◽  
Nicole Dubilier
Keyword(s):  
Hydrothermal Vents ◽  
Annual Review ◽  
Publication Date ◽  
Metabolic Diversity ◽  
Research Directions ◽  
Physiological Diversity ◽  
Living Together ◽  
Gain Energy ◽  
Chemosynthetic Bacteria ◽  
Ecological Success

Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Small sinking particles control anammox rates in the Peruvian oxygen minimum zone

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Clarissa Karthäuser ◽  
Soeren Ahmerkamp ◽  
Hannah K. Marchant ◽  
Laura A. Bristow ◽  
Helena Hauss ◽  
...  
Keyword(s):  
Nitrogen Loss ◽  
Anammox Bacteria ◽  
Small Particles ◽  
Free Living ◽  
Major Pathway ◽  
Oxygen Minimum Zones ◽  
Anoxic Waters ◽  
Sinking Particles ◽  
Minimum Zone ◽  
Oxygen Minimum

AbstractAnaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.

scholarly journals Genome-resolved viral ecology in a marine oxygen minimum zone (OMZ)

2020 ◽  
Author(s):  
Dean Vik ◽  
Maria Consuelo Gazitúa ◽  
Christine L. Sun ◽  
Montserrat Aldunate ◽  
Margaret R. Mulholland ◽  
...  
Keyword(s):  
Community Structure ◽  
Global Climate ◽  
South Pacific ◽  
Ecological Change ◽  
Alpha And Beta Diversity ◽  
Oxygen Minimum Zones ◽  
Anoxic Waters ◽  
Viral Community ◽  
Viral Communities ◽  
Oxygen Minimum

SummaryOxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of surface oxygenated to anoxic waters (< 0.02 μmol/L O2) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46,127 viral populations (>5 kb), which augments the known viruses at this site by 10-fold. ETSP viral communities clustered into 6 groups that correspond to oceanographic features, with 3 clusters representing samples from suboxic to anoxic waters. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. Viruses were largely endemic as few (6% of viruses from this study) were found in at least another marine metagenome, and of those, most (77%) were restricted to other OMZs. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.Originality-Significance StatementMarine oxygen minimum zones (OMZs) are unique and important ocean ecosystems where microbes drive climate-altering nutrient transformations. This study provides a baseline, deeply sequenced viral metagenomic dataset and reference viral genomes to assess ecological change and drivers across the oxygenated surface to de-oxygenated deep waters of the Eastern Tropical South Pacific (ETSP) OMZ. Community ecological assessment of the ETSP viromes reveals a relatively low diversity viral community with a high degree of endemic populations in the OMZ waters.

scholarly journals Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones

2021 ◽  
Author(s):  
Xin Sun ◽  
Claudia Frey ◽  
Emilio Garcia-Robledo ◽  
Amal Jayakumar ◽  
Bess B. Ward
Keyword(s):  
Nitrogen Loss ◽  
Niche Differentiation ◽  
Nitrite Reduction ◽  
Nitrite Oxidation ◽  
Fixed Nitrogen ◽  
Anoxic Waters ◽  
Biogeochemical Models ◽  
Nitrite Oxidizing Bacteria ◽  
Oxygen Addition ◽  
Oxygen Minimum

AbstractNitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals In situ quantification of ultra‐low O 2 concentrations in oxygen minimum zones: Application of novel optodes

2016 ◽  
Vol 14 (12) ◽  
pp. 784-800 ◽  
Author(s):  
Morten Larsen ◽  
Philipp Lehner ◽  
Sergey M. Borisov ◽  
Ingo Klimant ◽  
Jan P. Fischer ◽  
...  
Keyword(s):  
Oxygen Minimum Zones ◽  
Oxygen Minimum

scholarly journals Expanded oxygen minimum zones during the late Paleocene-early Eocene: Hints from multiproxy comparison and ocean modeling

2016 ◽  
Vol 31 (12) ◽  
pp. 1532-1546 ◽  
Author(s):  
X. Zhou ◽  
E. Thomas ◽  
A. M. E. Winguth ◽  
A. Ridgwell ◽  
H. Scher ◽  
...  
Keyword(s):  
Ocean Modeling ◽  
Early Eocene ◽  
Oxygen Minimum Zones ◽  
Late Paleocene ◽  
Oxygen Minimum

scholarly journals Growth and Phylogenetic Properties of Novel Bacteria Belonging to the Epsilon Subdivision of the Proteobacteria Enriched fromAlvinella pompejana and Deep-Sea Hydrothermal Vents

2001 ◽  
Vol 67 (10) ◽  
pp. 4566-4572 ◽  
Author(s):  
Barbara J. Campbell ◽  
Christian Jeanthon ◽  
Joel E. Kostka ◽  
George W. Luther ◽  
S. Craig Cary
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Heterotrophic Bacteria ◽  
Geographic Location ◽  
Optimal Growth ◽  
Small Subunit ◽  
Ribosomal Gene ◽  
Moderately Thermophilic ◽  
Novel Bacteria

ABSTRACT Recent molecular characterizations of microbial communities from deep-sea hydrothermal sites indicate the predominance of bacteria belonging to the epsilon subdivision of Proteobacteria(epsilon Proteobacteria). Here, we report the first enrichments and characterizations of four epsilonProteobacteria that are directly associated withAlvinella pompejana, a deep sea hydrothermal vent polychete, or with hydrothermal vent chimney samples. These novel bacteria were moderately thermophilic sulfur-reducing heterotrophs growing on formate as the energy and carbon source. In addition, two of them (Am-H and Ex-18.2) could grow on sulfur lithoautrotrophically using hydrogen as the electron donor. Optimal growth temperatures of the bacteria ranged from 41 to 45°C. Phylogenetic analysis of the small-subunit ribosomal gene of the two heterotrophic bacteria demonstrated 95% similarity to Sulfurospirillum arcachonense, an epsilon Proteobacteria isolated from an oxidized marine surface sediment. The autotrophic bacteria grouped within a deeply branching clade of the epsilonProteobacteria, to date composed only of uncultured bacteria detected in a sample from a hydrothermal vent along the mid-Atlantic ridge. A molecular survey of various hydrothermal vent environments demonstrated the presence of two of these bacteria (Am-N and Am-H) in more than one geographic location and habitat. These results suggest that certain epsilonProteobacteria likely fill important niches in the environmental habitats of deep-sea hydrothermal vents, where they contribute to overall carbon and sulfur cycling at moderate thermophilic temperatures.

Advancing Socioeconomic Rights Through Interdisciplinary Factfinding: Opportunities and Challenges

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Sarah Knuckey ◽  
Joshua D. Fisher ◽  
Amanda M. Klasing ◽  
Tess Russo ◽  
Margaret L. Satterthwaite
Keyword(s):  
Human Rights ◽  
Mixed Methods ◽  
Social Science ◽  
Science Volume ◽  
Lessons Learned ◽  
Limited Resources ◽  
Annual Review ◽  
Publication Date ◽  
Socioeconomic Rights ◽  
Human Rights Movement

The human rights movement is increasingly using interdisciplinary, multidisciplinary, mixed-methods, and quantitative factfinding. There has been too little analysis of these shifts. This article examines some of the opportunities and challenges of these methods, focusing on the investigation of socioeconomic human rights. By potentially expanding the amount and types of evidence available, factfinding's accuracy and persuasiveness can be strengthened, bolstering rights claims. However, such methods can also present significant challenges and may pose risks in individual cases and to the human rights movement generally. Interdisciplinary methods can be costly in human, financial, and technical resources; are sometimes challenging to implement; may divert limited resources from other work; can reify inequalities; may produce “expertise” that disempowers rightsholders; and could raise investigation standards to an infeasible or counterproductive level. This article includes lessons learned and questions to guide researchers and human rights advocates considering mixed-methods human rights factfinding. Expected final online publication date for the Annual Review of Law and Social Science, Volume 17 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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