0
selected
-
1.
The Complexity of Spills: The Fate of the Deepwater Horizon Oil.
Passow, U, Overton, EB
Annual review of marine science. 2021;:109-136
Abstract
The Deepwater Horizon oil spill was the largest, longest-lasting, and deepest oil accident to date in US waters. As oil and natural gas jetted from release points at 1,500-m depth in the northern Gulf of Mexico, entrainment of the surrounding ocean water into a buoyant plume, rich in soluble hydrocarbons and dispersed microdroplets of oil, created a deep (1,000-m) intrusion layer. Larger droplets of liquid oil rose to the surface, forming a slick of mostly insoluble, hydrocarbon-type compounds. A variety of physical, chemical, and biological mechanisms helped to transform, remove, and redisperse the oil and gas that was released. Biodegradation removed up to 60% of the oil in the intrusion layer but was less efficient in the surface slick, due to nutrient limitation. Photochemical processes altered up to 50% (by mass) of the floating oil. The surface oil expression changed daily due to wind and currents, whereas the intrusion layer flowed southwestward. A portion of the weathered surface oil stranded along shorelines. Oil from both surface and intrusion layers were deposited onto the seafloor via sinking marine oil snow. The biodegradation rates of stranded or sedimented oil were low, with resuspension and redistribution transiently increasing biodegradation. The subsequent research efforts increased our understanding of the fate of spilled oil immensely, with novel insights focusing on the importance of photooxidation, the microbial communities driving biodegradation, and the formation of marine oil snow that transports oil to the seafloor.
-
2.
New Microbial Biodiversity in Marine Sediments.
Baker, BJ, Appler, KE, Gong, X
Annual review of marine science. 2021;:161-175
Abstract
Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.
-
3.
Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria.
Ford, BA, Sullivan, GJ, Moore, L, Varkey, D, Zhu, H, Ostrowski, M, Mabbutt, BC, Paulsen, IT, Shah, BS
Biochemical Society transactions. 2021;(6):2465-2481
-
-
Free full text
-
Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
-
4.
The ambivalent role of water at the origins of life.
do Nascimento Vieira, A, Kleinermanns, K, Martin, WF, Preiner, M
FEBS letters. 2020;(17):2717-2733
-
-
Free full text
-
Abstract
Life as we know it would not exist without water. However, water molecules not only serve as a solvent and reactant but can also promote hydrolysis, which counteracts the formation of essential organic molecules. This conundrum constitutes one of the central issues in origin of life. Hydrolysis is an important part of energy metabolism for all living organisms but only because, inside cells, it is a controlled reaction. How could hydrolysis have been regulated under prebiotic settings? Lower water activities possibly provide an answer: geochemical sites with less free and more bound water can supply the necessary conditions for protometabolic reactions. Such conditions occur in serpentinising systems, hydrothermal sites that synthesise hydrogen gas via rock-water interactions. Here, we summarise the parallels between biotic and abiotic means of controlling hydrolysis in order to narrow the gap between biochemical and geochemical reactions and briefly outline how hydrolysis could even have played a constructive role at the origin of molecular self-organisation.
-
5.
Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater.
Li, SH, Song, J, Kang, I, Hwang, J, Cho, JC
Journal of microbiology (Seoul, Korea). 2020;(6):463-471
Abstract
A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088T, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1BT (94.5%) and Halioglobus pacificus S1-72T (94.5%), followed by 92.3-94.3% sequence similarities with other species within the aforementioned family. Phylogenetic analyses demonstrated that strain IMCC3088T was robustly clustered with Luminiphilus syltensis NOR5-1BT within the family Halieaceae. However, average amino acid identity (AAI), percentages of conserved proteins (POCP), average nucleotide identity (ANI), and alignment fraction (AF) between strain IMCC3088T and Luminiphilus syltensis NOR5-1BT were 54.5%, 47.7%, 68.0%, and 16.5%, respectively, suggesting that they belonged to different genera. Whole-genome sequencing of strain IMCC3088T revealed a 3.1 Mbp genome size with a DNA G + C content of 51.7 mol%. The genome encoded diverse metabolic pathways including sulfur oxidation, phenol degradation, and proteorhodopsin phototrophy. Mono-unsaturated fatty acids were found to be the predominant cellular fatty acid components in the strain. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the primarily identified polar lipids, and ubiquinone-8 was identified as a major respiratory quinone. The taxonomic data collected herein suggested that strain IMCC3088T represented a novel genus and species of the family Halieaceae, for which the name Aequoribacter fuscus gen. nov., sp. nov. is proposed with the type strain (= KACC 15529T = NBRC 108213T).
-
6.
Progress in the Study and Use of Seawater Vegetables.
Li, L, Zhao, Y, Han, G, Guo, J, Meng, Z, Chen, M
Journal of agricultural and food chemistry. 2020;(22):5998-6006
Abstract
As global soil salinization increases, halophytes that can grow in saline soils are the primary choice for improving soil quality. Some halophytes can even be irrigated with seawater and used as vegetables. These so-called seawater vegetables include those that can be planted on saline and alkali soils and some edible halophytes and ordinary vegetables that are salt-tolerant. The cultivation of seawater vegetables on saline soil has become a matter of increasing interest. In this review, we focus on the salt-tolerance mechanisms and potential applications of some seawater vegetables. We also summarize their value to health, medicine, industry, and the economy as a whole. Further improvement and development to support the use of seawater vegetables will require in-depth research at the cellular and molecular levels.
-
7.
GEOTRACES: Accelerating Research on the Marine Biogeochemical Cycles of Trace Elements and Their Isotopes.
Anderson, RF
Annual review of marine science. 2020;:49-85
Abstract
The biogeochemical cycles of trace elements and their isotopes (TEIs) constitute an active area of oceanographic research due to their role as essential nutrients for marine organisms and their use as tracers of oceanographic processes. Selected TEIs also provide diagnostic information about the physical, geological, and chemical processes that supply or remove solutes in the ocean. Many of these same TEIs provide information about ocean conditions in the past, as their imprint on marine sediments can be interpreted to reflect changes in ocean circulation, biological productivity, the ocean carbon cycle, and more. Other TEIs have been introduced as the result of human activities and are considered contaminants. The development and implementation of contamination-free methods for collecting and analyzing samples for TEIs revolutionized marine chemistry, revealing trace element distributions with oceanographically consistent features and new insights about the processes regulating them. Despite these advances, the volume and geographic coverage of high-quality TEI data by the end of the twentieth century were insufficient to constrain their global biogeochemical cycles. To accelerate progress in this field of research, marine geochemists developed a coordinated international effort to systematically study the marine biogeochemical cycles of TEIs-the GEOTRACES program. Following a decade of planning and implementation, GEOTRACES launched its main field effort in 2010. This review, roughly midway through the field program, summarizes the steps involved in designing the program, its management structure, and selected findings.
-
8.
Upwelling Bays: How Coastal Upwelling Controls Circulation, Habitat, and Productivity in Bays.
Largier, JL
Annual review of marine science. 2020;:415-447
Abstract
Bays in coastal upwelling regions are physically driven and biochemically fueled by their interaction with open coastal waters. Wind-driven flow over the shelf imposes a circulation in the bay, which is also influenced by local wind stress and thermal bay-ocean density differences. Three types of bays are recognized based on the degree of exposure to coastal currents and winds (wide-open bays, square bays, and elongated bays), and the characteristic circulation and stratification patterns of each type are described. Retention of upwelled waters in bays allows for dense phytoplankton blooms that support productive bay ecosystems. Retention is also important for the accumulation of larvae, which accounts for high recruitment in bays. In addition, bays are coupled to the shelf ecosystem through export of plankton-rich waters during relaxation events. Ocean acidification and deoxygenation are a concern in bays because local extrema can develop beneath strong stratification.
-
9.
Sulfur metabolites in the pelagic ocean.
Moran, MA, Durham, BP
Nature reviews. Microbiology. 2019;(11):665-678
Abstract
Marine microorganisms play crucial roles in Earth's element cycles through the production and consumption of organic matter. One of the elements whose fate is governed by microbial activities is sulfur, an essential constituent of biomass and a crucial player in climate processes. With sulfur already being well studied in the ocean in its inorganic forms, organic sulfur compounds are emerging as important chemical links between marine phytoplankton and bacteria. The high concentration of inorganic sulfur in seawater, which can readily be reduced by phytoplankton, provides a freely available source of sulfur for biomolecule synthesis. Mechanisms such as exudation and cell lysis release these phytoplankton-derived sulfur metabolites into seawater, from which they are rapidly assimilated by marine bacteria and archaea. Energy-limited bacteria use scavenged sulfur metabolites as substrates or for the synthesis of vitamins, cofactors, signalling compounds and antibiotics. In this Review, we examine the current knowledge of sulfur metabolites released into and taken up from the marine dissolved organic matter pool by microorganisms, and the ecological links facilitated by their diversity in structures, oxidation states and chemistry.
-
10.
Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities.
Stal, LJ, Bolhuis, H, Cretoiu, MS
Environmental microbiology. 2019;(5):1529-1551
Abstract
Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.