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1.
Ann Rev Mar Sci ; 16: 577-599, 2024 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-37722713

RESUMO

The speciation of most biologically active trace metals in seawater is dominated by complexation by organic ligands. This review traces the history of work in this area, from the early observations that showed surprisingly poor recoveries using metal preconcentration protocols to the present day, where advances in mass spectroscopy and stable isotope geochemistry are providing new insights into the structure, origin, fate, and biogeochemical impact of organic ligands. Many long-standing hypotheses about the specific biological origin of ligands such as siderophores in seawater are finally being validated. This work has revealed the complexity of organic complexation, with multiple ligands and, in some cases, timescales of ligand exchange that are much slower than originally thought. The influence of organic complexation on scavenging is now a key parameter in biogeochemical models of biologically essential metals, especially iron. New insights about the sources and sinks of ligands are required to enhance the usefulness of these models.


Assuntos
Água do Mar , Oligoelementos
3.
Environ Microbiol Rep ; 10(4): 453-457, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30022612

RESUMO

Cobalamin (vitamin B12 ) is a precious resource in natural systems that is produced by select prokaryotes and required by a broad range of organisms. In this way, the production of cobalamin reinforces numerous microbial interdependencies. Here we report the accumulation of an unusual form of cobalamin, nitrocobalamin (NO2 -cobalamin), in a marine oxygen deficient zone (ODZ), isolates of ammonia-oxidizing archaea (AOA), and an anaerobic ammonium-oxidizing (anammox) bacteria enriched bioreactor. Low oxygen waters were enriched in NO2 -cobalamin, and AOA isolates experiencing ammonia or copper stress produced more NO2 -cobalamin, though there is wide strain-to-strain and batch-to-batch variability. NO2 -cobalamin has no known biochemical role. We hypothesize that AOA and anammox bacteria are a source of marine NO2 -cobalamin in the environment via a reactive nitrogen intermediate. These findings suggest connections between cobalamin forms and nitrogen transformations, physiological stress and ocean deoxygenation.


Assuntos
Archaea/metabolismo , Água do Mar/química , Estresse Fisiológico , Vitamina B 12/análogos & derivados , Amônia/metabolismo , Archaea/fisiologia , Reatores Biológicos , Cobre/deficiência , Cobre/metabolismo , Hipóxia , Oxirredução , Oceano Pacífico , Clima Tropical , Vitamina B 12/análise , Vitamina B 12/química , Vitamina B 12/metabolismo
4.
ISME J ; 12(2): 508-519, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29053148

RESUMO

High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu stress was downregulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.


Assuntos
Amônia/metabolismo , Archaea/metabolismo , Estresse Fisiológico , Archaea/efeitos dos fármacos , Archaea/enzimologia , Archaea/genética , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Ciclo do Carbono , Cobre/toxicidade , Oxirredução , Oxirredutases/genética , Oxirredutases/metabolismo , Proteômica , Estresse Fisiológico/genética , Transcriptoma , Vitamina B 12/biossíntese , Microbiologia da Água
5.
Int J Syst Evol Microbiol ; 67(12): 5067-5079, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-29034851

RESUMO

Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1T, HCA1T, HCE1T and PS0T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1T, HCE1T, and PS0T. Strain PS0T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0-34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1T (=ATCC TSD-97T =NCIMB 15022T), HCA1T (=ATCC TSD-96T), HCE1T (=ATCC TSD-98T), and PS0T (=ATCC TSD-99T) are type strains of the species Nitrosopumilusmaritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.


Assuntos
Archaea/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Amônia/metabolismo , Archaea/genética , Archaea/isolamento & purificação , Composição de Bases , DNA Arqueal/genética , Estuários , Éteres de Glicerila/química , Oxirredução , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Washington
6.
Environ Microbiol Rep ; 9(3): 250-256, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28211189

RESUMO

Recent studies point to the importance of oxygen (O2 ) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O2 tension in oceanic oxygen minimum zones (OMZs), and O2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2 O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low µM O2 concentrations, characteristic of suboxic regions of OMZs (<10 µM O2 ), and that atmospheric concentrations of O2 may inhibit the growth of some environmental populations. We quantify the increasing N2 O production by marine AOA with decreasing O2 tensions, consistent with the plausibility of an AOA contribution to the accumulation of N2 O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations.


Assuntos
Amônia/metabolismo , Anaerobiose/fisiologia , Archaea/metabolismo , Óxido Nitroso/metabolismo , Oxigênio/metabolismo , Archaea/crescimento & desenvolvimento , Peróxido de Hidrogênio/farmacologia , Oceanos e Mares , Oxirredução
7.
Proc Natl Acad Sci U S A ; 114(2): 364-369, 2017 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-28028206

RESUMO

Organisms within all domains of life require the cofactor cobalamin (vitamin B12), which is produced only by a subset of bacteria and archaea. On the basis of genomic analyses, cobalamin biosynthesis in marine systems has been inferred in three main groups: select heterotrophic Proteobacteria, chemoautotrophic Thaumarchaeota, and photoautotrophic Cyanobacteria. Culture work demonstrates that many Cyanobacteria do not synthesize cobalamin but rather produce pseudocobalamin, challenging the connection between the occurrence of cobalamin biosynthesis genes and production of the compound in marine ecosystems. Here we show that cobalamin and pseudocobalamin coexist in the surface ocean, have distinct microbial sources, and support different enzymatic demands. Even in the presence of cobalamin, Cyanobacteria synthesize pseudocobalamin-likely reflecting their retention of an oxygen-independent pathway to produce pseudocobalamin, which is used as a cofactor in their specialized methionine synthase (MetH). This contrasts a model diatom, Thalassiosira pseudonana, which transported pseudocobalamin into the cell but was unable to use pseudocobalamin in its homolog of MetH. Our genomic and culture analyses showed that marine Thaumarchaeota and select heterotrophic bacteria produce cobalamin. This indicates that cobalamin in the surface ocean is a result of de novo synthesis by heterotrophic bacteria or via modification of closely related compounds like cyanobacterially produced pseudocobalamin. Deeper in the water column, our study implicates Thaumarchaeota as major producers of cobalamin based on genomic potential, cobalamin cell quotas, and abundance. Together, these findings establish the distinctive roles played by abundant prokaryotes in cobalamin-based microbial interdependencies that sustain community structure and function in the ocean.


Assuntos
Vitamina B 12/metabolismo , 5-Metiltetra-Hidrofolato-Homocisteína S-Metiltransferase/metabolismo , Archaea/metabolismo , Cianobactérias/metabolismo , Diatomáceas/metabolismo , Ecossistema , Processos Heterotróficos/fisiologia , Oceanos e Mares
8.
J Plankton Res ; 38(2): 167-182, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27275023

RESUMO

The Costa Rica Dome (CRD) is an open-ocean upwelling system in the Eastern Tropical Pacific that overlies the ocean's largest oxygen minimum zone (OMZ). The region has unique characteristics, biomass dominance by picophytoplankton, suppressed diatoms, high biomass of higher consumers and presumptive trace metal limitation, but is poorly understood in terms of pelagic stock and process relationships, including productivity and production controls. Here, we describe the goals, project design, physical context and major findings of the Flux and Zinc Experiments cruise conducted in June-July 2010 to assess trophic flux relationships and elemental controls on phytoplankton in the CRD. Despite sampling during a year of suppressed summertime surface chlorophyll, cruise results show high productivity (∼1 g C m-2 day-1), high new production relative to export, balanced production and grazing, disproportionate biomass-specific productivity of large phytoplankton and high zooplankton stocks. Zinc concentrations are low in surface waters relative to phosphorous and silicate in other regions, providing conditions conducive to picophytoplankton, like Synechococcus, with low Zn requirements. Experiments nonetheless highlight phytoplankton limitation or co-limitation by silicic acid, driven by a strong silica pump that is linked to low dissolution of biogenic silica in the cold shallow thermocline of the lower euphotic zone.

9.
J Plankton Res ; 38(2): 244-255, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27275028

RESUMO

The Costa Rica Dome (CRD) is a wind-driven feature characterized by high primary production and an unusual cyanobacterial bloom in surface waters. It is not clear whether this bloom arises from top-down or bottom-up processes. Several studies have argued that trace metal geochemistry within the CRD contributes to the composition of the phytoplankton assemblages, since cyanobacteria and eukaryotic phytoplankton have different transition metal requirements. Here, we report that total dissolved zinc (Zn) is significantly depleted relative to phosphate (P) and silicate (Si) within the upper water column of the CRD compared with other oceanic systems, and this may create conditions favorable for cyanobacteria, which have lower Zn requirements than their eukaryotic competitors. Shipboard grow-out experiments revealed that while Si was a limiting factor under our experimental conditions, additions of Si and either iron (Fe) or Zn led to higher biomass than Si additions alone. The addition of Fe and Zn alone did not lead to significant enhancements. Our results suggest that the depletion of Zn relative to P in upwelled waters may create conditions in the near-surface waters that favor phytoplankton with low Zn requirements, including cyanobacteria.

10.
ISME J ; 10(2): 333-45, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26208139

RESUMO

Marine picocyanobacteria, comprised of the genera Synechococcus and Prochlorococcus, are the most abundant and widespread primary producers in the ocean. More than 20 genetically distinct clades of marine Synechococcus have been identified, but their physiology and biogeography are not as thoroughly characterized as those of Prochlorococcus. Using clade-specific qPCR primers, we measured the abundance of 10 Synechococcus clades at 92 locations in surface waters of the Atlantic and Pacific Oceans. We found that Synechococcus partition the ocean into four distinct regimes distinguished by temperature, macronutrients and iron availability. Clades I and IV were prevalent in colder, mesotrophic waters; clades II, III and X dominated in the warm, oligotrophic open ocean; clades CRD1 and CRD2 were restricted to sites with low iron availability; and clades XV and XVI were only found in transitional waters at the edges of the other biomes. Overall, clade II was the most ubiquitous clade investigated and was the dominant clade in the largest biome, the oligotrophic open ocean. Co-occurring clades that occupy the same regime belong to distinct evolutionary lineages within Synechococcus, indicating that multiple ecotypes have evolved independently to occupy similar niches and represent examples of parallel evolution. We speculate that parallel evolution of ecotypes may be a common feature of diverse marine microbial communities that contributes to functional redundancy and the potential for resiliency.


Assuntos
Ferro/metabolismo , Água do Mar/química , Água do Mar/microbiologia , Synechococcus/isolamento & purificação , Synechococcus/metabolismo , Primers do DNA/genética , Ecótipo , Ferro/análise , Oceanos e Mares , Oceano Pacífico , Filogenia , Prochlorococcus/genética , Prochlorococcus/metabolismo , Synechococcus/classificação , Synechococcus/genética , Temperatura
11.
Front Microbiol ; 6: 998, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26441925

RESUMO

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

12.
Proc Natl Acad Sci U S A ; 112(35): 10979-84, 2015 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-26283385

RESUMO

Marine ammonia-oxidizing archaea (AOA) are among the most abundant of marine microorganisms, spanning nearly the entire water column of diverse oceanic provinces. Historical patterns of abundance are preserved in sediments in the form of their distinctive glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids. The correlation between the composition of GDGTs in surface sediment and the overlying annual average sea surface temperature forms the basis for a paleotemperature proxy (TEX86) that is used to reconstruct surface ocean temperature as far back as the Middle Jurassic. However, mounting evidence suggests that factors other than temperature could also play an important role in determining GDGT distributions. We here use a study set of four marine AOA isolates to demonstrate that these closely related strains generate different TEX86-temperature relationships and that oxygen (O2) concentration is at least as important as temperature in controlling TEX86 values in culture. All of the four strains characterized showed a unique membrane compositional response to temperature, with TEX86-inferred temperatures varying as much as 12 °C from the incubation temperatures. In addition, both linear and nonlinear TEX86-temperature relationships were characteristic of individual strains. Increasing relative abundance of GDGT-2 and GDGT-3 with increasing O2 limitation, at the expense of GDGT-1, led to significant elevations in TEX86-derived temperature. Although the adaptive significance of GDGT compositional changes in response to both temperature and O2 is unclear, this observation necessitates a reassessment of archaeal lipid-based paleotemperature proxies, particularly in records that span low-oxygen events or underlie oxygen minimum zones.


Assuntos
Archaea/metabolismo , Biologia Marinha , Oxigênio/metabolismo , Temperatura , Amônia/metabolismo , Archaea/crescimento & desenvolvimento , Fatores de Confusão Epidemiológicos
13.
Nature ; 523(7559): 200-3, 2015 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-26156374

RESUMO

Hydrothermal venting along mid-ocean ridges exerts an important control on the chemical composition of sea water by serving as a major source or sink for a number of trace elements in the ocean. Of these, iron has received considerable attention because of its role as an essential and often limiting nutrient for primary production in regions of the ocean that are of critical importance for the global carbon cycle. It has been thought that most of the dissolved iron discharged by hydrothermal vents is lost from solution close to ridge-axis sources and is thus of limited importance for ocean biogeochemistry. This long-standing view is challenged by recent studies which suggest that stabilization of hydrothermal dissolved iron may facilitate its long-range oceanic transport. Such transport has been subsequently inferred from spatially limited oceanographic observations. Here we report data from the US GEOTRACES Eastern Pacific Zonal Transect (EPZT) that demonstrate lateral transport of hydrothermal dissolved iron, manganese, and aluminium from the southern East Pacific Rise (SEPR) several thousand kilometres westward across the South Pacific Ocean. Dissolved iron exhibits nearly conservative (that is, no loss from solution during transport and mixing) behaviour in this hydrothermal plume, implying a greater longevity in the deep ocean than previously assumed. Based on our observations, we estimate a global hydrothermal dissolved iron input of three to four gigamoles per year to the ocean interior, which is more than fourfold higher than previous estimates. Complementary simulations with a global-scale ocean biogeochemical model suggest that the observed transport of hydrothermal dissolved iron requires some means of physicochemical stabilization and indicate that hydrothermally derived iron sustains a large fraction of Southern Ocean export production.


Assuntos
Fontes Hidrotermais/química , Metais/química , Modelos Teóricos , Água do Mar/química , Oceano Pacífico , Movimentos da Água
14.
Environ Microbiol ; 17(7): 2261-74, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25420929

RESUMO

Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia-oxidizing archaea (AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide (NO) by Nitrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi-steady state concentrations between 0.05 and 0.08 µM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea (ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub-micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism.


Assuntos
Amônia/metabolismo , Archaea/metabolismo , Óxidos N-Cíclicos/farmacologia , Imidazóis/farmacologia , Óxido Nítrico/metabolismo , Nitrificação , Tioureia/análogos & derivados , Compostos de Amônio/metabolismo , Organismos Aquáticos/metabolismo , Betaproteobacteria/metabolismo , Desnitrificação , Óxido Nítrico/biossíntese , Nitrogênio/metabolismo , Oxirredução , Tioureia/farmacologia
15.
Rapid Commun Mass Spectrom ; 28(22): 2398-404, 2014 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-25303468

RESUMO

RATIONALE: Vitamin B(12) is an essential nutrient for more than half of surveyed marine algae species, but methods for directly measuring this important cofactor in seawater are limited. Current mass spectrometry methods do not quantify all forms of B(12), potentially missing a significant portion of the B(12) pool. METHODS: We present a method to measure vitamins B(1), B(2), B(6), B(7) and four forms of B(12) dissolved in seawater. The method entails solid-phase extraction, separation by ultra-performance liquid chromatography, and detection by triple-quadrupole tandem mass spectrometry using stable-isotope-labeled internal standards. We demonstrated the use of this method in the environment by analyzing B(12) concentrations at different depths in the Hood Canal, part of the Puget Sound estuarine system in Washington State. RESULTS: Recovery of vitamin B(12) forms during the preconcentration steps was >71% and the limits of detection were <0.275 pM in seawater. Standard addition calibration curves in three different seawater matrices were used to determine analytical response and to quantify samples from the environment. Hydroxocobalamin was the main form of B(12) in seawater at our field site. CONCLUSIONS: We developed a method for quantifying four forms of B(12) in seawater by liquid chromatography/mass spectrometry with the option of simultaneous analysis of vitamins B(1), B(2), B(6), and B(7). We validated the method and demonstrated its application in the field.


Assuntos
Cromatografia Líquida/métodos , Água do Mar/química , Espectrometria de Massas em Tandem/métodos , Vitamina B 12/análise , Complexo Vitamínico B/análise , Limite de Detecção , Modelos Lineares , Reprodutibilidade dos Testes , Temperatura , Vitamina B 12/química , Complexo Vitamínico B/química
16.
Proc Natl Acad Sci U S A ; 111(34): 12504-9, 2014 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-25114236

RESUMO

Ammonia-oxidizing archaea (AOA) are now implicated in exerting significant control over the form and availability of reactive nitrogen species in marine environments. Detailed studies of specific metabolic traits and physicochemical factors controlling their activities and distribution have not been well constrained in part due to the scarcity of isolated AOA strains. Here, we report the isolation of two new coastal marine AOA, strains PS0 and HCA1. Comparison of the new strains to Nitrosopumilus maritimus strain SCM1, the only marine AOA in pure culture thus far, demonstrated distinct adaptations to pH, salinity, organic carbon, temperature, and light. Strain PS0 sustained nearly 80% of ammonia oxidation activity at a pH as low as 5.9, indicating that coastal strains may be less sensitive to the ongoing reduction in ocean pH. Notably, the two novel isolates are obligate mixotrophs that rely on uptake and assimilation of organic carbon compounds, suggesting a direct coupling between chemolithotrophy and organic matter assimilation in marine food webs. All three isolates showed only minor photoinhibition at 15 µE ⋅ m(-2) ⋅ s(-1) and rapid recovery of ammonia oxidation in the dark, consistent with an AOA contribution to the primary nitrite maximum and the plausibility of a diurnal cycle of archaeal ammonia oxidation activity in the euphotic zone. Together, these findings highlight an unexpected adaptive capacity within closely related marine group I Archaea and provide new understanding of the physiological basis of the remarkable ecological success reflected by their generally high abundance in marine environments.


Assuntos
Amônia/metabolismo , Archaea/metabolismo , Archaea/classificação , Archaea/genética , Ecossistema , Concentração de Íons de Hidrogênio , Microscopia Eletrônica de Transmissão , Dados de Sequência Molecular , Oxirredução , Filogenia , RNA Arqueal/genética , RNA Ribossômico 16S/genética , Salinidade , Água do Mar/microbiologia , Temperatura
17.
ISME J ; 7(10): 2023-33, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23657360

RESUMO

Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis-Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l(-1) was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used (15)NH4(+) dilution technique.


Assuntos
Amônia/metabolismo , Archaea/fisiologia , Água do Mar/microbiologia , Temperatura , Archaea/genética , Archaea/metabolismo , Cinética , Oxirredução , Oxirredutases/genética , Oxirredutases/metabolismo , Água do Mar/química
18.
ISME J ; 6(9): 1728-39, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-22402399

RESUMO

The activity of the N(2)-fixing cyanobacterial genus Trichodesmium is critical to the global nitrogen (N) and carbon (C) cycles. Although iron (Fe) has been shown to be an important element limiting the growth and N(2) fixation of Trichodesmium, there have been no specific data demonstrating the in situ affect of Fe on Trichodesmium. We surveyed Trichodesmium populations from the Atlantic and Pacific Oceans for Fe limitation using a novel quantitative reverse transcriptase-PCR (qRT-PCR) method monitoring the expression of an Fe limitation-induced gene, isiB. Here we report the first molecular evidence of in situ Fe limitation of Trichodesmium N(2) fixation, which was evident in samples from the Pacific Ocean, whereas limitation appeared minimal to nonexistent in Atlantic Ocean samples. As our method is Trichodesmium clade specific, we were also able to determine that representatives from the Trichodesmium tenue clade were the most biologically active group of Trichodesmium in the majority of our samples, which speaks to their dominance in open ocean regimes. Furthermore, comparisons of our field expression and chemical data with laboratory studies suggest that the majority of dissolved Fe in the open ocean is available to Trichodesmium colonies regardless of Fe complexation.


Assuntos
Cianobactérias/genética , Cianobactérias/metabolismo , Ferro/metabolismo , Microbiologia da Água , Oceano Atlântico , Disponibilidade Biológica , Cianobactérias/classificação , Cianobactérias/crescimento & desenvolvimento , Meio Ambiente , Genes Bacterianos/genética , Oceano Pacífico , Filogenia , Estresse Fisiológico
19.
Environ Sci Technol ; 42(7): 2387-93, 2008 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-18504970

RESUMO

Superoxide, formed by the single electron reduction of oxygen, is important due to its ability to act as a mild reductant under typical environmental conditions. Using chemiluminescence detection with the reagent methyl Cypridina luciferin analog (MCLA), we have measured superoxide at picomolar concentrations in the water column of the Costa Rica Dome (CRD) seasonal upwelling region of the eastern equatorial Pacific Ocean. After 0.45 microm filtration, superoxide decayed in a pseudofirst order manner but more slowly than expected (rate constants varied from <10(-4) to 9.7 x 10(-3) s(-1)), which we hypothesize is due to complexation of metals that could otherwise scavenge superoxide, and the noncatalytic nature of superoxide decay at subnanomolar concentrations. Depth profiles revealed a particle-associated and nonphotochemically generated source of superoxide, implicating biological processes in its production. Superoxide in surface waters exhibited a diel cycle but concentrations were comparable to those in samples stored in the dark for at least 30 min, suggesting that the nonphotochemical source may dominate over abiotic photochemical superoxide production in the CRD. Elevated concentrations of superoxide in localized zones of the ocean may promote the reduction of several biologically important trace metals, thereby increasing their solubility and potential bioavailability.


Assuntos
Superóxidos/química , Indicadores e Reagentes/química , Oceano Pacífico , Superóxidos/metabolismo , Synechococcus/metabolismo
20.
Anal Chim Acta ; 614(2): 143-52, 2008 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-18420044

RESUMO

Zinc speciation is considered to be an important determinant of the biological availability of zinc. Yet in oceanic surface waters, characterization of zinc speciation is difficult due to the low concentrations of this essential micronutrient. In this study, an anodic stripping voltammetry method previously developed for the total determination of cadmium and lead was successfully adapted to the measurement of zinc speciation. The method differs from previous zinc speciation anodic stripping voltammetry methods in that a fresh mercury film is plated with each sample aliquot. The fresh film anodic stripping voltammetry method was compared to competitive ligand exchange cathodic stripping voltammetry in a profile from the North Atlantic Ocean. Results using the fresh film anodic stripping voltammetry method were similar to those determined using the cathodic stripping voltammetry method, though ligand concentrations determined by fresh film anodic stripping voltammetry were generally slightly higher than those determined by cathodic stripping voltammetry. There did not seem to be a systematic difference between methods for the estimates of conditional stability constants. The ligand concentration in the North Atlantic profile ranged from 0.9 to 1.5 nmol L(-1) as determined by fresh film anodic stripping voltammetry and 0.6 to 1.3 nmol L(-1) as determined by cathodic stripping voltammetry. The conditional stability constants determined by fresh film anodic stripping voltammetry were 10(9.8)-10(10.5) and by cathodic stripping voltammetry were 10(9.8)-10(11.3).


Assuntos
Água do Mar/química , Zinco/análise , Oceano Atlântico , Eletroquímica , Eletrodos , Ligantes , Reprodutibilidade dos Testes
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