scholarly journals Phylogenomics Suggests the Origin of Obligately Anaerobic Anammox Bacteria Correlates with the Great Oxidation Event

2021 ◽  
Author(s):  
Tianhua Liao ◽  
Sishuo Wang ◽  
Haiwei Luo
Keyword(s):  
Sequence Data ◽  
Atmospheric Oxygen ◽  
Nitrogen Loss ◽  
Anaerobic Bacteria ◽  
Anammox Bacteria ◽  
Ammonium Oxidation ◽  
Data Set ◽  
Origin And Evolution ◽  
Great Oxidation Event ◽  
Obligate Anaerobic

The anaerobic ammonium oxidation (anammox) bacteria transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for nearly half of global nitrogen loss. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remains enigmatic. Here, we compile a comprehensive sequence data set of anammox bacteria, and confirm their single origin within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates with different statistical methods, we estimate that anammox bacteria originated at 2.0 - 2.6 Ga, broadly coinciding with the Great Oxidation Event (GOE) which is thought to have fundamentally changed global biogeochemical cycles. We further show that during the origin of anammox bacteria, genes involved in oxidative stress, bioenergetics and anammox granules formation were recruited, which may have contributed to their survival in an increasingly oxic Earth. Our findings suggest the rising level of atmospheric oxygen, which made nitrite increasingly available, as a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link GOE to the evolution of obligate anaerobic bacteria.

scholarly journals Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

2016 ◽  
Vol 113 (40) ◽  
pp. E5925-E5933 ◽  
Author(s):  
Stilianos Louca ◽  
Alyse K. Hawley ◽  
Sergei Katsev ◽  
Monica Torres-Beltran ◽  
Maya P. Bhatia ◽  
...  
Keyword(s):  
Sequence Data ◽  
Nitrogen Loss ◽  
Expression Patterns ◽  
Molecular Techniques ◽  
Ecosystem Functions ◽  
Biogeochemical Model ◽  
Sequence Information ◽  
Ammonium Oxidation ◽  
Wide Range ◽  
Oxygen Minimum

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet—a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite “leakage” during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.

Global impact and application of the anaerobic ammonium-oxidizing (anammox) bacteria

2006 ◽  
Vol 34 (1) ◽  
pp. 174-178 ◽  
Author(s):  
H.J.M. Op den Camp ◽  
B. Kartal ◽  
D. Guven ◽  
L.A.M.P. van Niftrik ◽  
S.C.M. Haaijer ◽  
...  
Keyword(s):  
Nitrogen Loss ◽  
Low Cost ◽  
High Strength ◽  
Immunogold Labelling ◽  
Primary Electron ◽  
Freshwater Ecosystems ◽  
Anammox Bacteria ◽  
Ammonium Oxidation ◽  
Short Supply ◽  
Anammox Process

In the anaerobic ammonium oxidation (anammox) process, ammonia is oxidized with nitrite as primary electron acceptor under strictly anoxic conditions. The reaction is catalysed by a specialized group of planctomycete-like bacteria. These anammox bacteria use a complex reaction mechanism involving hydrazine as an intermediate. The reactions are assumed to be carried out in a unique prokaryotic organelle, the anammoxosome. This organelle is surrounded by ladderane lipids, which make the organelle nearly impermeable to hydrazine and protons. The localization of the major anammox protein, hydrazine oxidoreductase, was determined via immunogold labelling to be inside the anammoxosome. The anammox bacteria have been detected in many marine and freshwater ecosystems and were estimated to contribute up to 50% of oceanic nitrogen loss. Furthermore, the anammox process is currently implemented in water treatment for the low-cost removal of ammonia from high-strength waste streams. Recent findings suggested that the anammox bacteria may also use organic acids to convert nitrate and nitrite into dinitrogen gas when ammonia is in short supply.

scholarly journals RNA-seq of a lung sample from a male COVID19 deceased patient (age 74) submitted by Icahn School of Medicine at Mount Sinai does not show the anaerobic/aerobic homeostasis disruption observed in other patient samples - an artifact of post-mortem procedures?

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
Atmospheric Oxygen ◽  
Anaerobic Bacteria ◽  
Rna Seq ◽  
Patient Age ◽  
School Of Medicine ◽  
Lung Sample ◽  
Obligate Anaerobic ◽  
Patient Âgé ◽  
Mount Sinai ◽  
Deceased Patient

Here, I have analyzed the RNA-seq of a lung sample from a male COVID19 deceased patient (age 74) submitted by Icahn School of Medicine at Mount Sinai (Accid:PRJNA615032). There are two replicates, which I have pooled into a single sample. The analysis (Table 1, SI/bact.txt) does not show the anaero- bic/aerobic homeostasis disruption observed in some patient samples [1–3]. Although not all samples show anaerobic/aerobic homeostasis disruption [4–6], they are possibly patients in the early phase of the disease. The findings in the current deceased patient (viral load is very low, SI/viralreads.fa) however does not align with the hypothesis [7], unless there are artifacts arising from obtaining the lung sample. Since obligate anaerobic bacteria cant tolerate more than 5% oxygen, and atmospheric oxygen is much higher, could these have been killed after atmospheric exposure? Note, anaerobic bacteria are present - its just that they don’t seem to have colonized the lung of the deceased patient.

Anaerobic ammonium oxidation (anammox) in different natural ecosystems

2011 ◽  
Vol 39 (6) ◽  
pp. 1811-1816 ◽  
Author(s):  
Bao-lan Hu ◽  
Li-dong Shen ◽  
Xiang-yang Xu ◽  
Ping Zheng
Keyword(s):  
Nitrogen Loss ◽  
Terrestrial Ecosystems ◽  
Influential Factors ◽  
Anaerobic Ammonium Oxidation ◽  
Anammox Bacteria ◽  
Ammonium Oxidation ◽  
Natural Ecosystems ◽  
Natural Habitats ◽  
Water Columns ◽  
Anammox Process

Anammox (anaerobic ammonium oxidation), which is a reaction that oxidizes ammonium to dinitrogen gas using nitrite as the electron acceptor under anoxic conditions, was an important discovery in the nitrogen cycle. The reaction is mediated by a specialized group of planctomycete-like bacteria that were first discovered in man-made ecosystems. Subsequently, many studies have reported on the ubiquitous distribution of anammox bacteria in various natural habitats, including anoxic marine sediments and water columns, freshwater sediments and water columns, terrestrial ecosystems and some special ecosystems, such as petroleum reservoirs. Previous studies have estimated that the anammox process is responsible for 50% of the marine nitrogen loss. Recently, the anammox process was reported to account for 9–40% and 4–37% of the nitrogen loss in inland lakes and agricultural soils respectively. These findings indicate the great potential for the anammox process to occur in freshwater and terrestrial ecosystems. The distribution of different anammox bacteria and their contribution to nitrogen loss have been described in different natural habitats, demonstrating that the anammox process is strongly influenced by the local environmental conditions. The present mini-review summarizes the current knowledge of the ecological distribution of anammox bacteria, their contribution to nitrogen loss in various natural ecosystems and the effects of major influential factors on the anammox process.

Earth’s Middle Ages: What Came after the GOE

2017 ◽  
Author(s):  
Donald Eugene Canfield
Keyword(s):  
Organic Matter ◽  
Organic Carbon ◽  
Middle Ages ◽  
Atmospheric Oxygen ◽  
Iron Formation ◽  
Banded Iron Formation ◽  
Dissolved Iron ◽  
Great Oxidation Event ◽  
Low Levels ◽  
Substantial Rise

This chapter considers the aftermath of the great oxidation event (GOE). It suggests that there was a substantial rise in oxygen defining the GOE, which may, in turn have led to the Lomagundi isotope excursion, which was associated with high rates of organic matter burial and perhaps even higher concentrations of oxygen. This excursion was soon followed by a crash in oxygen to very low levels and a return to banded iron formation deposition. When the massive amounts of organic carbon buried during the excursion were brought into the weathering environment, they would have represented a huge oxygen sink, drawing down levels of atmospheric oxygen. There appeared to be a veritable seesaw in oxygen concentrations, apparently triggered initially by the GOE. The GOE did not produce enough oxygen to oxygenate the oceans. Dissolved iron was removed from the oceans not by reaction with oxygen but rather by reaction with sulfide. Thus, the deep oceans remained anoxic and became rich in sulfide, instead of becoming well oxygenated.

scholarly journals Colonocyte metabolism shapes the gut microbiota

Science ◽  
2018 ◽  
Vol 362 (6418) ◽  
pp. eaat9076 ◽  
Author(s):  
Yael Litvak ◽  
Mariana X. Byndloss ◽  
Andreas J. Bäumler
Keyword(s):  
Gut Microbiota ◽  
Anaerobic Bacteria ◽  
Enteric Pathogens ◽  
Metabolic Reprogramming ◽  
Human Diseases ◽  
Fermentation Products ◽  
Colonic Microbiota ◽  
Obligate Anaerobic ◽  
Control Switch ◽  
Facultative Anaerobic Bacteria

An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

scholarly journals Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul M. Magyar ◽  
Damian Hausherr ◽  
Robert Niederdorfer ◽  
Nicolas Stöcklin ◽  
Jing Wei ◽  
...  
Keyword(s):  
Isotope Effect ◽  
Isotope Composition ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Anammox Bacteria ◽  
Ammonium Oxidation ◽  
Experimental Conditions ◽  
N Transformations ◽  
Natural Systems ◽  
Inverse Isotope Effect

AbstractAnaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (15N/14N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor 15ε for the reduction of nitrite to N2 is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of 15ε for the oxidation of nitrite to nitrate (inverse isotope effect, − 16 to − 43‰) and for the reduction of ammonium to N2 (normal isotope effect, 19–32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.

Diversity of anammox bacteria and contribution to the nitrogen loss in surface sediment

2019 ◽  
Vol 142 ◽  
pp. 227-234 ◽  
Author(s):  
Jiapeng Wu ◽  
Yiguo Hong ◽  
Jiaqi Ye ◽  
Yiben Li ◽  
Xiaohan Liu ◽  
...  
Keyword(s):  
Surface Sediment ◽  
Nitrogen Loss ◽  
Anammox Bacteria

Frequent Closed Partial Orders Mining in Sequences

2013 ◽  
Vol 846-847 ◽  
pp. 1304-1307
Author(s):  
Ye Wang ◽  
Yan Jia ◽  
Lu Min Zhang
Keyword(s):  
Sequence Data ◽  
Real Data ◽  
Partial Orders ◽  
Hard Problem ◽  
Important Data ◽  
Data Set ◽  
Pruning Algorithm ◽  
Equal Chance ◽  
Np Hard Problem ◽  
General Sequences

Mining partial orders from sequence data is an important data mining task with broad applications. As partial orders mining is a NP-hard problem, many efficient pruning algorithm have been proposed. In this paper, we improve a classical algorithm of discovering frequent closed partial orders from string. For general sequences, we consider items appearing together having equal chance to calculate the detecting matrix used for pruning. Experimental evaluations from a real data set show that our algorithm can effectively mine FCPO from sequences.

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