Modelling and Simulation


Publications (10)

Deciphering Symbiotic Interactions of “ Candidatus Aenigmarchaeota” with Inferred Horizontal Gene Transfers and Co-occurrence Networks

Citation
Li et al. (2021). mSystems 6 (4)
Names
Ca. Aenigmarchaeota
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modeling and Simulation Modelling and Simulation Molecular Biology Physiology
Abstract
Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites , Parvarchaeota , Aenigmarchaeota , Nanoarchaeota , and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community.

Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon “ Candidatus Nitrosocosmicus agrestis”

Citation
Liu et al. (2021). mSystems 6 (1)
Names
Ca. Nitrosocosmicus agrestis Ca. Nitrosocosmicus
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modelling and Simulation Molecular Biology Physiology
Abstract
Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N 2 O emission. Recently, some AOA species from the genus “ Ca. Nitrosocosmicus” were also found to have high ammonia tolerance.

Genomes of the “ Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria

Citation
López-Pérez et al. (2020). mSystems 5 (6)
Names
Ca. Actinomarinales
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modelling and Simulation Molecular Biology Physiology
Abstract
Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge.

Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts

Citation
Zuñiga et al. (2020). npj Systems Biology and Applications 6 (1)
Names
Ca. Liberibacter asiaticus
Subjects
Applied Mathematics Computer Science Applications Drug Discovery General Biochemistry, Genetics and Molecular Biology Modelling and Simulation
Abstract
AbstractCandidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.

Integrated Omic Analyses Provide Evidence that a “ Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions

Citation
Camejo et al. (2019). mSystems 4 (1)
Names
Ca. Accumulibacter phosphatis
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modelling and Simulation Molecular Biology Physiology
Abstract
“ Candidatus Accumulibacter phosphatis” is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that “ Ca . Accumulibacter phosphatis” is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”

Citation
Camejo et al. (2017). mSystems 2 (5)
Names
Ca. Nitrospira nitrosa
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modelling and Simulation Molecular Biology Physiology
Abstract
Nitrospira -like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.

Metatranscriptomics Supports the Mechanism for Biocathode Electroautotrophy by “ Candidatus Tenderia electrophaga”

Citation
Eddie et al. (2017). mSystems 2 (2)
Names
Ca. Tenderia electrophaga
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modelling and Simulation Molecular Biology Physiology
Abstract
Bacteria that directly use electrodes as metabolic electron donors (biocathodes) have been proposed for applications ranging from microbial electrosynthesis to advanced bioelectronics for cellular communication with machines. However, just as we understand very little about oxidation of analogous natural insoluble electron donors, such as iron oxide, the organisms and extracellular electron transfer (EET) pathways underlying the electrode-cell direct electron transfer processes are almost completely unknown. Biocathodes are a stable biofilm cultivation platform to interrogate both the rate and mechanism of EET using electrochemistry and to study the electroautotrophic organisms that catalyze these reactions. Here we provide new evidence supporting the hypothesis that the uncultured bacterium “ Candidatus Tenderia electrophaga” directly couples extracellular electron transfer to CO 2 fixation. Our results provide insight into developing biocathode technology, such as microbial electrosynthesis, as well as advancing our understanding of chemolithoautotrophy.

Proteome Remodeling in Response to Sulfur Limitation in “ Candidatus Pelagibacter ubique”

Citation
Smith et al. (2016). mSystems 1 (4)
Names
Ca. Pelagibacter ubique
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modelling and Simulation Molecular Biology Physiology
Abstract
“ Ca . Pelagibacter ubique” is a key driver of marine biogeochemistry cycles and a model for understanding how minimal genomes evolved in free-living anucleate organisms. This study explores the unusual sulfur acquisition strategy that has evolved in these cells, which lack assimilatory sulfate reduction and instead rely on reduced sulfur compounds found in oxic marine environments to meet their cellular quotas. Our findings demonstrate that the sulfur acquisition systems are constitutively expressed but the enzymatic steps leading to the essential sulfur-containing amino acid methionine are regulated by a unique array of riboswitches and genes, many of which are encoded in a rapidly evolving genome region. These findings support mounting evidence that streamlined cells have evolved regulatory mechanisms that minimize transcriptional switching and, unexpectedly, localize essential sulfur acquisition genes in a genome region normally associated with adaption to environmental variation.