Biology subjects

Ouboter, H. T.

Publications and source records attributed to Ouboter, H. T..

3 recordsLinked to original sources

bioRxiv2022

A widespread group of large plasmids in methanotrophic Methanoperedens archaea

Anaerobic methanotrophic (ANME) archaea conserve energy from the breakdown of methane, an important driver of global warming, yet the extrachromosomal genetic elements that impact the activities of ANME archaea are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus. These have been maintained in two bioreactors that contain enrichment cultures dominated by different Methanoperedens species and co-occur with Methanoperedens species in other anoxic environments. By manual curation we show that two of the plasmids are large (155,607 bp and 191,912 bp), circular, and replicate bidirectionally. The group of Methanoperedens species that carry these plasmids is related to "Ca. Methanoperedens nitroreducens", "Ca. Methanoperedens ferrireducens", "Ca. Methanoperedens manganicus" and the plasmids occur in the same copy number as the main chromosome. The larger plasmid encodes transporters that potentially enhance access to Ni, which is required for the methyl-CoM reductase (Mcr), Co required for the cobalamin cofactor needed for methyltransferases, and amino acid uptake. We show that many plasmid genes are actively transcribed, including genes involved in plasmid chromosome maintenance and segregation, a Co2+/Ni2+ transporter and cell protective proteins. Notably, one plasmid carries three tRNAs and two colocalized genes encoding ribosomal protein uL16 and elongation factor eEF2. These are not encoded in the host Methanoperedens genome and uL16 and eEF2 were highly expressed, indicating an obligate interdependence between this plasmid and its host. The finding of plasmids of Methanoperedens opens the way for the development of genetic vectors that could be used to probe little understood aspects of Methanoperedens physiology. Ultimately, this may provide a route to introduce or alter genes that may enhance growth and overall metabolism to accelerate methane oxidation rates.

microbiology↗

bioRxiv2021

Unraveling nitrogen, sulfur and carbon metabolic pathways and microbial community transcriptional responses to substrate deprivation and toxicity stresses in a bioreactor mimicking anoxic brackish coastal sediment conditions

Microbial communities are key drivers of carbon, sulfur and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Candidatus Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The methanotroph Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). After the ammonium removal experiment, a novel methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila and the anaerobic ammonium oxidizer (anammox) Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductase. Our results indicate that some community members could be more resilient to stresses than others in coastal ecosystems, leading to dynamic microbial community shifts and novel functional states. Methane and sulfide oxidation could be ecosystem functions preserved across the investigated disturbances, while differing nitrogen cycling pathways might be favored in response to stresses. ImportanceCoastal ecosystems are primary zones of biogeochemical cycling, processing inputs of nutrients both generated in situ and derived from land runoff. Microbial communities that inhabit costal sediments perform these biogeochemical reactions, but microbial responses to dynamic, periodic substrate deprivation and exposure to toxic compounds remain elusive. In this study, we sought to address this knowledge gap in a controlled bioreactor system, unraveling microbial metabolic pathways and monitoring microbial responses to stresses that might occur in costal sediments. We identified key microbial players and shifts in their abundance and transcriptional activity. Our results indicated that methanotrophs were particularly resilient to stresses, sulfide oxidizers differed in resiliency but the community maintained sulfide oxidation function across stresses, and that anaerobic ammonium oxidizing (anammox) bacteria were sensitive to substrate deprivation but could restore activity once favorable conditions were reestablished. These insights will help to understand and predict coastal ecosystem responses to future disturbances.

microbiology↗

bioRxiv2020

Effects of light/dark diel cycles on the photoorganoheterotrophic metabolism of Rhodopseudomonas palustris for differential electron allocation to PHAs and H2

Light/dark cycles can impact the electron distribution in Rhodopseudomonas palustris, a hyperversatile photoorganoheterotrophic purple non-sulfur bacterium (PNSB). Dynamic conditions during diel cycles are important for the physiology of PNSB, but the coupling between illumination patterns and redox balancing has not been extensively studied. For survival and growth, Rhodopseudomonas has developed different mechanisms to allocate electrons under dynamic growth conditions. Products such as hydrogen and poly-{beta}-hydroxyalkanoates (PHAs) can form alternative electron sinks. A continuous culture, fed with a balanced nutrients medium, was exposed to three different conditions: 24 h continuous infrared illumination, 16h light/8h dark, and 8h light/16h dark. Light and dark phase durations in a cycle determined the energy availability level (light) and the attainment of a stationary state. Under long dark phases, the acetate substrate accumulated to levels that could not be depleted by growth in the light. Under short dark phases, acetate was rapidly consumed in the light with most of the phototrophic growth occurring under acetate-limiting conditions. Under diel cycles, substrate uptake and growth were unbalanced and Rhodopseudomonas shunted the excess of carbon and electron flow first toward PHAs production. Only secondarily, when PHA storage got saturated, the electron excess was redirected toward H2. A numerical model described well the dynamics of biomass and nutrients during the different light/dark cycle regimes. The model simulations allowed determination of stoichiometric and kinetic parameters for conversion by Rhodopseudomonas. Understanding the inherent process dynamics of diel light cycles in purple sulfur bacteria cultures would enable optimization procedures for targeted bioproduct formation. ImportancePurple non-sulfur bacteria (PNSB) are important anoxygenic phototrophic microorganisms that take part in numerous environmental processes, based on their metabolic versatility. Rhodopseudomonas palustris is a model photosynthetic bacterium of the PNSB guild. Light cycles influence deeply its physiology. Poly-{beta}-hydroxyalkanoates (PHAs) and biohydrogen are two of the most studied metabolic products of Rhodopseudomonas, because of their biotechnology potential besides involvement in carbon and electron allocations in its metabolism. Their production mechanisms have often been described as competitive, but the rationale behind the production of one or the other compound has not been elucidated. Here, we found that under light / dark cycles an excess of organic substrate was first directed toward PHAs production, and only when this pathway was saturated H2 was produced. Understanding the dynamics of carbon and electron allocation under intermittent light cycles enhances our knowledge on PNSB metabolisms and paves ways to manage the formation of targeted bioproducts.

microbiology↗