Studies of the Ecophysiology of Single Cells in Microbial Communities by (Quantitative) Microautoradiography and Fluorescence In Situ Hybridization (MAR-FISH)

Nierychlo, Marta; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

doi:10.1007/8623_2015_66

Cited by 8 publications

(8 citation statements)

References 30 publications

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“…Marine cable bacteria enrichments were incubated with 10 μCi mL −1 14 C-bicarbonate for 8 h at 15°C. Cable bacteria were then fixed and immobilized, and MAR-FISH, imaging, and quantification of silver grains was done as previously described (99). Further details are provided in SI Appendix, Methods.…”

Section: Methodsmentioning

confidence: 99%

On the evolution and physiology of cable bacteria

Kjeldsen

Schreiber

Thorup

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood–Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.

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Section: Methodsmentioning

confidence: 99%

On the evolution and physiology of cable bacteria

Kjeldsen

Schreiber

Thorup

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

158

228

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“…Samples were stored at 4°C and microautoradiography (MAR) analyses performed within 24 h of sampling. The MAR protocol was essentially as detailed by Nierychlo et al (2015) . Activated sludge was aerated for 40 min at room temperature prior to MAR incubation, to reduce any residual substrates, oxygen, and NO x present.…”

Section: Methodsmentioning

confidence: 99%

Genomic and in Situ Analyses Reveal the Micropruina spp. as Abundant Fermentative Glycogen Accumulating Organisms in Enhanced Biological Phosphorus Removal Systems

et al. 2018

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Enhanced biological phosphorus removal (EBPR) involves the cycling of biomass through carbon-rich (feast) and carbon-deficient (famine) conditions, promoting the activity of polyphosphate accumulating organisms (PAOs). However, several alternate metabolic strategies, without polyphosphate storage, are possessed by other organisms, which can compete with the PAO for carbon at the potential expense of EBPR efficiency. The most studied are the glycogen accumulating organisms (GAOs), which utilize aerobically stored glycogen to energize anaerobic substrate uptake and storage. In full-scale systems the Micropruina spp. are among the most abundant of the proposed GAO, yet little is known about their ecophysiology. In the current study, genomic and metabolomic studies were performed on Micropruina glycogenica str. Lg2T and compared to the in situ physiology of members of the genus in EBPR plants using state-of-the-art single cell techniques. The Micropruina spp. were observed to take up carbon, including sugars and amino acids, under anaerobic conditions, which were partly fermented to lactic acid, acetate, propionate, and ethanol, and partly stored as glycogen for potential aerobic use. Fermentation was not directly demonstrated for the abundant members of the genus in situ, but was strongly supported by the confirmation of anaerobic uptake of carbon and glycogen storage in the absence of detectable polyhydroxyalkanoates or polyphosphate reserves. This physiology is markedly different from the classical GAO model. The amount of carbon stored by fermentative organisms has potentially important implications for phosphorus removal – as they compete for substrates with the Tetrasphaera PAO and stored carbon is not made available to the “Candidatus Accumulibacter” PAO under anaerobic conditions. This study shows that the current models of the competition between PAO and GAO are too simplistic and may need to be revised to take into account the impact of potential carbon storage by fermentative organisms.

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“…For example, Fortunato and Huber (2016) coupled stable isotope probing with metatranscriptomics to identify taxa and pathways involved in chemolithotrophic processes at hydrothermal vents. Methods for visualization of radioisotope (Microautoradiography, (Nierychlo et al 2016) or stable isotope (Nanoscale secondary ion mass spectrometry, Gao et al 2016) enrichments in single cells coupled to CARD-FISH could be another method to quantify biogeochemical fluxes of certain taxonomic groups.…”

Section: Advances In Microbial Ecologymentioning

confidence: 99%

Progress in Microbial Ecology in Ice-Covered Seas

Vonnahme

Dietrich

Hassett

2019

YOUMARES 9 - The Oceans: Our Research, Our Future

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Sea ice seasonally covers 10% of the earth's oceans and shapes global ocean chemistry. The unique physical processes associated with sea ice growth and development shape the associated biological diversity and ecosystem function. Microbes make up the base of all marine food webs and the overwhelming majority of biomass in the sea ice ecosystem. Despite their biomass, microbial processes are not fully integrated into marine ecosystem models. Recent applications of novel molecular biology technologies to studies of marine ecology have elucidated numerous microbial-mediated processes interfaced by previously unknown organisms and processes. These discoveries are yielding more in-depth studies on the relevance of mixotrophy, the ecology of fungi, and the interplay between major microbial clades. In ecosystem studies, the basis of the food web is frequently neglected even though the accessibility of energy, recycling of nutrients, and parasitism are crucial factors shaping the environment for grazers and higher trophic levels. In this review, we focus on the species composition, abundance, and functions of microalgae, bacteria, archaea, fungi, and viruses in the sea ice-covered seas throughout the year. A strong emphasis will be put on advances in molecular methods that empower scientists to further investigate microorganisms in more detail. Since microbes make up the majority of all oceanic biomass, we believe that it is impossible to accurately forecast the biological fate of polar marine ecosystems without placing a proportional emphasis on microbes relative to their biomass.

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Studies of the Ecophysiology of Single Cells in Microbial Communities by (Quantitative) Microautoradiography and Fluorescence In Situ Hybridization (MAR-FISH)

Cited by 8 publications

References 30 publications

On the evolution and physiology of cable bacteria

On the evolution and physiology of cable bacteria

Genomic and in Situ Analyses Reveal the Micropruina spp. as Abundant Fermentative Glycogen Accumulating Organisms in Enhanced Biological Phosphorus Removal Systems

Progress in Microbial Ecology in Ice-Covered Seas

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