In situ growth of anammox bacteria in subseafloor sediments

2019 ◽  
Author(s):  
Rui Zhao ◽  
José M. Mogollón ◽  
Sophie S. Abby ◽  
Christa Schleper ◽  
Jennifer F. Biddle ◽  
...  
Keyword(s):  
Environmental Stressors ◽  
Anammox Bacteria ◽  
Deep Biosphere ◽  
Active Growth ◽  
Subsurface Sediments ◽  
Cell Energy ◽  
Energy Limitation ◽  
Microbial Groups ◽  
Favorable Conditions

The deep biosphere buried in marine sediments was estimated to host an equal number of microbes as found in the above oceans 1. It has been debated if these cells are alive and active 2, and their per cell energy availability does not seem to allow for net population growth 3. Here, we report the growth of anammox bacteria in ∼80,000 year old subsurface sediments indicated by their four orders of magnitude abundance increase in the nitrate-ammonia transition zone (NATZ). Their growth coincides with a local increase in anammox power supply. The genome of the dominant anammox bacterium from the NATZ was reconstructed and showed an increased index of replication confirming in situ active growth. The genome belongs to a new Scalindua species so far exclusively found in marine environments, which has the genetic capacity of urea and cyanate utilization and is enriched in genes allowing it to cope with external environmental stressors, such as energy limitation. Our results suggest that specific microbial groups are not only able to survive over geological timescales, but also thrive in the deep subsurface when encountering favorable conditions.

scholarly journals Geochemical transition zone powering microbial growth in subsurface sediments

2020 ◽  
Vol 117 (51) ◽  
pp. 32617-32626
Author(s):  
Rui Zhao ◽  
José M. Mogollón ◽  
Sophie S. Abby ◽  
Christa Schleper ◽  
Jennifer F. Biddle ◽  
...  
Keyword(s):  
Transition Zone ◽  
Draft Genome ◽  
Reaction Rates ◽  
The Arctic ◽  
Marker Genes ◽  
Anammox Bacteria ◽  
Subsurface Sediments ◽  
Microbial Proliferation ◽  
Microbial Groups

No other environment hosts as many microbial cells as the marine sedimentary biosphere. While the majority of these cells are expected to be alive, they are speculated to be persisting in a state of maintenance without net growth due to extreme starvation. Here, we report evidence for in situ growth of anaerobic ammonium-oxidizing (anammox) bacteria in ∼80,000-y-old subsurface sediments from the Arctic Mid-Ocean Ridge. The growth is confined to the nitrate–ammonium transition zone (NATZ), a widespread geochemical transition zone where most of the upward ammonium flux from deep anoxic sediments is being consumed. In this zone the anammox bacteria abundances, assessed by quantification of marker genes, consistently displayed a four order of magnitude increase relative to adjacent layers in four cores. This subsurface cell increase coincides with a markedly higher power supply driven mainly by intensified anammox reaction rates, thereby providing a quantitative link between microbial proliferation and energy availability. The reconstructed draft genome of the dominant anammox bacterium showed an index of replication (iRep) of 1.32, suggesting that 32% of this population was actively replicating. The genome belongs to aScalinduaspecies which we nameCandidatus Scalindua sediminis, so far exclusively found in marine sediments. It has the capacity to utilize urea and cyanate and a mixotrophic lifestyle. Our results demonstrate that specific microbial groups are not only able to survive unfavorable conditions over geological timescales, but can proliferate in situ when encountering ideal conditions with significant consequences for biogeochemical nitrogen cycling.

scholarly journals FISH investigation of the bacterial groups anammox and Azoarcus-Thauera at treatment of landfill leachate

2021 ◽  
Vol Volume 53 (Special Issue A) ◽  
pp. 27-34
Author(s):  
M. Belouhova ◽  
N. Dinova ◽  
I. Yotinov ◽  
S. Lincheva ◽  
I. Schneider ◽  
...  
Keyword(s):  
Landfill Leachate ◽  
Waste Treatment ◽  
Treatment Plant ◽  
Anammox Bacteria ◽  
Leachate Treatment ◽  
Complex Information ◽  
Microbial Groups ◽  
Bacterial Groups ◽  
Transformation Processes

The landfill leachate is heavily polluted wastewater produced in the landfills. The management of the purification of the leachate is especially challenging and that is why new approaches and indicators are needed. The quantity, localization, interaction, clustering of the key microbial groups, responsible for the critical transformation processes can be used as indication leading to better performance of the technology. This study is focused on two bacterial groups (Anammox and Azoarcus-Thauera cluster) which have potential to serve as indicators for the landfill leachate treatment. Their quantity and activity were studied by FISH during lab-scale treatment of leachate from the Municipal Enterprise for Waste Treatment (MEWT), Sofia, Bulgaria. Two activated sludges (AS) were used – one from the MEWT and another form the WWTP (wastewater treatment plant) of Sofia. The obtained results showed that 74% of the COD was eliminated when leachate was diluted 50 and 25 times and 31% - when undiluted leachate was used. At the end of the process (21 day) the Azoarcus-Thauera group formed large aggregations in the AS from MEWT. They were 17.50% of the bacteria there while in the AS from the WWTP of Sofia they represented only 2.61%. The quantity of the anammox bacteria remained almost unchanged during the process and was 10.75% of the community from MEWT which eliminated 98 mg/L more ammonium ions at the end of the process and 6% from the community from the WWTP of Sofia. The two studied groups gave more complex information about the processes in the AS related to the elimination of the nitrogen and carbon containing pollutants. They could be used for better management of the biological processes during landfill leachate treatment. Key words: landfill leachate; anammox, Azoarcus-Thauera; activated sludge; fluorescence in-situ hybridization

scholarly journals Temperature response of denitrification and anammox reveals the adaptation of microbial communities to in situ temperatures in permeable marine sediments that span 50° in latitude

2013 ◽  
Vol 10 (9) ◽  
pp. 14595-14626 ◽  
Author(s):  
A. Canion ◽  
J. E. Kostka ◽  
T. M. Gihring ◽  
M. Huettel ◽  
J. E. E. van Beusekom ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Marine Sediments ◽  
Metabolic Response ◽  
Anammox Bacteria ◽  
Advective Flow ◽  
Permeable Sediments ◽  
N Removal ◽  
In Situ Conditions ◽  
Wide Range

Abstract. Despite decades of research on the physiology and biochemistry of nitrate/nitrite-respiring microorganisms, little is known regarding their metabolic response to temperature, especially under in situ conditions. The temperature regulation of microbial communities that mediate anammox and denitrification was investigated in near shore permeable sediments at polar, temperate, and subtropical sites with annual mean temperatures ranging from −5 to 23 °C. Total N2 production rates were determined using the isotope pairing technique in intact core incubations under diffusive and simulated advection conditions and ranged from 2 to 359 μmol N m−2 d−1. For the majority of sites studied, N2 removal was 2 to 7 times more rapid under advective flow conditions. Anammox comprised 6 to 14% of total N2 production at temperate and polar sites and was not detected at the subtropical site. Potential rates of denitrification and anammox were determined in anaerobic slurries in a temperature gradient block incubator across a temperature range of −1 to 42 °C. The highest optimum temperature (Topt) for denitrification was 36 °C and was observed in subtropical sediments, while the lowest Topt of 21 °C was observed at the polar site. Seasonal variation in the Topt was observed at the temperate site with values of 26 and 34 °C in winter and summer, respectively. The Topt values for anammox were 9 and 26 °C at the polar and temperate sites, respectively. The results demonstrate adaptation of denitrifying communities to in situ temperatures in permeable marine sediments across a wide range of temperatures, whereas marine anammox bacteria may be predominately psychrophilic to psychrotolerant. To our knowledge, we provide the first rates of denitrification and anammox from permeable sediments of a polar permanently cold ecosystem. The adaptation of microbial communities to in situ temperatures suggests that the relationship between temperature and rates of N removal is highly dependent on community structure.

scholarly journals Re-Evaluating the Age of Deep Biosphere Fossils in the Lockne Impact Structure

Geosciences ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 202 ◽  
Author(s):  
Mikael Tillberg ◽  
Magnus Ivarsson ◽  
Henrik Drake ◽  
Martin J. Whitehouse ◽  
Ellen Kooijman ◽  
...  
Keyword(s):  
Hydrothermal Activity ◽  
Crystalline Rock ◽  
Hydrothermal Systems ◽  
Fungal Colonization ◽  
Precambrian Basement ◽  
Impact Event ◽  
Deep Biosphere ◽  
Microbial Ecosystems ◽  
The Impact

Impact-generated hydrothermal systems have been suggested as favourable environments for deep microbial ecosystems on Earth, and possibly beyond. Fossil evidence from a handful of impact craters worldwide have been used to support this notion. However, as always with mineralized remains of microorganisms in crystalline rock, certain time constraints with respect to the ecosystems and their subsequent fossilization are difficult to obtain. Here we re-evaluate previously described fungal fossils from the Lockne crater (458 Ma), Sweden. Based on in-situ Rb/Sr dating of secondary calcite-albite-feldspar (356.6 ± 6.7 Ma) we conclude that the fungal colonization took place at least 100 Myr after the impact event, thus long after the impact-induced hydrothermal activity ceased. We also present microscale stable isotope data of 13C-enriched calcite suggesting the presence of methanogens contemporary with the fungi. Thus, the Lockne fungi fossils are not, as previously thought, related to the impact event, but nevertheless have colonized fractures that may have been formed or were reactivated by the impact. Instead, the Lockne fossils show similar features as recent findings of ancient microbial remains elsewhere in the fractured Swedish Precambrian basement and may thus represent a more general feature in this scarcely explored habitat than previously known.

scholarly journals Simultaneous Nitrite-Dependent Anaerobic Methane and Ammonium Oxidation Processes

2011 ◽  
Vol 77 (19) ◽  
pp. 6802-6807 ◽  
Author(s):  
Francisca A. Luesken ◽  
Jaime Sánchez ◽  
Theo A. van Alen ◽  
Janeth Sanabria ◽  
Huub J. M. Op den Camp ◽  
...  
Keyword(s):  
Enrichment Culture ◽  
Anammox Bacteria ◽  
Anaerobic Oxidation Of Methane ◽  
Ammonium Oxidation ◽  
Content Type ◽  
Oxidation Of Methane ◽  
Activity Measurements ◽  
Near Future ◽  
Damo Bacteria

ABSTRACTNitrite-dependent anaerobic oxidation of methane (n-damo) and ammonium (anammox) are two recently discovered processes in the nitrogen cycle that are catalyzed by n-damo bacteria, including “CandidatusMethylomirabilis oxyfera,” and anammox bacteria, respectively. The feasibility of coculturing anammox and n-damo bacteria is important for implementation in wastewater treatment systems that contain substantial amounts of both methane and ammonium. Here we tested this possible coexistence experimentally. To obtain such a coculture, ammonium was fed to a stable enrichment culture of n-damo bacteria that still contained some residual anammox bacteria. The ammonium supplied to the reactor was consumed rapidly and could be gradually increased from 1 to 20 mM/day. The enriched coculture was monitored by fluorescencein situhybridization and 16S rRNA andpmoAgene clone libraries and activity measurements. After 161 days, a coculture with about equal amounts of n-damo and anammox bacteria was established that converted nitrite at a rate of 0.1 kg-N/m3/day (17.2 mmol day−1). This indicated that the application of such a coculture for nitrogen removal may be feasible in the near future.

scholarly journals Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate

2004 ◽  
Vol 70 (8) ◽  
pp. 4911-4920 ◽  
Author(s):  
Nadia N. North ◽  
Sherry L. Dollhopf ◽  
Lainie Petrie ◽  
Jonathan D. Istok ◽  
David L. Balkwill ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Quantitative Pcr ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Clone Libraries ◽  
Subsurface Sediments

ABSTRACT Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells. In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed that sediment pH increased substantially (by 1 to 2 pH units) while nitrate was largely depleted. A large diversity of 16S rRNA gene sequences were retrieved from subsurface sediments, including species from the α, β, δ, and γ subdivisions of the class Proteobacteria, as well as low- and high-G+C gram-positive species. Following in situ biostimulation of microbial communities within contaminated sediments, sequences related to previously cultured metal-reducing δ-Proteobacteria increased from 5% to nearly 40% of the clone libraries. Quantitative PCR revealed that Geobacter-type 16S rRNA gene sequences increased in biostimulated sediments by 1 to 2 orders of magnitude at two of the four sites tested. Evidence from the quantitative PCR analysis corroborated information obtained from 16S rRNA gene clone libraries, indicating that members of the δ-Proteobacteria subdivision, including Anaeromyxobacter dehalogenans-related and Geobacter-related sequences, are important metal-reducing organisms in acidic subsurface sediments. This study provides the first cultivation-independent analysis of the change in metal-reducing microbial communities in subsurface sediments during an in situ bioremediation experiment.

scholarly journals Suspension Array Analysis of 16S rRNA from Fe- and SO42-Reducing Bacteria in Uranium-Contaminated Sediments Undergoing Bioremediation

2006 ◽  
Vol 72 (7) ◽  
pp. 4672-4687 ◽  
Author(s):  
Darrell P. Chandler ◽  
Ann E. Jarrell ◽  
Eric R. Roden ◽  
Julia Golova ◽  
Boris Chernov ◽  
...  
Keyword(s):  
16S Rrna ◽  
Total Rna ◽  
Iron Reducing Bacteria ◽  
Suspension Array ◽  
Sulfate Reducing ◽  
Subsurface Sediments ◽  
Reducing Bacteria ◽  
Bead Arrays ◽  
Microbiological Analyses

ABSTRACT A 16S rRNA-targeted tunable bead array was developed and used in a retrospective analysis of metal- and sulfate-reducing bacteria in contaminated subsurface sediments undergoing in situ U(VI) bioremediation. Total RNA was extracted from subsurface sediments and interrogated directly, without a PCR step. Bead array validation studies with total RNA derived from 24 isolates indicated that the behavior and response of the 16S rRNA-targeted oligonucleotide probes could not be predicted based on the primary nucleic acid sequence. Likewise, signal intensity (absolute or normalized) could not be used to assess the abundance of one organism (or rRNA) relative to the abundance of another organism (or rRNA). Nevertheless, the microbial community structure and dynamics through time and space and as measured by the rRNA-targeted bead array were consistent with previous data acquired at the site, where indigenous sulfate- and iron-reducing bacteria and near neighbors of Desulfotomaculum were the organisms that were most responsive to a change in injected acetate concentrations. Bead array data were best interpreted by analyzing the relative changes in the probe responses for spatially and temporally related samples and by considering only the response of one probe to itself in relation to a background (reference) environmental sample. By limiting the interpretation of the data in this manner and placing it in the context of supporting geochemical and microbiological analyses, we concluded that ecologically relevant and meaningful information can be derived from direct microarray analysis of rRNA in uncharacterized environmental samples, even with the current analytical uncertainty surrounding the behavior of individual probes on tunable bead arrays.

scholarly journals Potential Interactions of Particle-Associated Anammox Bacteria with Bacterial and Archaeal Partners in the Namibian Upwelling System

2007 ◽  
Vol 73 (14) ◽  
pp. 4648-4657 ◽  
Author(s):  
Dagmar Woebken ◽  
Bernhard M. Fuchs ◽  
Marcel M. M. Kuypers ◽  
Rudolf Amann
Keyword(s):  
16S Rrna ◽  
Free Water ◽  
Water Phase ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Anammox Bacteria ◽  
Upwelling System ◽  
Group I ◽  
Anammox Activity

ABSTRACT Recent studies have shown that the anaerobic oxidation of ammonium by anammox bacteria plays an important role in catalyzing the loss of nitrogen from marine oxygen minimum zones (OMZ). However, in situ oxygen concentrations of up to 25 μM and ammonium concentrations close to or below the detection limit in the layer of anammox activity are hard to reconcile with the current knowledge of the physiology of anammox bacteria. We therefore investigated samples from the Namibian OMZ by comparative 16S rRNA gene analysis and fluorescence in situ hybridization. Our results showed that “Candidatus Scalindua” spp., the typical marine anammox bacteria, colonized microscopic particles that were likely the remains of either macroscopic marine snow particles or resuspended particles. These particles were slightly but significantly (P < 0.01) enriched in Gammaproteobacteria (11.8% ± 5.0%) compared to the free-water phase (8.1% ± 1.8%). No preference for the attachment to particles could be observed for members of the Alphaproteobacteria and Bacteroidetes, which were abundant (12 to 17%) in both habitats. The alphaproteobacterial SAR11 clade, the Euryarchaeota, and group I Crenarchaeota, were all significantly depleted in particles compared to their presence in the free-water phase (16.5% ± 3.5% versus 2.6% ± 1.7%, 2.7% ± 1.9% versus <1%, and 14.9% ± 4.6% versus 2.2% ± 1.8%, respectively, all P < 0.001). Sequence analysis of the crenarchaeotal 16S rRNA genes showed a 99% sequence identity to the nitrifying “Nitrosopumilus maritimus.” Even though we could not observe conspicuous consortium-like structures of anammox bacteria with particle-enriched bacterioplankton groups, we hypothesize that members of Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes play a critical role in extending the anammox reaction to nutrient-depleted suboxic water layers in the Namibian upwelling system by creating anoxic, nutrient-enriched microniches.

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