Growth at Low Ammonium Concentrations and Starvation Response as Potential Factors Involved in Niche Differentiation among Ammonia-Oxidizing Bacteria

ABSTRACT In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with N. europaea and the ammonia oxidizer G5-7, a close relative of Nitrosomonas oligotropha belonging to Nitrosomonas cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of N. europaea. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete N. europaea at growth-limiting substrate concentrations of about 10 μM ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However, N. europaea displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation, N. europaea became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The Nitrosomonas cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of N. europaea, belonging to Nitrosomonas cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of N. europaea to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.

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Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

Applied and Environmental Microbiology ◽

10.1128/aem.01038-21 ◽

2021 ◽

Author(s):

Elizabeth French ◽

Jessica A. Kozlowski ◽

Annette Bollmann

Keyword(s):

Ammonia Oxidation ◽

Heterotrophic Bacteria ◽

Ammonia Oxidizer ◽

Ammonium Concentration ◽

Natural Environments ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers ◽

Batch Cultures ◽

Freshwater Systems ◽

Ammonia Oxidizing Archaea

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group ( Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite – can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

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Effect of Toxic Metals on Indigenous Soil β-Subgroup Proteobacterium Ammonia Oxidizer Community Structure and Protection against Toxicity by Inoculated Metal-Resistant Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.65.1.95-101.1999 ◽

1999 ◽

Vol 65 (1) ◽

pp. 95-101 ◽

Cited By ~ 210

Author(s):

John R. Stephen ◽

Yun-Juan Chang ◽

Sarah J. Macnaughton ◽

George A. Kowalchuk ◽

Kam T. Leung ◽

...

Keyword(s):

Community Structure ◽

Toxic Metals ◽

Heterotrophic Bacteria ◽

Ammonia Oxidizer ◽

Resistant Bacteria ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers ◽

Gene Encoding ◽

Α Subunit ◽

Mining Sites

ABSTRACT Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia oxidizers that are members of the beta subgroup of the Proteobacteria (β-subgroup ammonia oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4 + levels in soil samples. The gene encoding the α-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the β-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from culturedNitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of β-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of β-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment.

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Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox

ISME Communications ◽

10.1038/s43705-021-00008-0 ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

A. E. Bernhard ◽

J. Beltz ◽

A. E. Giblin ◽

B. J. Roberts

Keyword(s):

Gulf Of Mexico ◽

New England ◽

Salt Marshes ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ammonia Oxidizer ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers ◽

Biogeographic Patterns ◽

Potential Nitrification

AbstractFew studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.

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Volunteering among Older Lesbian and Gay Adults: Associations with Mental, Physical and Social Well-Being

Journal of Aging and Health ◽

10.1177/0898264320952910 ◽

2020 ◽

pp. 089826432095291

Author(s):

Anthony Lyons ◽

Beatrice Alba ◽

Andrea Waling ◽

Victor Minichiello ◽

Mark Hughes ◽

...

Keyword(s):

Gay Men ◽

Nationwide Survey ◽

Well Being ◽

Lesbian Women ◽

Community Connectedness ◽

Factors Associated ◽

Lesbian And Gay ◽

Survey Results ◽

Potential Factors ◽

Insight Into

Objectives: Volunteering is associated with positive well-being among older people, providing opportunities to stay active and socially connected. This may be especially relevant for older lesbian and gay people, who are less likely than heterosexual people to have a partner, children or support from their family of origin. Methods: Patterns of volunteering and mental, physical and social well-being were examined in a sample of 754 lesbian and gay adults in Australia aged 60 years and older who completed a nationwide survey. Results: Volunteers reported greater positive mental health than non-volunteers. Among the gay men, volunteers additionally reported higher self-rated health and social support and lower psychological distress. Both the lesbian women and gay men who volunteered for lesbian, gay, bisexual, transgender or intersex (LGBTI) organisations also reported greater LGBTI community connectedness than volunteers for non-LGBTI organisations. Discussion: These findings provide further insight into potential factors associated with the well-being of older lesbian and gay adults.

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Molecular Analysis of Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in Compost and Composted Materials

Applied and Environmental Microbiology ◽

10.1128/aem.65.2.396-403.1999 ◽

1999 ◽

Vol 65 (2) ◽

pp. 396-403 ◽

Cited By ~ 159

Author(s):

George A. Kowalchuk ◽

Zinaida S. Naoumenko ◽

Piet J. L. Derikx ◽

Andreas Felske ◽

John R. Stephen ◽

...

Keyword(s):

Denaturing Gradient Gel Electrophoresis ◽

Ammonia Oxidizer ◽

Ammonia Oxidizing Bacteria ◽

Nitrogen Transformations ◽

Rt Pcr ◽

Gene Encoding ◽

Specific Pcr ◽

Pcr Products ◽

Gradient Gel Electrophoresis ◽

Almost All

ABSTRACT Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous compound in composting material, and the conversion of this compound to nitrite in the environment by chemolithotrophic ammonia-oxidizing bacteria is an essential step in nitrogen cycling. Therefore, the distribution of ammonia-oxidizing members of the β subdivision of the class Proteobacteriain a variety of composting materials was assessed by amplifying 16S ribosomal DNA (rDNA) and 16S rRNA by PCR and reverse transcriptase PCR (RT-PCR), respectively. The PCR and RT-PCR products were separated by denaturing gradient gel electrophoresis (DGGE) and were identified by hybridization with a hierarchical set of oligonucleotide probes designed to detect ammonia oxidizer-like sequence clusters in the genera Nitrosospira and Nitrosomonas. Ammonia oxidizer-like 16S rDNA was detected in almost all of the materials tested, including industrial and experimental composts, manure, and commercial biofertilizers. A comparison of the DGGE and hybridization results after specific PCR and RT-PCR suggested that not all of the different ammonia oxidizer groups detected in compost are equally active. amoA, the gene encoding the active-site-containing subunit of ammonia monooxygenase, was also targeted by PCR, and template concentrations were estimated by competitive PCR. Detection of ammonia-oxidizing bacteria in the composts tested suggested that such materials may not be biologically inert with respect to nitrification and that the fate of nitrogen during composting and compost storage may be affected by the presence of these organisms.

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Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

Biogeosciences ◽

10.5194/bg-10-7395-2013 ◽

2013 ◽

Vol 10 (11) ◽

pp. 7395-7410 ◽

Cited By ~ 47

Author(s):

A. E. Santoro ◽

C. M. Sakamoto ◽

J. M. Smith ◽

J. N. Plant ◽

A. L. Gehman ◽

...

Keyword(s):

Ammonia Oxidation ◽

Heterotrophic Bacteria ◽

California Current ◽

Euphotic Zone ◽

Ammonia Oxidizing Bacteria ◽

Central California ◽

Oxidation Rates ◽

Ammonia Oxidizing Archaea ◽

Nitrite Production ◽

Nh3 Oxidation

Abstract. Nitrite (NO2−) is a substrate for both oxidative and reductive microbial metabolism. NO2− accumulates at the base of the euphotic zone in oxygenated, stratified open-ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2− production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria and archaea as well as assimilatory nitrate (NO3−) reduction by phytoplankton and heterotrophic bacteria. Measurements of NH3 oxidation and NO3− reduction to NO2− were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2− production in the PNM. Sensitive (< 10 nmol L−1), precise measurements of [NH4+] and [NO2−] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2− producing process, with rates of NH3 oxidation to NO2− of up to 31 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2− production from NO3− was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2− production from NO3− were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2− production agreed with production determined from 15N bottle incubations within the PNM, but a modeled net biological sink for NO2− just below the PNM was not captured in the incubations. Residence time estimates of NO2− within the PNM ranged from 18 to 470 days at the mesotrophic station and was 40 days at the oligotrophic station. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

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Combining fluorescent in situ hybridization (fish) with cultivation and mathematical modeling to study population structure and function of ammonia-oxidizing bacteria in activated sludge

Water Science & Technology ◽

10.2166/wst.1998.0689 ◽

1998 ◽

Vol 37 (4-5) ◽

pp. 441-449 ◽

Cited By ~ 17

Author(s):

Michael Wagner ◽

Daniel R. Noguera ◽

Stefan Juretschko ◽

Gabriele Rath ◽

Hans-Peter Koops ◽

...

Keyword(s):

Mathematical Modeling ◽

In Situ Hybridization ◽

Activated Sludge ◽

Heterotrophic Bacteria ◽

Sewage Treatment Plant ◽

Laser Scanning Microscopy ◽

Industrial Plant ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers

16S rRNA-targeted oligonucleotide probes for phylogenetically defined groups of autotrophic ammonia-oxidizing bacteria were used for analyzing the natural diversity of nitrifiers in an industrial sewage treatment plant receiving sewage with high ammonia concentrations. In this facility discontinuous aeration is used to allow for complete nitrification and denitrification. In situ hybridization revealed a yet undescribed diversity of ammonia oxidizers occurring in the plant. Surprisingly, the majority of the ammonia oxidizers were detected with probe combinations which indicate a close affiliation of these cells with Nitrosococcus mobilis. In addition, low numbers of ammonia-oxidizers related to the Nitrosomonas europaea - Nitrosomonas eutropha cluster were present. Interestingly, we also observed hybridization patterns which suggested the occurrence of a novel population of ammonia oxidizers. Confocal laser scanning microscopy revealed that all specifically stained ammonia oxidizers were clustered in microcolonies formed by rod-shaped bacteria. Combination of FISH and mathematical modeling was used to investigate diffusion limitation of ammonia and O2 within these aggregates. Model simulations suggest that mass transfer limitations inside the clusters are not as significant as the substrate limitations due to the activity of surrounding heterotrophic bacteria. To learn more about the ammonia-oxidizers of the industrial plant, we enriched and isolated ammonia-oxidizing bacteria from the activated sludge by combining classical cultivation techniques and FISH. Monitoring the isolates with the nested probe set allowed us to specifically identify those ammonia oxidizers which were found in situ to be numerically dominant. The phylogenetic relationship of these isolates determined by comparative 16S rDNA sequence analysis confirmed the affiliation suggested by FISH.

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Autophagy is involved in starvation response and cell death in Blastocystis

Microbiology ◽

10.1099/mic.0.033944-0 ◽

2010 ◽

Vol 156 (3) ◽

pp. 665-677 ◽

Cited By ~ 16

Author(s):

Jing Yin ◽

Angeline J. J. Ye ◽

Kevin S. W. Tan

Keyword(s):

Cell Death ◽

Amino Acid ◽

Morphological Changes ◽

Central Vacuole ◽

Starvation Response ◽

The Core ◽

Large Size ◽

Transmission Electron ◽

Membrane Bound ◽

Insight Into

Previous studies have demonstrated that colony forms of Blastocystis undergo cell death with numerous membrane-bound vesicles containing organelles located within the central vacuole, resembling morphological features of autophagy. In this study, we investigated whether Blastocystis underwent autophagy upon amino acid starvation and rapamycin treatment. Concurrently, we provide new insight into a possible function of the central vacuole. The use of the autophagy marker monodansylcadaverine, and the autophagy inhibitors3-methyladenine and wortmannin, showed the existence of autophagy in amino-acid-starved and rapamycin-treated Blastocystis. Confocal microscopy and transmission electron microscopy studies also showed morphological changes that were suggestive of autophagy. The unusually large size of the autophagic compartments within the parasite central vacuole was found to be unique in Blastocystis. In addition, autophagy was found to be triggered when cells were exposed to the cytotoxic antibody mAb 1D5, and autophagy was intensified in the presence of the caspase inhibitor zVAD.fmk. Taken together, our results suggest that the core machinery for autophagy is conserved in Blastocystis, and that it plays an important role in the starvation response and cell death of the parasite.

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Enigmatic dual symbiosis in the excretory organ of Nautilus macromphalus (Cephalopoda: Nautiloidea)

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2006.0353 ◽

2007 ◽

Vol 274 (1614) ◽

pp. 1143-1152 ◽

Cited By ~ 13

Author(s):

Mathieu Pernice ◽

Silke Wetzel ◽

Olivier Gros ◽

Renata Boucher-Rodoni ◽

Nicole Dubilier

Keyword(s):

Sequence Similarity ◽

Ammonia Oxidizing Bacteria ◽

Living Fossil ◽

Symbiotic Associations ◽

Transmission Electron ◽

Physiological Adaptations ◽

Excretory Organ ◽

Pericardial Villi ◽

Insight Into

Symbiosis is an important driving force in metazoan evolution and the study of ancient lineages can provide an insight into the influence of symbiotic associations on morphological and physiological adaptations. In the ‘living fossil’ Nautilus , bacterial associations are found in the highly specialized pericardial appendage. This organ is responsible for most of the excretory processes (ultrafiltration, reabsorption and secretion) and secretes an acidic ammonia-rich excretory fluid. In this study, we show that Nautilus macromphalus pericardial appendages harbour a high density of a β-proteobacterium and a coccoid spirochaete using transmission electron microscopy, comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH). These two bacterial phylotypes are phylogenetically distant from any known bacteria, with ammonia-oxidizing bacteria as the closest relatives of the β-proteobacterium (above or equal to 87.5% sequence similarity) and marine Spirochaeta species as the closest relatives of the spirochaete (above or equal to 89.8% sequence similarity), and appear to be specific to Nautilus . FISH analyses showed that the symbionts occur in the baso-medial region of the pericardial villi where ultrafiltration and reabsorption processes take place, suggesting a symbiotic contribution to the excretory metabolism.

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Characterization of bacterial biofilm communities in tertiary treatment processes for wastewater reclamation and reuse

Water Science & Technology ◽

10.2166/wst.2008.457 ◽

2008 ◽

Vol 58 (5) ◽

pp. 1023-1030 ◽

Cited By ~ 7

Author(s):

Tadashi Shoji ◽

Shuichi Ochi ◽

Masaaki Ozaki

Keyword(s):

Urban Areas ◽

Heterotrophic Bacteria ◽

Bacterial Biofilm ◽

Nitrifying Bacteria ◽

Water Supply Systems ◽

Ammonia Oxidizing Bacteria ◽

Tertiary Treatment ◽

Treatment Processes ◽

Related Group ◽

Biofilm Development

The concern with wastewater reuse as a sustainable water resource in urban areas has been growing. For the reclamation and distribution of wastewater, biofilm development deserves careful attention from the point of view of its promotion (e.g. biofiltration) and inhibition (e.g. clogging and hygiene problems). As the first step to control biofilm development, bacterial biofilm communities in tertiary treatment processes were characterized by using molecular biological methods. The result of clone library analysis showed that Nitrospirae-related (nitrite-oxydizing bacteria) and Acidobacteria-related (probably oligotrophic bacteria) groups were dominant. The ratio of the Nitrospirae-related group to the Acidobacteria-related group was associated with ammonia load, whereas other operational conditions (process, media, temperature, salt) did not clearly affect the phylum-level community or the dominant sequence of nitrifying bacteria. The result of real-time PCR also indicated that high ammonia load promotes the proliferation of nitrite- and ammonia-oxidizing bacteria. Regarding water supply systems, some researchers also have suggested the dominance of Nitrospirae- and Acidobacteria-related groups in biofilm formed on water distribution pipes. In tertiary wastewater treatment, therefore, it is concluded that oligotrophic and autotrophic bacteria are the dominant groups in biofilm samples because assimilable organic carbon is too poor to proliferate various heterotrophic bacteria.

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