scholarly journals Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature

2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Ling Wu ◽  
Cheng Han ◽  
Guangwei Zhu ◽  
Wenhui Zhong
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Nitrogen Input ◽  
Nitrification Activity ◽  
Ammonia Oxidizing Archaea ◽  
Nitrogen Inputs

ABSTRACTAmmonium concentrations and temperature drive the activities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), but their effects on these microbes in eutrophic freshwater sediments are unclear. In this study, surface sediments collected from areas of Taihu Lake (China) with different degrees of eutrophication were incubated under three levels of nitrogen input and temperature, and the autotrophic growth of ammonia oxidizers was assessed using13C-labeled DNA-based stable-isotope probing (SIP), while communities were characterized using MiSeq sequencing and phylogenetic analysis of 16S rRNA genes. Nitrification rates in sediment microcosms were positively correlated with nitrogen inputs, but there was no marked association with temperature. Incubation of SIP microcosms indicated that AOA and AOBamoAgenes were labeled by13C at 20°C and 30°C in the slightly eutrophic sediment, and AOBamoAgenes were labeled to a much greater extent than AOAamoAgenes in the moderately eutrophic sediment after 56 days. Phylogenetic analysis of13C-labeled 16S rRNA genes revealed that the active AOA were mainly affiliated with theNitrosopumiluscluster, with theNitrososphaeracluster dominating in the slightly eutrophic sediment at 30°C with low ammonium input (1 mM). Active AOB communities were more sensitive to nitrogen input and temperature than were AOA communities, and they were exclusively dominated by theNitrosomonascluster, which tended to be associated withNitrosomonadaceae-like lineages.Nitrosomonassp. strain Is79A3 tended to dominate the moderately eutrophic sediment at 10°C with greater ammonium input (2.86 mM). The relative abundance responses of the major active communities to nitrogen input and temperature gradients varied, indicating niche differentiation and differences in the physiological metabolism of ammonia oxidizers that are yet to be described.IMPORTANCEBoth archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.

scholarly journals Autotrophic Growth of Bacterial and Archaeal Ammonia Oxidizers in Freshwater Sediment Microcosms Incubated at Different Temperatures

2013 ◽  
Vol 79 (9) ◽  
pp. 3076-3084 ◽  
Author(s):  
Yucheng Wu ◽  
Xiubin Ke ◽  
Marcela Hernández ◽  
Baozhan Wang ◽  
Marc G. Dumont ◽  
...  
Keyword(s):  
Lake Taihu ◽  
Microbial Community Composition ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Autotrophic Growth ◽  
Ammonia Oxidizing Archaea ◽  
Different Temperatures

ABSTRACTBoth bacteria and archaea potentially contribute to ammonia oxidation, but their roles in freshwater sediments are still poorly understood. Seasonal differences in the relative activities of these groups might exist, since cultivated archaeal ammonia oxidizers have higher temperature optima than their bacterial counterparts. In this study, sediment collected from eutrophic freshwater Lake Taihu (China) was incubated at different temperatures (4°C, 15°C, 25°C, and 37°C) for up to 8 weeks. We examined the active bacterial and archaeal ammonia oxidizers in these sediment microcosms by using combined stable isotope probing (SIP) and molecular community analysis. The results showed that accumulation of nitrate in microcosms correlated negatively with temperature, although ammonium depletion was the same, which might have been related to enhanced activity of other nitrogen transformation processes. Incubation at different temperatures significantly changed the microbial community composition, as revealed by 454 pyrosequencing targeting bacterial 16S rRNA genes. After 8 weeks of incubation, [13C]bicarbonate labeling of bacterialamoAgenes, which encode the ammonia monooxygenase subunit A, and an observed increase in copy numbers indicated the activity of ammonia-oxidizing bacteria in all microcosms.Nitrosomonassp. strain Is79A3 andNitrosomonas communislineages dominated the heavy fraction of CsCl gradients at low and high temperatures, respectively, indicating a niche differentiation of active bacterial ammonia oxidizers along the temperature gradient. The13C labeling of ammonia-oxidizing archaea in microcosms incubated at 4 to 25°C was minor. In contrast, significant13C labeling ofNitrososphaera-like archaea and changes in the abundance and composition of archaealamoAgenes were observed at 37°C, implicating autotrophic growth of ammonia-oxidizing archaea under warmer conditions.

scholarly journals Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Valsamma Joseph ◽  
Geethu Chellappan ◽  
S. Aparajitha ◽  
R. N. Ramya ◽  
S. Vrinda ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Water Exchange ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Shrimp Culture ◽  
Ammonia Oxidizing Archaea ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

AbstractIn the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.

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

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.

Amplification of 16S rRNA genes of Anaplasma species in China for phylogenetic analysis

2005 ◽  
Vol 107 (1-2) ◽  
pp. 145-148 ◽  
Author(s):  
Zhijie Liu ◽  
Jianxun Luo ◽  
Qi Bai ◽  
Miling Ma ◽  
Guiguan Guan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes

scholarly journals Quantitative Assessment of Ammonia-Oxidizing Bacterial Communities in the Epiphyton of Submerged Macrophytes in Shallow Lakes

2010 ◽  
Vol 76 (6) ◽  
pp. 1813-1821 ◽  
Author(s):  
M. Coci ◽  
G. W. Nicol ◽  
G. N. Pilloni ◽  
M. Schmid ◽  
M. P. Kamst-van Agterveld ◽  
...  
Keyword(s):  
16S Rrna ◽  
Shallow Lakes ◽  
Submerged Macrophytes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gene Copy ◽  
Potamogeton Pectinatus ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Potential Nitrification

ABSTRACT In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However, the diversity, numbers, and activity of epiphytic ammonia-oxidizing bacteria have long been overlooked. In the present study, we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On the basis of the m2 of the lake surface, the gene copy numbers of epiphytic ammonia oxidizers were not significantly different from those in the benthic and pelagic compartments. The potential ammonia-oxidizing activities measured in the epiphytic compartment were also not significantly different from the activities determined in the benthic compartment. No potential ammonia-oxidizing activities were observed in the pelagic compartment. No activity was detected in the epiphyton of Chara aspera, the dominant submerged macrophyte in Lake Nuldernauw in The Netherlands. The presence of ammonia-oxidizing bacterial cells in the epiphyton of Potamogeton pectinatus was also demonstrated by fluorescent in situ hybridization microscopy images. By comparing the community composition as assessed by the 16S rRNA gene PCR-denaturing gradient gel electrophoresis approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Of the environmental parameters examined, only the water retention time, the Kjeldahl nitrogen content, and the total phosphorus content correlated with potential ammonia-oxidizing activities. None of these parameters correlated with the numbers of gene copies related to ammonia-oxidizing betaproteobacteria.

scholarly journals Census of the Viral Metagenome within an Activated Sludge Microbial Assemblage

2010 ◽  
Vol 76 (8) ◽  
pp. 2673-2677 ◽  
Author(s):  
Larissa C. Parsley ◽  
Erin J. Consuegra ◽  
Stephen J. Thomas ◽  
Jaysheel Bhavsar ◽  
Andrew M. Land ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Activated Sludge ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Isolates ◽  
Microbial Assemblage ◽  
Culture Independent ◽  
Culture Dependent

ABSTRACT The viral metagenome within an activated sludge microbial assemblage was sampled using culture-dependent and culture-independent methods and compared to the diversity of activated sludge bacterial taxa. A total of 70 unique cultured bacterial isolates, 24 cultured bacteriophages, 829 bacterial metagenomic clones of 16S rRNA genes, and 1,161 viral metagenomic clones were subjected to a phylogenetic analysis.

scholarly journals Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon

2013 ◽  
Vol 80 (5) ◽  
pp. 1684-1691 ◽  
Author(s):  
Baozhan Wang ◽  
Yan Zheng ◽  
Rong Huang ◽  
Xue Zhou ◽  
Dongmei Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
Buoyant Density ◽  
Stable Isotope Probing ◽  
Acidic Soil ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Metabolic Versatility

ABSTRACTAll cultivated ammonia-oxidizing archaea (AOA) within theNitrososphaeracluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence ofNitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth ofNitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis ofamoAgenes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that13CO2assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both13C-labeledamoAand 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strainsNitrososphaera viennensisEN76 and JG1 within theNitrososphaeracluster. Our results provide strong evidence for the adaptive growth ofNitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.

Phylogenetic analysis of several Thermus strains from Rehai of Tengchong, Yunnan, China

2005 ◽  
Vol 51 (10) ◽  
pp. 881-886 ◽  
Author(s):  
Lianbing Lin ◽  
Jie Zhang ◽  
Yunlin Wei ◽  
Chaoyin Chen ◽  
Qian Peng
Keyword(s):  
Phylogenetic Analysis ◽  
Secondary Structure ◽  
16S Rrna ◽  
Hot Springs ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Structure Comparison ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Rehai Geothermal Area

Several Thermus strains were isolated from 10 hot springs of the Rehai geothermal area in Tengchong, Yunnan province. The diversity of Thermus strains was examined by sequencing the 16S rRNA genes and comparing their sequences. Phylogenetic analysis showed that the 16S rDNA sequences from the Rehai geothermal isolates form four branches in the phylogenetic tree and had greater than 95.9% similarity in the phylogroup. Secondary structure comparison also indicated that the 16S rRNA from the Rehai geothermal isolates have unique secondary structure characteristics in helix 6, helix 9, and helix 10 (reference to Escherichia coli). This research is the first attempt to reveal the diversity of Thermus strains that are distributed in the Rehai geothermal area.Key words: Thermus, diversity, phylogenetic analysis, RNA secondary structure.

scholarly journals Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean

2000 ◽  
Vol 66 (5) ◽  
pp. 1960-1969 ◽  
Author(s):  
Nasreen Bano ◽  
James T. Hollibaugh
Keyword(s):  
Arctic Ocean ◽  
16S Rrna Genes ◽  
The Arctic ◽  
Rrna Genes ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Major Band ◽  
Pcr Product ◽  
The Arctic Ocean

ABSTRACT The spatial distribution and diversity of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria(hereinafter referred to as ammonia oxidizers) in the Arctic Ocean were determined. The presence of ammonia oxidizers was detected by PCR amplification of 16S rRNA genes using a primer set specific for this group of organisms (nitA and nitB, which amplifies a 1.1-kb fragment between positions 137 and 1234, corresponding to Escherichia coli 16S rDNA numbering). We analyzed 246 samples collected from the upper water column (5 to 235 m) during March and April 1995, September and October 1996, and September 1997. Ammonia oxidizers were detected in 25% of the samples from 5 m, 80% of the samples from 55 m, 88% of the samples from 133 m, and 50% of the samples from 235 m. Analysis of nitA-nitB PCR product by nested PCR-denaturing gradient gel electrophoresis (DGGE) showed that all positive samples contained the same major band (band A), indicating the presence of a dominant, ubiquitous ammonia oxidizer in the Arctic Ocean basin. Twenty-two percent of the samples contained additional major bands. These samples were restricted to the Chukchi Sea shelf break, the Chukchi cap, and the Canada basin; areas likely influenced by Pacific inflow. The nucleotide sequence of the 1.1-kb nitA-nitB PCR product from a sample that contained only band A grouped with sequences designated group 1 marine Nitrosospira-like sequences. PCR-DGGE analysis of 122 clones from four libraries revealed that 67 to 71% of the inserts contained sequences with the same mobility as band A. Nucleotide sequences (1.1 kb) of another distinct group of clones, found only in 1995 samples (25%), fell into the group 5 marineNitrosomonas-like sequences. Our results suggest that the Arctic Ocean β-proteobacterial ammonia oxidizers have low diversity and are dominated by marine Nitrosospira-like organisms. Diversity appears to be higher in Western Arctic Ocean regions influenced by inflow from the Pacific Ocean through the Bering and Chukchi seas.

Phylogenetic Differentiation of Two Closely RelatedNitrosomonas spp. That Inhabit Different Sediment Environments in an Oligotrophic Freshwater Lake

1999 ◽  
Vol 65 (11) ◽  
pp. 4855-4862 ◽  
Author(s):  
Corinne B. Whitby ◽  
Jon R. Saunders ◽  
Juana Rodriguez ◽  
Roger W. Pickup ◽  
Alan McCarthy
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Freshwater Lake ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Relative Distribution ◽  
Sediment Samples ◽  
Oligonucleotide Hybridization

ABSTRACT The population of ammonia-oxidizing bacteria in a temperate oligotrophic freshwater lake was analyzed by recovering 16S ribosomal DNA (rDNA) from lakewater and sediment samples taken throughout a seasonal cycle. Nitrosospira and Nitrosomonas16S rRNA genes were amplified in a nested PCR, and the identity of the products was confirmed by oligonucleotide hybridization.Nitrosospira DNA was readily identified in all samples, and nitrosomonad DNA of the Nitrosomonas europaea-Nitrosomonas eutropha lineage was also directly detected, but during the summer months only. Phylogenetic delineation with partial (345 bp) 16S rRNA gene sequences of clones obtained from sediments confirmed the fidelity of the amplified nitrosomonad DNA and identified two sequence clusters closely related to either N. europaea or N. eutropha that were equated with the littoral and profundal sediment sites, respectively. Determination of 701-bp sequences for 16S rDNA clones representing each cluster confirmed this delineation. A PCR-restriction fragment length polymorphism (RFLP) system was developed that enabled identification of clones containing N. europaea and N. eutropha 16S rDNA sequences, including subclasses therein. It proved possible to analyze 16S rDNA amplified directly from sediment samples to determine the relative abundance of each species compared with that of the other. N. europaea and N. eutropha are very closely related, and direct evidence for their presence in lake systems is limited. The correlation of each species with a distinct spatial location in sediment is an unusual example of niche adaptation by two genotypically similar bacteria. Their occurrence and relative distribution can now be routinely monitored in relation to environmental variation by the application of PCR-RFLP analysis.

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