scholarly journals Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

2018 ◽  
Author(s):  
Zhirong Zhao ◽  
Guohe Huang ◽  
Mingyuan Wang ◽  
Nan Zhou ◽  
Shishi He ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
River Sediments ◽  
High Specificity ◽  
Single Step ◽  
Ammonia Oxidizing Bacteria ◽  
Water And Wastewater Treatment ◽  
Universal Primer ◽  
Real Time Quantitative Pcr ◽  
Clade B ◽  
Abundance And Diversity

AbstractComplete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting the both clades of CAOBamoAgene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in whichN. nitrosacluster dominated CAOBamoAin activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.

scholarly journals Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary

2021 ◽  
Vol 11 ◽  
Author(s):  
Xinxin Wang ◽  
Lu Lu ◽  
Xue Zhou ◽  
Xiufeng Tang ◽  
Lu Kuang ◽  
...  
Keyword(s):  
Yangtze River ◽  
Ammonia Oxidation ◽  
Agricultural Soils ◽  
River Estuary ◽  
Niche Differentiation ◽  
Yangtze River Estuary ◽  
Ammonia Oxidizing Bacteria ◽  
Community Structures ◽  
Dominant Group ◽  
Clade B

The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.

scholarly journals Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Laibin Huang ◽  
Seemanti Chakrabarti ◽  
Jennifer Cooper ◽  
Ana Perez ◽  
Sophia M. John ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Ammonia Oxidizing Bacteria ◽  
Central Process ◽  
Soil Nitrification ◽  
Plant Nitrogen ◽  
Ammonia Oxidizing Archaea ◽  
Activity Measurements ◽  
Nitrite Oxidizing Bacteria

AbstractNitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

scholarly journals Magnetic Signatures on River Sediments and Agricultural Soils as Proxy Indicators of Anthropogenic-derived Pollution (Case Study: Cikijing River, Rancaekek, West Java)

2021 ◽  
Vol 7 (3) ◽  
pp. 381
Author(s):  
Dini Fitriani ◽  
Widya Utami ◽  
Kartika Hajar Kirana ◽  
Eleonora Agustine ◽  
Siti Zulaikah
Keyword(s):  
Magnetic Properties ◽  
Magnetic Susceptibility ◽  
Agricultural Soils ◽  
River Sediments ◽  
Paddy Fields ◽  
Composition Analysis ◽  
Magnetic Minerals ◽  
West Java ◽  
Anthropogenic Pollutants ◽  
Magnetic Signatures

A number of activities occur around the Cikijing River in Rancaekek area, West Java, such as industrial and domestic activities. The various activities could decrease the quality of the river and surrounding environment due to anthropogenic pollutants that might be produced. Since the Cikijing River is also used as the source of irrigation, paddy fields around the river could be also be affected. The presence of pollutants in river sediments and agricultural soils over a long period could change their magnetic properties. Magnetic susceptibility of Cikijing River sediments and soils of the paddy fields in the surrounding have been examined considering that magnetic properties could represent environmental conditions. The results show that river sediments have magnetic susceptibility (cLF) in range of 356.2-456.3 (×10-8) m3kg-1, whereas soils samples have cLF varying from 94.1 to 347.1 (×10-8) m3kg-1, suggesting domination of ferrimagnetic minerals. The cFD (%) is <4% indicating the anthropogenic origin of magnetic minerals.  Electron microscopy images show the imperfect octahedral and spherules shapes of magnetic grains that supports magnetic susceptibility analysis about the source of magnetic minerals. Elemental composition analysis reveals Fe and O’s content as main elements, including minor elements of Ca, Mg, Al. Si, Ti and Cr

Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice

2015 ◽  
Vol 70 (4) ◽  
pp. 971-980 ◽  
Author(s):  
Hongzhao Yuan ◽  
Tida Ge ◽  
Xiangbi Chen ◽  
Shoulong Liu ◽  
Zhenke Zhu ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Management Practice ◽  
Abundance And Diversity

scholarly journals Tuber melanosporum shapes nirS-type denitrifying and ammonia-oxidizing bacterial communities in Carya illinoinensis ectomycorrhizosphere soils

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9457
Author(s):  
Zongjing Kang ◽  
Jie Zou ◽  
Yue Huang ◽  
Xiaoping Zhang ◽  
Lei Ye ◽  
...  
Keyword(s):  
Denitrifying Bacteria ◽  
Ammonium Nitrogen ◽  
Carya Illinoinensis ◽  
Tuber Melanosporum ◽  
Ammonia Oxidizing Bacteria ◽  
Community Structures ◽  
Ectomycorrhizal Symbiosis ◽  
Rhizosphere Soils ◽  
Abundance And Diversity ◽  
Next Generation Sequencing Ngs

Background NirS-type denitrifying bacteria and ammonia-oxidizing bacteria (AOB) play a key role in the soil nitrogen cycle, which may affect the growth and development of underground truffles. We aimed to investigate nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of Carya illinoinensis seedlings inoculated with the black truffle (Tuber melanosporum) during the early symbiotic stage. Methods The C. illinoinensis seedlings inoculated with or without T. melanosporum were cultivated in a greenhouse for six months. Next-generation sequencing (NGS) technology was used to analyze nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of these seedlings. Additionally, the soil properties were determined. Results The results indicated that the abundance and diversity of AOB were significantly reduced due to the inoculation of T. melanosporum, while these of nirS-type denitrifying bacteria increased significantly. Proteobacteria were the dominant bacterial groups, and Rhodanobacter, Pseudomonas, Nitrosospira and Nitrosomonas were the dominant classified bacterial genera in all the soil samples. Pseudomonas was the most abundant classified nirS-type denitrifying bacterial genus in ectomycorrhizosphere soils whose relative abundance could significantly increase after T. melanosporum inoculation. A large number of unclassified nirS-type denitrifying bacteria and AOB were observed. Moreover, T. melanosporum inoculation had little effect on the pH, total nitrogen (TN), nitrate-nitrogen (NO${}_{3}^{-}$-N) and ammonium-nitrogen (NH${}_{4}^{+}$-N) contents in ectomycorrhizosphere soils. Overall, our results showed that nirS-type denitrifying bacterial and AOB communities in C. illinoinensis rhizosphere soils were significantly affected by T. melanosporum on the initial stage of ectomycorrhizal symbiosis, without obvious variation of soil N contents.

scholarly journals Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon “Candidatus Nitrosocosmicus agrestis”

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Liangting Liu ◽  
Mengfan Liu ◽  
Yiming Jiang ◽  
Weitie Lin ◽  
Jianfei Luo
Keyword(s):  
Agricultural Soils ◽  
Metagenomic Data ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Polyamine Synthesis ◽  
Ammonia Oxidizing Archaea ◽  
High Ammonia ◽  
Genes Encoding ◽  
High Concentrations ◽  
Ammonia Tolerance

ABSTRACT Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus “Candidatus Nitrosocosmicus.” However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species “Candidatus Nitrosocosmicus agrestis,” obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH3 (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus “Ca. Nitrosocosmicus.” When “Ca. Nitrosocosmicus agrestis” was grown with high levels of ammonia, the genes that participate in CO2/HCO3− conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of “Ca. Nitrosocosmicus agrestis,” and even of the genus “Ca. Nitrosocosmicus.” IMPORTANCE Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N2O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species “Ca. Nitrosocosmicus agrestis” was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.

scholarly journals Genomic analysis of red-tide water bloomed with Heterosigma akashiwo in Geoje

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4854 ◽  
Author(s):  
Hye-Eun Kang ◽  
Tae-Ho Yoon ◽  
Sunyoung Yoon ◽  
Hak Jun Kim ◽  
Hyun Park ◽  
...  
Keyword(s):  
Microbial Community ◽  
Harmful Algal Bloom ◽  
High Specificity ◽  
Cross Reactivity ◽  
Heterosigma Akashiwo ◽  
Universal Primer ◽  
Abundant Otus ◽  
Phytoplankton Communities ◽  
Genomic Analyses ◽  
Primer Sets

Microbial community structures of harmful algal bloom (HAB) caused by Heterosigma akashiwo in Geoje were analyzed using the MiSeq platform. To analyze phytoplankton communities without cross-reactivity with predominant bacteria, a new phytoplankton-specific 23S universal primer set was designed by modifying two previously used ones. The new universal primer set turned out to be a useful tool for the analysis of the phytoplankton community; it showed a high specificity for phytoplankton without cross-reactivity to bacterial sequences as well as the wide taxon coverage presenting from prokaryotic cyanobacteria to eukaryotic algae. Next Generation Sequencing (NGS) data generated by two universal primer sets (16S and 23S) provided useful information about the H. akashiwo bloom. According to the 23S universal primer set, proportions of H. akashiwo increased by more than 200-fold as the bloom occurred and its numbers were high enough to detect in control sites. Its operational taxonomic units (OTUs) were detected in the bloom sites at low proportions suggesting that the 16S universal primer set may not be as effective for monitoring harmful algal blooming (HAB) as the 23S universal primer set. In addition, several abundant OTUs in Chlorophyta were not presented by the 16S universal primer set in this study. However, the 16S primer set was useful for detecting decreases in Foraminifera as HAB occurred suggesting that genomic analyses using two universal primer sets would provide more reliable data for understanding microbial community changes by various environmental or ecological events, including HAB. Genomic analyses using two universal primer sets was also useful for determining a correlation between microbial components as HAB occurred. Heterosigma akashiwo was positively correlated with other bloom species, including Karenia mikimotoi, Teleaulax amphioxeia, and bacteria in Verrucomicrobia.

Sign in / Sign up

Export Citation Format

Share Document