Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt

Herfort, Lydie; Kim, Jung-Hyun; Coolen, Marco J. L.; Abbas, Ben; Schouten, Stefan; Herndl, Gerhard J.; Damsté, Jaap S. Sinninghe

doi:10.3354/ame01294

Cited by 48 publications

(44 citation statements)

References 53 publications

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“…However, owing to the short hydraulic residence time in the JRE (2-3 days), it seems not possible to develop an autochthonous planktonic archaeal communities in the freshwater region of this estuary, and therefore may represent allochthonous inputs of river populations [5]. Although this finding is unexpected, it is in line with the results of previous works which observed MCG and methanogens in oxygen-rich water of lakes [11,[64][65][66] and rivers [57,[67][68][69], suggesting that these two archaeal populations may have a more cosmopolitan distribution than conventional observations. Indeed, we also observed that MCG and some groups of methanogens are consistent components of archaeal communities in water and sediments of the Jiulong River (our unpublished data).…”

Section: Discussionsupporting

confidence: 91%

“…Previous studies have demonstrated that some typical soil archaeal lineages such as group 1.1b, which was also retrieved from JRE planktonic communities (Fig. 3c), have a patchy distribution in freshwater plankton [11,14,16,67]. In addition, it is very likely that JRE sediments and surrounding mangroves are important sources of archaeaplankton in the freshwater zone of the JRE, because a high proportion of OTUs was found to share between planktonic and benthic archaeal communities (Fig.…”

Section: Discussionmentioning

confidence: 86%

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Biogeography of Planktonic and Benthic Archaeal Communities in a Subtropical Eutrophic Estuary of China

Hou

2015

Microb Ecol

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Mounting evidence suggests that Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles, yet the pattern and its ecological drivers of biogeographic distribution of archaeal community in estuarine ecosystem are still not well understood. Here, we investigated planktonic and benthic archaeal communities in the human-impacted Jiulong River estuary (JRE), southern China by using real-time PCR (RT-PCR) and Illumina 16S ribosomal RNA (rRNA) amplicon sequencing. RT-PCR analysis indicated that Archaea accounted for an average of 0.79 and 5.31 % of prokaryotic biomass in water and sediment samples of the JRE, respectively. The diversity of planktonic archaeal community decreased gradually from the river runoff to seawater, whereas that of benthic community did not show the similar pattern. The results of taxonomic assignments indicated that Thaumarchaeota (Nitrosopumilus and Cenarchaeum), Methanocorpusculum, and Methanospirillum were significantly more abundant in planktonic than benthic communities, whereas the relative abundances of Miscellaneous Crenarchaeotic Group, Marine Benthic Group-B/-D, anaerobic methane-oxidizing Archaea -1/-2D, and South Africa Gold Mine Euryarchaeotic Group 1 were higher in sediments than in surface waters. Moreover, planktonic archaeal community composition varied significantly at broad and finer-scale taxonomic levels along the salinity gradient. Multivariate statistical analyses revealed that salinity is the main factor structuring the JRE planktonic but not benthic archaeal community at both total community and population level. SourceTrakcer analysis indicated that river might be a major source of archaea in the freshwater zone of the JRE. Overall, this study advances our understanding of the biogeographic patterns and its ecological drivers of estuarine archaeal communities.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 86%

Biogeography of Planktonic and Benthic Archaeal Communities in a Subtropical Eutrophic Estuary of China

Hou

2015

Microb Ecol

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“…The total bacterioplankton cell numbers ranged from 6.1 × 10 5 to 5.4 × 10 6 cells per milliliter, which was equivalent to typical bacterioplankton cell numbers reported from other rivers and lakes [3,[25][26][27]. The cell numbers were not significantly different among seasons, which coincided with a previous report from Tampa Bay, FL, USA [28].…”

Section: Bacterioplankton Cell Numbers Along the Estuary Salinitysupporting

confidence: 74%

Shifts of Bacterioplankton Metabolic Profiles along the Salinity Gradient in a Subtropical Estuary

et al. 2013

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Understanding the biodegradation potential of river bacterioplankton communities is crucial for watershed management. We investigated the shifts in bacterioplankton metabolic profiles along the salinity gradient of the Caloosahatchee River Estuary, Florida. The carbon source utilization patterns of river bacterioplankton communities were determined by using Biolog EcoPlates. The number of utilized substrates was generally high in the upstream freshwater dominated zone and low in the downstream zone, suggesting a shift in metabolic profiles among bacterioplankton assemblages along the estuarine gradient. The prokaryotic cell numbers also decreased along the estuarine salinity gradient. Seasonal and site-specific differences were found in the numbers of utilized substrates, which were similar in summer and fall (wet season) and winter and spring (dry season). Bacterioplankton assemblages in summer and fall showed more versatile substrate utilization patterns than those of winter and spring communities. Therefore, our data suggest that microbial metabolic patterns in the subtropical estuary are likely influenced by the water discharge patterns created by dry and wet seasons along the salinity gradient.

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“…Only a few freshwater planktonic environments have been prospected so far, but AOA have been detected in rivers (26,31), in the oligotrophic African Lake Kivu (44), in groundwater (57), and in drinking water (66). Here, we have extended the survey to ultraoligotrophic mountain lakes, showing that freshwater amoA sequences mainly formed coherent freshwater clusters (Fig.…”

Section: Discussionmentioning

confidence: 98%

Seasonal Changes of Freshwater Ammonia-Oxidizing Archaeal Assemblages and Nitrogen Species in Oligotrophic Alpine Lakes

Auguet

Nomokonova

Camarero

et al. 2011

Appl Environ Microbiol

105

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The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ؎ 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.For almost 30 years, the ubiquity of nitrification, particularly in the most oligotrophic environments, had constituted an enigma for ecologists (28,52). First, because of very low natural abundances of ammonia-oxidizing bacteria (AOB), the a priori unique microorganisms with the potential to catalyze the first step of nitrification had been reported (e.g., 0.1% of total bacterial assemblage in oceanic habitats) (9, 38), and second, because field measurements indicated that the oxidation of ammonia (NH 4 ϩ ) to nitrate was feasible in situ even in the most oligotrophic habitats, where NH 4 ϩ concentrations were below the affinity threshold for AOB (8). Five years ago, metagenomics provided an answer to the enigma and radically changed the general perception of the nitrification process (65, 67). The presence of putative ammonia monooxygenase subunits (amoA, amoB, and amoC) within the genomes of widespread and abundant microorganisms of the domain Archaea (65, 67), as well as the chemolithoautotrophic growth using ammonia as an energy source observed in the recently isolated Crenarchaeota Nitrosopumilus maritimus (37), has fuelled...

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Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt

Cited by 48 publications

References 53 publications

Biogeography of Planktonic and Benthic Archaeal Communities in a Subtropical Eutrophic Estuary of China

Biogeography of Planktonic and Benthic Archaeal Communities in a Subtropical Eutrophic Estuary of China

Shifts of Bacterioplankton Metabolic Profiles along the Salinity Gradient in a Subtropical Estuary

Seasonal Changes of Freshwater Ammonia-Oxidizing Archaeal Assemblages and Nitrogen Species in Oligotrophic Alpine Lakes

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