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The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

Reis MP, Ávila MP, Keijzer RM, Barbosa FA, Chartone-Souza E, Nascimento AM, Laanbroek HJ - Front Microbiol (2015)

Bottom Line: In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them.Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH.These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands.

ABSTRACT
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

No MeSH data available.


Unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) band sequences from the samples. (A) archaeal 16S rRNA gene; (B) archaeal amoA gene; (C) bacterial 16S rRNA gene; (D) bacterial amoA gene. CS, Carrapatos sediment; MS, Mina sediment; S1, Site 1 sediment; S2, Site 2 sediment; TS, Tulipa sediment; MTS, Mutuca sediment.
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Figure 4: Unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) band sequences from the samples. (A) archaeal 16S rRNA gene; (B) archaeal amoA gene; (C) bacterial 16S rRNA gene; (D) bacterial amoA gene. CS, Carrapatos sediment; MS, Mina sediment; S1, Site 1 sediment; S2, Site 2 sediment; TS, Tulipa sediment; MTS, Mutuca sediment.

Mentions: The DGGE banding profiles demonstrated a higher number of bands in the AOA communities than in the AOB communities based on both 16S rRNA and amoA genes (Figure 4). Moreover, only one bacterial amoA gene band was detected in the non-impacted S1 sample, whereas no bands were observed for the AOB community in the non-impacted S2 and MTS samples (Figure 4D).


The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

Reis MP, Ávila MP, Keijzer RM, Barbosa FA, Chartone-Souza E, Nascimento AM, Laanbroek HJ - Front Microbiol (2015)

Unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) band sequences from the samples. (A) archaeal 16S rRNA gene; (B) archaeal amoA gene; (C) bacterial 16S rRNA gene; (D) bacterial amoA gene. CS, Carrapatos sediment; MS, Mina sediment; S1, Site 1 sediment; S2, Site 2 sediment; TS, Tulipa sediment; MTS, Mutuca sediment.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4553384&req=5

Figure 4: Unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) band sequences from the samples. (A) archaeal 16S rRNA gene; (B) archaeal amoA gene; (C) bacterial 16S rRNA gene; (D) bacterial amoA gene. CS, Carrapatos sediment; MS, Mina sediment; S1, Site 1 sediment; S2, Site 2 sediment; TS, Tulipa sediment; MTS, Mutuca sediment.
Mentions: The DGGE banding profiles demonstrated a higher number of bands in the AOA communities than in the AOB communities based on both 16S rRNA and amoA genes (Figure 4). Moreover, only one bacterial amoA gene band was detected in the non-impacted S1 sample, whereas no bands were observed for the AOB community in the non-impacted S2 and MTS samples (Figure 4D).

Bottom Line: In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them.Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH.These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands.

ABSTRACT
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

No MeSH data available.