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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.


Canonical correspondence analysis (CCA) ordination diagram of the archaeal and bacterial ammonia-oxidizing communities’ composition data in relation to the five selected environmental variables: (A) archaeal 16S rRNA gene; (B) bacterial16S rRNA gene; (C) archaeal amoA 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 7: Canonical correspondence analysis (CCA) ordination diagram of the archaeal and bacterial ammonia-oxidizing communities’ composition data in relation to the five selected environmental variables: (A) archaeal 16S rRNA gene; (B) bacterial16S rRNA gene; (C) archaeal amoA 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: Figure 7 shows the correlation of the five selected environmental parameters with both AOA and AOB community compositions based on the banding profile of both the 16S rRNA and amoA genes. The CCA for the archaeal 16S rRNA gene community showed S2 and CS to be positively correlated with Fe, TP, and NO3-. Moreover, S1 was positively correlated with DO and negatively correlated with NH4+, whereas the opposite was observed for the MS community (Figure 7A). The bacterial 16S rRNA gene communities from CS, S2, and MTS were positively correlated with Fe, TP, and NO3-. Again, MS was positively correlated with NH4+ and negatively with DO, and S1 was positively correlated with DO (Figure 7B).


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)

Canonical correspondence analysis (CCA) ordination diagram of the archaeal and bacterial ammonia-oxidizing communities’ composition data in relation to the five selected environmental variables: (A) archaeal 16S rRNA gene; (B) bacterial16S rRNA gene; (C) archaeal amoA 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 7: Canonical correspondence analysis (CCA) ordination diagram of the archaeal and bacterial ammonia-oxidizing communities’ composition data in relation to the five selected environmental variables: (A) archaeal 16S rRNA gene; (B) bacterial16S rRNA gene; (C) archaeal amoA 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: Figure 7 shows the correlation of the five selected environmental parameters with both AOA and AOB community compositions based on the banding profile of both the 16S rRNA and amoA genes. The CCA for the archaeal 16S rRNA gene community showed S2 and CS to be positively correlated with Fe, TP, and NO3-. Moreover, S1 was positively correlated with DO and negatively correlated with NH4+, whereas the opposite was observed for the MS community (Figure 7A). The bacterial 16S rRNA gene communities from CS, S2, and MTS were positively correlated with Fe, TP, and NO3-. Again, MS was positively correlated with NH4+ and negatively with DO, and S1 was positively correlated with DO (Figure 7B).

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.