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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.


Neighbor-joining tree of AOA based on the partial 16S rRNA gene of DGGE bands. Nodes with a bootstrap value greater than 0.90 or 0.50 are indicated by closed and open circles, respectively. 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 5: Neighbor-joining tree of AOA based on the partial 16S rRNA gene of DGGE bands. Nodes with a bootstrap value greater than 0.90 or 0.50 are indicated by closed and open circles, respectively. CS, Carrapatos sediment; MS, Mina sediment; S1, Site 1 sediment; S2, Site 2 sediment; TS, Tulipa sediment; MTS, Mutuca sediment.

Mentions: To identify the phylogenetic affiliations of members of the AOA and AOB communities selected bands from the DGGE gels were excised and sequenced. No chimeras were detected among the sequences. For the archaeal 16S rRNA gene, 36 sequences were subjected to phylogenetic analysis (Figure 5). It should be noted that all the archaeal sequences from the TS and S2 samples were affiliated with the Thaumarchaeota, whereas the MTS sample, which is oligotrophic and is not influenced by human settlement, was comprised of Crenarchaeota-related sequences. Sequences recovered from the other stream sediments were scattered throughout the Thaumarchaeota and Crenarchaeota phyla. Most sequences from the S1 and S2 samples grouped together in the Group 1.1a-associated clade (Figure 5).


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)

Neighbor-joining tree of AOA based on the partial 16S rRNA gene of DGGE bands. Nodes with a bootstrap value greater than 0.90 or 0.50 are indicated by closed and open circles, respectively. 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 5: Neighbor-joining tree of AOA based on the partial 16S rRNA gene of DGGE bands. Nodes with a bootstrap value greater than 0.90 or 0.50 are indicated by closed and open circles, respectively. CS, Carrapatos sediment; MS, Mina sediment; S1, Site 1 sediment; S2, Site 2 sediment; TS, Tulipa sediment; MTS, Mutuca sediment.
Mentions: To identify the phylogenetic affiliations of members of the AOA and AOB communities selected bands from the DGGE gels were excised and sequenced. No chimeras were detected among the sequences. For the archaeal 16S rRNA gene, 36 sequences were subjected to phylogenetic analysis (Figure 5). It should be noted that all the archaeal sequences from the TS and S2 samples were affiliated with the Thaumarchaeota, whereas the MTS sample, which is oligotrophic and is not influenced by human settlement, was comprised of Crenarchaeota-related sequences. Sequences recovered from the other stream sediments were scattered throughout the Thaumarchaeota and Crenarchaeota phyla. Most sequences from the S1 and S2 samples grouped together in the Group 1.1a-associated clade (Figure 5).

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.