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

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.

Resistant ammonia‐oxidizing archaea endure, but adapting ammonia‐oxidizing bacteria thrive in boreal lake sediments receiving nutrient‐rich effluents

“…When unclassified Nitrosomonadacaea was excluded, the abundance of Nitrosomonas was higher than that of Nitrosospira in wastewater‐ influenced sediments. These two AOB clades are physiologically distinct, Nitrosospira ‐like AOB being more abundant in low ammonium conditions, while Nitrosomonas ‐like AOB have been suggested to be adapted to grow in ammonium‐rich environments, for example, in eutrophic sediments (Peng et al ., ; Reis et al ., ). Altogether, these results indicate that although wastewater can promote the abundance of certain AOB groups ( Nitrosomonas ) through habitat modification and migration from WWTP, other groups can still coexist.…”

“…Although a proportion of AOB was suggested to originate from wastewater treatment plant (see also Mußmann et al ., ; Pan et al ., ), the dynamics between AOA and AOB abundance were mainly directly driven by wastewater itself. Previous studies have reported that AOA thrive under stable and oligotrophic conditions, while dynamic and nitrogen‐rich conditions favour AOB in aquatic environments (Laanbroek et al ., ; Bollman et al ., ; Reis et al ., ). From an ecological perspective, these results indicate that there might be some differences in the stability of AOA and AOB communities, seen as different resistance to changes in environmental conditions.…”

“…Our second objective was to specifically examine how AOA and AOB communities respond to wastewater. As AOA communities have been found to exhibit low diversity under disturbance (Newell et al, 2014), and their abundance to be suppressed under nutrient-rich conditions (French et al, 2012;Reis et al, 2015;Soares et al, 2016), we hypothesized that AOA would be more sensitive to nutrient-rich wastewater, showing decreasing diversity as well as decreasing overall abundance. We expected the abundance of AOB to increase in wastewater-influenced sediments, and hypothesized that it would be due to altered environmental conditions and/or introduction of novel AOB from wastewater treatment plant (WWTP).…”

Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake

“…The distribution of sediment ammonia-oxidizing archaeal and bacterial populations has been investigated in a variety of freshwater ecosystems, such as river (Reis et al 2015;Sonthiphand et al 2013;Sun et al 2013;Xie et al 2014), reservoir , lake (Bollmann et al 2014;Hou et al 2013;Liu et al 2015;Mukherjee et al 2016;Zhao et al 2013Zhao et al , 2014, wetland (Liu et al 2014a;Wang et al 2013;Yang et al 2014), and pond (Lu et al 2015), yet the relative importance of AOA and AOB to nitrification process in freshwater sediments remains under debate. Several previous studies indicated that AOA amoA gene abundance was usually greater than AOB in lake sediments (Herrmann et al 2009;Hou et al 2013;Zhao et al 2014), while the numerical dominance of AOB over AOA amoA gene abundance was observed in sediments of many freshwater lakes on the Yunnan Plateau (Liu et al 2015).…”

Archaea in Natural and Impacted Brazilian Environments

“…and Methanosarcina sp., suggesting that both acetate and other compounds such as methanol and methylamines were being used as substrate for methanogenesis. A subsequent study by the same group [71] investigated the effect of human settlement in mining areas on ammonia oxidizing microorganisms present in these kinds of sediments. Archaeal amoA genes were detected in both impacted and nonimpacted sediments, but most abundantly in the nonimpacted sediment.…”