Microbial nitrification in urban streams: from single cell activity to ecosystem

Abstract

[spa] El objetivo de esta tesis ha sido el estudio de los mecanismos y factores reguladores del proceso microbiano de oxidación del amonio (NH4) en ríos urbanos afectados por vertidos de depuradoras. Arqueas (AOA) y bacterias (AOB) oxidadoras de amonio (OA) fueron detectadas en comunidades microbianas (biofilms) desarrolladas sobre los cantos rodados del río. Su abundancia, composición, distribución y actividad fueron examinadas, con técnicas de ecología microbiana molecular y de biogeoquímica fluvial, en estudios realizados con cultivos, microcosmos e in situ. Tanto la concentración natural de amonio (NH4) como la radiación solar fueron factores clave en la regulación de dichos parámetros de los AO. En condiciones ambientales de baja concentración de NH4, las AOA (cluster Nitrososophaera) dominaron la comunidad de OA, mostrando una baja actividad nitifricante. Bajo altas concentraciones de NH4, las AOB eran dominantes (clusters Nitrosospira y N. oligotropha) y mostraban una alta actividad. En cultivos monoespecíficos, el crecimiento de AOA y AOB fue inmediatamente inhibido por luz. Las AOA mostraron una mayor fotosensibilidad y una menor capacidad de recuperación que las AOB. Estos hallazgos sugerían que la luz podría ser un factor determinante en la distribución y actividad de OA en ecosistemas naturales. En concordancia, en biofilms naturales incipientes se observó mayor preferencia de las OA para colonizar las superficies orientadas hacia el sedimento que para colonizar superficies orientadas hacia la luz solar. Esta segregación espacial no se observó en biofilms maduros. Además, se observó una relación significativa entre biomasa total y abundancia de OA para los biofilms del lado luminoso pero no para los del lado oscuro. Este hecho sugiere la existencia de un efecto fotoprotector in situ (efecto “sombra”). Este efecto podría explicar porque la nitrificación medida a nivel de tramo fluvial fue independiente de la intensidad de la luz y del ciclo solar diario. Las poblaciones de OA fueron también abundantes en el sedimento. Sin embargo, la partición de la contribución de sedimento y biofilms a la nitrificación de un tramo fluvial desveló un papel proporcional preponderante de las poblaciones de OA que se desarrollan en biofilms protegidos de la luz.

[eng] The main goal of this PhD thesis was the study of the ammonium oxidation process in high nutrient loaded urban streams. We aimed to unveil regulating factors and driving mechanisms from the organisms to the ecosystem scales using a combined biogeochemistry-microbial ecology approach. Ammonia oxidization is the first and rate-limiting step of nitrification. Nitrification is the key process linking nitrogen (N) inputs (fixation, mineralization) and losses (denitrification, anamox) in the aquatic ecosystem. Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive this process through the enzyme ammonia monooxygenase. Although sharing a common function, AOB and AOA are phylogenetically distinct, suggesting different evolution and phenotypic characteristics. AOA and AOB were detected in the stream biofilms. The abundance, community composition and distribution of these microbial components were driven by environmental physical and chemical conditions, mainly ammonia (NH4) concentrations and sun irradiance. Ammonia oxidizing activity in biofilms under low NH4 availability was low and only 2 % of the inorganic NH4 was nitrified. Under these conditions AOA dominated ammonia oxidizing community and were key players of the observed ammonia oxidation (Nitrososophaera cluster). Conversely, under high NH4 load in the stream up to 100 % of the inorganic NH4 was oxidized to nitrate (NO3). Such high ammonia oxidizing activity was mostly driven by AOB (Nitrosospira and N. oligotropha clusters). Under these conditions AOB outnumbered AOA by orders of magnitude. AOA in contrast were poorly active under high NH4 concentrations and a consistent community composition shift was observed between high and low NH4 conditions. In laboratory cultures the growth of AOA and AOB was immediately inhibited by light. In particular, at lower light intensities, archaeal growth was much more photosensitive than bacterial growth and unlike AOB, AOA showed no evidence of recovery during dark phases. These findings provide evidence for niche differentiation in aquatic environments and suggested light as a main driving factor for the distribution and activity of ammonia oxidizers in the aquatic environment. Accordingly, in early stage biofilms developing on streams cobbles the percentage of ammonia oxidizers was higher in darkness (i.e., sediment facing side or dark-side biofilms) than in biofilms grown on the upper, light exposed side of the cobbles (light-side biofilm). However, this spatial segregation was missed in mature biofilms suggesting that the complex microbial structure present in light-side biofilms may protect both AOA and AOB against photoinhibition. This finding was further confirmed by a significant relationship found between light-side biofilm biomass and the abundance of ammonia oxidizers in situ. In contrast, for dark-side biofilms the relationship was missed. Therefore, irradiance was not an inhibitory factor for AOA and AOB in mature light-side biofilms probably due to an “umbrella effect”. The umbrella effect and the fact that AOA and AOB were highly abundant in the sediment (light avoiding strategy) are probably the reasons why nitrification at the ecosystem scale was independent from both light intensity and dial light cycling. Altogether these results highly contributed to improve the current knowledge on nitrification in urban streams and provided insights on niche differentiation between AOA and AOB.