Functionally distinct communities of ammonia‐oxidizing bacteria along an estuarine salinity gradient

Bernhard, Anne E.; Tucker, Jane; Giblin, Anne E.; Stahl, David A.

doi:10.1111/j.1462-2920.2007.01260.x

Cited by 144 publications

(131 citation statements)

References 57 publications

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“…Composition was highly variable over seasons and years, and compositional changes in response to the nutrient treatments were minor in comparison. High temporal variability in AOB communities (both abundance and composition) has been observed in both soils and the water column (Gray et al, 2003;O'Mullan and Ward, 2005) and in estuarine sediments (Bernhard et al, 2007;Ando et al, 2009;Fortunato et al, 2009). Given the importance of temperature on the spatial variability of AOB in soils (Fierer et al, 2009), we speculate that temperature could be one important factor contributing to this temporal variability.…”

Section: Temporal Variability and Nutrient Responsesmentioning

confidence: 88%

“…In general, microbial community-process relationships likely depend on environmental conditions. For instance, in estuarine sediments, Bernhard et al (2007) found that the strength of the correlation between AOB abundance and potential nitrification rates varies along a salinity gradient. Finally, AOB composition was highly variable within and across years, even in untreated plots.…”

Section: Discussionmentioning

confidence: 99%

“…Depending on the environmental conditions, nitrification can positively or negatively affect nitrogen retention in ecosystems (Kowalchuk et al, 2000;Templer et al, 2008;von Schiller et al, 2009). At the same time, the composition of nitrifying microorganisms can influence nitrification rates (Bottomley et al, 2004;Balser and Firestone, 2005;Bernhard et al, 2007). Therefore, knowledge about the interplay between nitrifiers and their environment is key to understanding the nitrification process.…”

Section: Introductionmentioning

confidence: 99%

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Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

et al. 2010

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Ammonia oxidation is a central process in the nitrogen cycle. Particularly in marine and estuarine environments, few experiments have been conducted to tease apart the factors influencing their abundance and composition. To investigate the effect of nitrogen and phosphorus availability on ammonia-oxidizing bacteria (AOB), we conducted a nutrient enrichment experiment in a Maine salt marsh and sampled sediment communities in three seasons over 2 years. We assessed community composition using terminal restriction fragment length polymorphism analysis and sequencing of cloned fragments of the ammonia monooxygenase (amoA) gene. Almost all of the amoA sequences fell within the marine and estuarine-specific Nitrosospira-like clade. Applied separately, nitrogen and phosphorus significantly altered AOB composition; however, together the nutrients had an interactive effect, and composition did not change. In contrast, nutrient enrichment did not alter AOB abundance. Furthermore, the response of AOB composition to nutrient enrichment varied over time. We conclude that closely related taxa within the marine/estuarine-specific Nitrosospira-like clade vary in their preference for nutrient concentrations, and this preference may depend on other temporally variable abiotic factors. Finally, AOB composition was highly variable within and across years even in untreated plots. Further studies are needed to test how these different aspects of compositional variability in AOB communities influence nitrogen cycling.

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Section: Temporal Variability and Nutrient Responsesmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

et al. 2010

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“…These counter results indicate that although the surrounding waters had permeated through the cages, sediment processes internal to the cages directly influenced ammonium concentrations. Microorganisms drive most processes in the nitrogen cycle, and previous studies provide evidence that their particular composition influences these processes rates (Cavigelli andRobertson, 2000, Avrahami et al, 2002;Balser and Firestone, 2005;Bernhard et al, 2007a). A related result is that sediment origin (either directly or interactively with environment) affected nitrification and methane flux, but not CO 2 production.…”

Section: Discussionmentioning

confidence: 99%

Microbial composition affects the functioning of estuarine sediments

2012

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Although microorganisms largely drive many ecosystem processes, the relationship between microbial composition and their functioning remains unclear. To tease apart the effects of composition and the environment directly, microbial composition must be manipulated and maintained, ideally in a natural ecosystem. In this study, we aimed to test whether variability in microbial composition affects functional processes in a field setting, by reciprocally transplanting riverbed sediments between low-and high-salinity locations along the Nonesuch River (Maine, USA). We placed the sediments into microbial 'cages' to prevent the migration of microorganisms, while allowing the sediments to experience the abiotic conditions of the surroundings. We performed two experiments, short-(1 week) and long-term (7 weeks) reciprocal transplants, after which we assayed a variety of functional processes in the cages. In both experiments, we examined the composition of bacteria generally (targeting the 16S rDNA gene) and sulfate-reducing bacteria (SRB) specifically (targeting the dsrAB gene) using terminal restriction fragment length polymorphism (T-RFLP). In the short-term experiment, sediment processes (CO 2 production, CH 4 flux, nitrification and enzyme activities) depended on both the sediment's origin (reflecting differences in microbial composition between salt and freshwater sediments) and the surrounding environment. In the long-term experiment, general bacterial composition (but not SRB composition) shifted in response to their new environment, and this composition was significantly correlated with sediment functioning. Further, sediment origin had a diminished effect, relative to the short-term experiment, on sediment processes. Overall, this study provides direct evidence that microbial composition directly affects functional processes in these sediments.

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“…Most of what is known about how biodiversity varies along environmental gradients stems from research on plants and animals, although recent studies suggest that microorganisms may exhibit similar gradient patterns. Within the bacteria, for instance, diversity and composition appear to vary along gradients of primary productivity (Horner-Devine et al, 2003), latitude (Blum et al, 2004;Yergeau et al, 2007), disturbance (Johnsen et al, 2001;Muller et al, 2001), climate (Yergeau et al, 2007) and salinity (Blum et al, 2004;Crump et al, 2004;Bernhard et al, 2005Bernhard et al, , 2007. However, even less is known about the variation of fungal diversity and composition along similar gradients.…”

Section: Introductionmentioning

confidence: 99%

Patterns of fungal diversity and composition along a salinity gradient

2010

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Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes-a salt, brackish and freshwater marsh-in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution.

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Functionally distinct communities of ammonia‐oxidizing bacteria along an estuarine salinity gradient

Cited by 144 publications

References 57 publications

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

Microbial composition affects the functioning of estuarine sediments

Patterns of fungal diversity and composition along a salinity gradient

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