Microbial composition affects the functioning of estuarine sediments

Abstract

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.

Microbial biomass in sediments affects greenhouse gas effluxes in Poyang Lake in China

“…This is consistent with other studies where microbial biomass influenced methane efflux and nitrification (Balser & Firestone 2005;Reed & Martiny 2013). These results can also be supported by Schimel (1995) as described above.…”

“…Previous studies found that fungi were involved in denitrification processes by reducing nitrate or nitrite to N 2 O in freshwater sediments (Takaya 2009;Seo & DeLaune 2010;Mouton et al 2012;Reed & Martiny 2013;S anchez-Andrea et al 2012). In particular, cell-free nitrate reductase (Nar) and nitrite reductase (Nir) activities which also included a unique cytochrome P450 acted as nitric oxide reductase played important roles in the anaerobic denitrification process of fungi (Usuda et al 1995).…”

“…Microbial biomass in soils and sediments plays a pivotal role in GHG emissions in ecosystems (Tong et al 2005;Liu et al 2009;Reed & Martiny 2013). For example, Urbanov a et al (2013) found that CH 4 efflux was positively associated with methanogenic biomass in Mountain Peatlands, Central Europe.…”

Global biogeography of microbial nitrogen-cycling traits in soil

“…Microbes catalyze most of the biological transformations of the major elements of life (7), and because of their sheer abundance they account for a large pool of elements in living matter (8). Furthermore, like plants and animals, microbial taxonomic composition varies over space (9,10), and this variation can influence ecosystem processes (11)(12)(13)(14). Thus, a consideration of microbial traits should improve efforts to connect biogeographic patterns and ecosystem processes (15).…”

“…If a gene from a pathway was detected, we assumed the presence of the entire pathway in the organism. To compare the frequencies among the N pathways, we standardized for the number of genes (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) in each pathway. Although metagenomic sequences provide a measure of a community's trait diversity (24), the presence of a trait does not indicate how it is being used in the community.…”