Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Estuarine sediments are the location for significant bacterial removal of anthropogenically derived inorganic nitrogen, in particular nitrate, from the aquatic environment. In this study, rates of benthic denitrification (DN), dissimilatory nitrate reduction to ammonium (DNRA), and anammox (AN) at three sites along a nitrate concentration gradient in the Colne estuary, United Kingdom, were determined, and the numbers of functional genes (narG, napA, nirS, and nrfA) and corresponding transcripts encoding enzymes mediating nitrate reduction were determined by reverse transcription-quantitative PCR. In situ rates of DN and DNRA decreased toward the estuary mouth, with the findings from slurry experiments suggesting that the potential for DNRA increased while the DN potential decreased as nitrate concentrations declined. AN was detected only at the estuary head, accounting for ϳ30% of N 2 formation, with 16S rRNA genes from anammox-related bacteria also detected only at this site. Numbers of narG genes declined along the estuary, while napA gene numbers were stable, suggesting that NAP-mediated nitrate reduction remained important at low nitrate concentrations. nirS gene numbers (as indicators of DN) also decreased along the estuary, whereas nrfA (an indicator for DNRA) was detected only at the two uppermost sites. Similarly, nitrate and nitrite reductase gene transcripts were detected only at the top two sites. A regression analysis of log(n ؉ 1) process rate data and log(n ؉ 1) mean gene abundances showed significant relationships between DN and nirS and between DNRA and nrfA. Although these log-log relationships indicate an underlying relationship between the genetic potential for nitrate reduction and the corresponding process activity, fine-scale environmentally induced changes in rates of nitrate reduction are likely to be controlled at cellular and protein levels.Estuaries are major conduits for the transport of anthropogenically derived nitrogen (e.g., from fertilizer runoff and from wastewater treatment plants) from land to sea (18,20). Estuarine sediments are now recognized as being an important location for the removal of inorganic nitrogen from this environment via benthic nitrate reduction to nitrogenous gases (21). Previously, we have utilized the isotope-pairing technique (22) to investigate rates of denitrification (DN) of nitrate to N 2 O and N 2 along the nitrate and salinity gradients in the hypernutrified Colne estuary, United Kingdom, and demonstrated that DN rates are highest at the estuary head, where nitrate levels are also at their highest (7, 9). However, DN represents only one of three key pathways relevant to nitrate reduction, with a recent review suggesting that the importance of DN in aquatic systems may be overstated (3). A substantial proportion of nitrate may alternatively be converted to ammonium (1, 16, 17) via dissimilatory nitrate reduction to ammonium (DNRA), in which case inorganic nitrogen is retained within the aquatic environment. Nitrite, usually derived from nitrate reduc...

The use of vanadium (III) has been proposed recently as a suitable alternative to cadmium for the reduction of NO 3 to NO 2 during spectrophotometric analysis. However, the methods proposed suffer from decreased sensitivity and additional steps for the measurements of nitrite and nitrate. We have developed an improved fast and sequential protocol that permits the determination of low concentrations of nitrite and nitrate in marine and freshwater samples using small volumes. NO 2 concentration is firstly determined using the common Griess reaction. The subsequent addition of a 2% VCl 3 solution in 6N HCl in the same sample and the reaction at 60ºC for 25 minutes results in an efficient reduction of the NO 3 to NO 2-(> 95%), which is also detected by the already added Griess reagents. The method has a detection limit <0.05 µM, a high precision (ranging from 0.2 to 11%) and accuracy (0.07 µM) for the determination of NO 3-+ NO 2 concentrations lower than 30 µM. Comparison of the proposed method with the established Cd column method using samples from a variety of environments (fresh water reservoir, sediment freeze lysable pore water, estuarine water samples and samples from an acid mine drainage impacted reservoir) showed good agreement between the two methods, with a difference between methods of 0.073 ± 0.099 µM. The analysis can be performed in large batches (~60 samples) using small sample volumes (≤1 mL) for the determination of both NO 3 and NO 2 in less than one hour.

Chemical properties of burrow wall sediment from burrows of the thalassinidean shrimp Pestarella (=Callianassa) tyrrhena located at Vravrona Bay (Aegean Sea, Greece) were studied and found to be very different from the sediment surface and ambient anoxic sediment. P. tyrrhena burrow walls had significantly higher amounts of silt and clay, while total organic carbon (TOC) was up to 6 times higher than in surrounding sediment. Chlorophyll a (chl a) accounted for a small fraction of TOC and showed similar values in burrow walls and surface sediment, whereas the low chl a: chl a + phaeopigment ratio indicated the presence of more fresh material in the latter. Biopolymers (carbohydrates, proteins and lipids) were 4 to 11 times higher in burrow walls than in the surrounding sediment, accounting for 47% of TOC. The low protein:carbohydrate ratio indicated that the high TOC in the burrow walls was caused by the presence of aged detritus of low nutritional quality, such as seagrass detritus. The distinct conditions along the burrow wall also affected the bacterial community and resulted in a 10-fold increase of bacterial abundance. Molecular fingerprints of the bacterial communities showed that the bacterial composition of the burrow wall was more similar to the ambient anoxic sediment and showed less seasonal change than the sediment surface. These results suggest that burrow walls have distinct properties and should not be considered merely as a simple extension of the sediment surface. KEY WORDS: Bioturbation · Organic matter · Seagrass detritus · Bacteria · PCR-DGGE · Pestarella tyrrhena Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 38: [181][182][183][184][185][186][187][188][189][190] 2005 ditions in the burrows (Kristensen 1988, Ziebis et al. 1996, Furukawa 2001. The availability of labile organic matter combined with steep chemical gradients and narrow redox zonation has a significant impact on the chemical and biological composition of the burrow environment. Bacterial abundances have been shown to be higher along burrow walls compared to either surface or ambient sediment (Aller & Aller 1986, Branch & Pringle 1987, Dworschak 2001. In addition, burrow walls show increased heterotrophic activity by both aerobic and anaerobic bacteria, resulting in increased rates of organic matter decomposition (Aller & Aller 1986, Reichardt 1988, Gribsholt et al. 2003.Thalassinidean ghost shrimps have been recognised in recent years as one of the most effective bioturbating groups of macrofaunal organisms, with significant impacts on the benthic environment (Griffis & Suchanek 1991, Reise 2002. Pestarella tyrrhena is an important bioturbator, commonly found in muddy and fine sandy intertidal and shallow subtidal coastal sediments, where it often creates dense monospecific populations. It is a selective deposit feeder that constructs deep and complex burrows, constantly digging new branches or filling up existing ones (Dworschak 1987). P. tyrrhena increases the organi...

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Diel primary production patterns of intertidal microphytobenthos (MPB) have been attributed to short-term physiological changes in the photosynthetic apparatus or to diel changes in the photoautotrophic biomass in the sediment photic layer due to vertical migration. Diel changes in primary production and vertical migration are entrained by external factors like photoperiod and tides. However, the role of photoperiod and tides has not been experimentally separated to date. Here, we performed laboratory experiments with sediment cores kept in immersion, in the absence of tides, with photoperiod or under continuous light. Measurements of net production, made with O2 microsensors, and of spectral reflectance at the sediment surface showed that, in intertidal sediments, the photoperiod signal was the major driver of the diel patterns of net primary production and sediment oxygen availability through the vertical migration of the MPB photoautotrophic biomass. Vertical migration was controlled by an endogenous circadian rhythm entrained by photoperiod in the absence of tides. The pattern progressively disappeared after 3 days in continuous light but was immediately reset by photoperiod. Even though a potential contribution of a subjective in situ tidal signal cannot be completely discarded, Fourier and cross spectral analysis of temporal patterns indicated that the photosynthetic circadian rhythm was mainly characterized by light/dark migratory cycles.

Intertidal areas support extensive diatom-rich biofilms. Such microphytobenthic (MPB) diatoms exude large quantities of extracellular polymeric substances (EPS) comprising polysaccharides, glycoproteins and other biopolymers, which represent a substantial carbon pool. However, degradation rates of different EPS components, and how they shape heterotrophic communities in sediments, are not well understood. An aerobic mudflat-sediment slurry experiment was performed in the dark with two different EPS carbon sources from a diatom-dominated biofilm: colloidal EPS (cEPS) and the more complex hot-bicarbonate-extracted EPS. Degradation rate constants determined over 9 days for three sediment fractions [dissolved organic carbon (DOC), total carbohydrates (TCHO), and (cEPS)] were generally higher in the colloidal-EPS slurries (0.105–0.123 d−1) compared with the hot-bicarbonate-extracted-EPS slurries (0.060–0.096 d−1). Addition of hot-bicarbonate-EPS resulted in large increases in dissolved nitrogen and phosphorous by the end of the experiment, indicating that the more complex EPS is an important source of regenerated inorganic nutrients. Microbial biomass increased ~4–6-fold over 9 days, and pyrosequencing of bacterial 16S rRNA genes revealed that the addition of both types of EPS greatly altered the bacterial community composition (from 0 to 9 days) compared to a control with no added EPS. Bacteroidetes (especially Tenacibaculum) and Verrucomicrobia increased significantly in relative abundance in both the hot-bicarbonate-EPS and colloidal-EPS treatments. These differential effects of EPS fractions on carbon-loss rates, nutrient regeneration and microbial community assembly improve our understanding of coastal-sediment carbon cycling and demonstrate the importance of diverse microbiota in processing this abundant pool of organic carbon.

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