Elsevier

Geochimica et Cosmochimica Acta

Volume 83, 15 April 2012, Pages 217-233
Geochimica et Cosmochimica Acta

Fate of microbial nitrogen, carbon, hydrolysable amino acids, monosaccharides, and fatty acids in sediment

https://doi.org/10.1016/j.gca.2011.12.016Get rights and content

Abstract

The fate of microbial carbon, nitrogen, hydrolysable amino acids (HAAs), monosaccharides, and fatty acids in sediment was investigated experimentally. The microbial community of a tidal flat sediment was labeled with 13C-enriched glucose and 15N-enriched ammonium, and sediment was incubated for up to 371 days. Analysis of total concentrations and 13C- and 15N content of bulk sediment, hydrolysable amino acids (including d-alanine), monosaccharides, total fatty acids (TFAs), and phospholipid-derived fatty acids (PLFAs) allowed us to trace the fate of microbial biomass and -detritus and the major biochemical groups therein (proteins, carbohydrates, and lipids) over intermediate time scales (weeks–months). Moreover, the unidentified fraction of the labeled material (i.e. not analyzed as HAA, FA, or carbohydrate) provided information on the formation and fate of molecularly uncharacterizable organic matter. Loss of 13C and 15N from the sediment was slow (half live of 433 days) which may have been due to the permanently anoxic conditions in the experiment. Loss rates for the different biochemical groups were also low with the following order of loss rate constants: PLFA > TFA > HAA > monosaccharides. The unidentified 13C-pool was rapidly formed (within days) and then decreased relatively slowly, resulting in a gradual relative accumulation of this pool over time. Degradation and microbial reworking of the labeled material resulted in subtle, yet consistent, diagenetic changes within the different biochemical groups. In the HAA pool, glycine, lysine, and proline were lost relatively slowly (i.e. best preserved) while there was no accumulation of d-alanine relative to l-alanine, indicating no relative accumulation of bacterial macromolecules rich in d-alanine. In the fatty acid pool, there was very little difference between PLFAs and TFAs, indicating a very similar lability of these pools. Differences between individual fatty acids included a relatively slow loss of i15:0, ai15:0 and 18:1ω7c which likely resulted from production of these bacterial fatty acids during bacterial reworking of the organic matter. Differences between loss rate constants for individual monosaccharides were not significant. An exception was ribose that was produced and lost relatively rapidly, which may be related to ribose being an important component of RNA. Losses of bulk 13C and 15N were closely coupled despite partly being present in different biochemicals and partly being derived from different microbial sources, indicating no selective preservation of either C or N during organic matter diagenesis.

Introduction

Microorganisms are the primary mediators of biogeochemical processes in sediments, including the processing of organic matter (degradation, remineralization, and reassimilation). Even though microbial biomass is only a small fraction of total organic matter in sediments, the continuous processing of organic matter by benthic microbes combined with turnover of microbial biomass results in a continuous flux of microbial detritus into the sediment organic matter pool. In this way, microbial reworking of organic matter can result in a substantial microbial contribution to the total organic matter pool and may also alter its composition and thereby change its long-term fate (Keil and Fogel, 2001, Burdige, 2007, Kaiser and Benner, 2008). Despite this strong potential impact on the quality and quantity of the sediment organic matter pool, microbial reworking and secondary production has been underappreciated in geochemical studies (Zonneveld et al., 2010). The short term fate of benthic bacterial biomass, in particular grazing by benthic fauna, has been investigated in a number of studies (e.g. Van Oevelen et al., 2006, Pascal et al., 2009) while the fate of bacterial biomass and detritus in natural sediments over longer time scales has remained largely unstudied.

The major biochemical components of microbial biomass and sediment detritus are proteins, carbohydrates, and lipids. Proteins are structural components consisting of amino acids. Hydrolysable amino acids (HAAs) are a major fraction of total proteinaceous material and account for 50–80% of total nitrogen in microbial biomass (Cowie and Hedges, 1992) and 10–20% of total organic matter in marine sediments (Burdige, 2007). The relative composition of the HAA pool can provide a good indication of the degradation state of organic matter (e.g. Dauwe and Middelburg, 1998, Keil et al., 2000 and references therein). A particularly interesting group of HAAs are the d-enantiomers, which are considered to be specific for bacterial macromolecules (Madigan et al., 2000, Kaiser and Benner, 2008).

Carbohydrates consist of monosaccharides and can serve both structural (e.g. cellulose) and energy storage functions (e.g. amylose). Total carbohydrates make up 20–40% of fresh marine organic matter and account for 5–20% of the sediment organic matter pool and sediment carbon remineralization (Burdige, 2006). The relative composition of the total carbohydrate pool can provide information about sources of organic matter in sediments (e.g. Cowie and Hedges, 1984) and can also show diagenetic changes (Jensen et al., 2005, Burdige, 2006). Carbohydrate diagenesis has not been investigated as extensively as that of amino acids. The recent introduction of a method for analysis of the 13C content of individual monosaccharides by HPLC-IRMS provides a powerful new tool for investigation of carbohydrates in stable isotope (13C) tracer studies (Boschker et al., 2008).

Lipids are complex structures with both structural functions and a role as energy source. Lipids make up 5–30% of fresh marine organic matter and <1% to 8% of the sediment organic matter pool (Burdige, 2007). Fatty acids are a major component of lipids and can be divided into various sub-fractions including phospholipid-derived fatty acids (PLFAs). PLFAs are derived from cell membranes and are amongst the most labile compounds in microbial biomass.

Proteins, carbohydrates, and lipids together with some minor biochemicals like amino sugars and nucleic acids, make up the identifiable fraction of microbial biomass and sediment organic matter. This identifiable fraction typically makes up 30–40% of total organic matter in surficial marine sediments, meaning that 60–70% is not identifiable with conventional analytical techniques (Hedges et al., 2000, Burdige, 2007). This so-called molecularly uncharacterized organic matter consists of compounds that are resistant to common extraction and separation techniques (Burdige, 2007). The formation, composition, and fate of molecularly uncharacterized organic matter is an intensively studied, but poorly understood, topic in sediment biogeochemistry.

The fate of microbial biomass and detritus and the associated changes in biochemical composition have been studied in two different ways that reflect distinctly different time scales. One approach involves analysis of the biochemical composition of fresh organic matter, usually algal-derived, as it gets degraded in laboratory experiments or in the field using a (stable) isotope tracer approach (Harvey et al., 1995, Sun et al., 2002, Oakes et al., 2010). These studies generally involve time scales of hours to weeks and results therefore reflect the earliest stages of organic matter degradation. The other approach involves investigation of the biochemical composition of organic matter along a given diagenetic gradient in the field (for example a sediment depth profile). This provides information about the alteration of organic matter, including microbial reworking, on the long term (months to geological time scales) (e.g. Wakeham et al., 1997a, Dauwe and Middelburg, 1998, Keil and Fogel, 2001). For both these approaches, studies usually focus on a specific biochemical group. Only a few studies have simultaneously investigated the fate of different biochemical groups from a given source in sediments (e.g. Henrichs and Doyle, 1986, Harvey et al., 1995), sinking particles (Wakeham et al., 2009) and soil (Kindler et al., 2009, Miltner et al., 2009). Moreover, most studies focus on the fate of algal biomass (primary producers) while the fate of organic matter derived from secondary producers, and thereby their potential effect on organic matter degradation in general, has been investigated only scarcely.

In the current study we investigate the fate of 13C- and 15N-labeled microbial biomass and detritus in sediment over a 1-year period. Alongside 13C and 15N, we also traced the specific fate of 13C and 15N in HAAs and 13C in monosaccharides, total fatty acids, and PLFAs, as well as concentrations of these different compounds. Sediment was homogenized, sieved, and incubated in vitro in order to exclude macrobiological loss processes (e.g. bioturbation, grazing) and physical loss processes (e.g. resuspension by currents and waves) typically encountered in the field. This unique approach allowed us to investigate the longer-term fate of C and N as well as proteins, carbohydrates, and lipids from a defined pool of microbial biomass in natural sediment. This study aims to bridge the gap between short-term experimental studies on degradation of defined pools of organic matter and observational studies assessing the net results of diagenesis on natural organic matter over long time scales.

Section snippets

Sediment collection and incubation

Sediment was collected from a tidal flat (Paulinapolder) in the mid region of the turbid, nutrient-rich, and heterotrophic Scheldt Estuary (The Netherlands). The sampling site is characteristic of tidal flats in this part of the estuary. Sediment at the sampling site was characterized as muddy with a silt content of 42% and a median grain size of 72 μm. On 14 June, 2006, 20 small sediment cores (2.5 cm i.d., 10 cm deep) were collected from the tidal flat at low tide. Sediment from the cores was

Results

Results comprise two distinct periods (Fig. 1). The period between day 1 and day 69 will hereafter be referred to as the ‘labeling phase’ while the period between day 69 and day 371 will be referred to as the ‘loss phase’. These two phases will be presented and discussed separately with the main focus on the loss phase as this was the most relevant phase with respect to the objectives of this study. The causes for the occurrence of these two phases and rationale for presenting the two phases

Methodological aspects and general setting

The chosen setup of glass bottles closed with a silicone liner proved to be easy and effective. The silicone liner prevented loss of water from the bottles while allowing gas exchange between the headspace in the bottles and the surrounding air. This means that the overlying water could remain oxygenated, which was confirmed by a 61% O2 saturation in the overlying water measured after two months of incubation. However, despite the overlying water being oxygenated, conditions in the 25–30 mm

Acknowledgments

We thank Pieter van Rijswijk, Marco Houtekamer, Peter van Breugel, Jan Peene and Lennart van IJzerloo for their help with field- and lab work, and three anonymous reviewers and associate editor David Burdige for their thorough evaluation of the paper. B.V. was financially supported by the Netherlands Organization for Scientific Research (Pionier 833.02.2002) and the Darwin Center for Biogeology (project 142.16.1052). D.v.O. was supported by the HERMIONE project (Grant Agreement No. 226354)

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