Sustainable Habitat Restoration: Fish, Farms, and Ecosystem Services

Biomass burning impacts biogeochemical cycling, vegetation dynamics and climate. However, interactions between fire, climate and vegetation are not well understood and therefore studies have attempted to reconstruct fire and vegetation history under different climatic conditions using sedimentary archives. Here we focus on levoglucosan, a thermal by-product of cellulose generated during biomass burning, and, therefore, a potential fire biomarker in the marine sedimentary archive. However, before levoglucosan can be applied as a biomass burning proxy in marine sediments, there is a need for studies on how levoglucosan is transported to the marine environment, how it is reflecting biomass burning on continents, as well as the fate of levoglucosan in the marine water column and during deposition in marine sediments. Here we present analyses of levoglucosan, using an improved Ultra High Pressure Liquid Chromatography-Electro Spray Ionization/High Resolution Mass Spectrometry (UHPLC-ESI/HRMS) method, in atmospheric particles, in particulate matter settling through the water column and in marine surface sediments on a longitudinal transect crossing the tropical North Atlantic Ocean at 12°N. Levoglucosan was detected in the atmosphere, although in low concentration, possibly due to the sampled particle size, the source area of the aerosols, or the short time interval of sampling by which large burning events may have been missed. In sinking particles in the tropical North Atlantic Ocean we find that levoglucosan deposition is influenced by a mineral ballast effect associated with marine biogenic particles, and that levoglucosan is not transported in association with mineral dust particles. Highest levoglucosan concentrations and seasonal differences in sinking particles were found close to continents and low concentrations and seasonal differences were found in the open ocean. Close to Africa, levoglucosan concentration is higher during winter, reflecting seasonal burning in northwestern Africa. However, close to South America levoglucosan concentrations appear to be affected by riverine transport from the Amazon River. In surface sediments close to South America, levoglucosan concentration is higher than in the middle of the Atlantic Ocean, implying that here the influence from the South American continent is important and perennial. Our study provides evidence that degradation of levoglucosan during settling in the marine water column is not substantial, but is substantial at the sediment–water interface. Nevertheless, levoglucosan was detected in all surface sediments throughout the tropical North Atlantic, indicating its presence in the marine sedimentary record, which reveals the potential for levoglucosan as a biomass burning proxy in marine sediments

Occurrence and distribution of ladderane oxidation products in different oceanic regimes

Ladderane fatty acids are commonly used as biomarkers for bacteria involved in anaerobic ammonium oxidation (anammox). These lipids have been experimentally shown to undergo aerobic microbial degradation to form short chain ladderane fatty acids. However, nothing is known of the production or the distribution of these oxic biodegradation products in the natural environment. In this study, we analysed marine water column particulate matter and sediment from three different oceanic regimes for the presence of ladderane oxidation products (C-14 ladderane fatty acids) and of original ladderane fatty acids (C-18 and C-20 ladderane fatty acids). We found that ladderane oxidation products, i.e. C-14 ladderane fatty acids, are already produced within the water column of the Arabian Sea oxygen minimum zone (OMZ) and thus only low amounts of oxygen (< 3 mu M) are needed for the beta-oxidation of original ladderane fatty acids to proceed. However, no short chain ladderane fatty acids were detected in the Cariaco Basin water column, where oxygen concentrations were below detection limit, suggesting that the beta-oxidation pathway is inhibited by the absence of molecular oxygen, or that the microbes performing the degradation are not proliferating under these conditions. Comparison of distributions of ladderane fatty acids indicates that short chain ladderane fatty acids are mostly produced in the water column and at the sediment surface, before being preserved deeper in the sediments. Short chain ladderane fatty acids were abundant in Arabian Sea and Peru Margin sediments (ODP Leg 201), often in higher concentrations than the original ladderane fatty acids. In a sediment core taken from within the Arabian Sea OMZ, short chain ladderanes made up more than 90% of the total ladderanes at depths greater than 5 cm below sea floor. We also found short chain ladderanes in higher concentrations in hydrolysed sediment residues compared to those freely occurring in lipid extracts, suggesting that they had become bound to the sediment matrix. Furthermore, these matrix-bound short chain ladderanes were found at greater sediment depths than short chain ladderanes in the lipid extract, suggesting that binding to the sediment matrix aids the preservation of these lipids. Though sedimentary degradation of short chain ladderane fatty acids did occur, it appeared to be at a slower rate than that of the original ladderane fatty acids, and short chain ladderane fatty acids were found in sediments from the Late Pleistocene (similar to 100 kyr). Together these results suggest that the oxic degradation products of ladderane fatty acids may be suitable biomarkers for past anammox activity in OMZs

Temperature and pH control on lipid composition of silica sinters from diverse hot springs in the Taupo Volcanic Zone, New Zealand

Microbial adaptations to environmental extremes, including high temperature and low pH conditions typical of geothermal settings, are of interest in astrobiology and origin of life investigations. The lipid biomarkers preserved in silica deposits associated with six geothermal areas in the Taupo Volcanic Zone were investigated and variations in lipid composition as a function of temperature and pH were assessed. Lipid analyses reveal highly variable abundances and distributions, reflecting community composition as well as adaptations to extremes of pH and temperature. Biomarker profiles reveal three distinct microbial assemblages across the sites: the first in Champagne Pool and Loop Road, the second in Orakei Korako, Opaheke and Ngatamariki, and the third in Rotokawa. Similar lipid distributions are observed in sinters from physicochemically similar springs. Furthermore, correlation between lipid distributions and geothermal conditions is observed. The ratio of archaeol to bacterial diether abundance, bacterial diether average chain length, degree of GDGT cyclisation and C31 and C32 hopanoic acid indices typically increase with temperature. At lower pH, the ratio of archaeol to bacterial diethers, degree of GDGT cyclisation and C31 and C32 hopanoic acid indices are typically higher. No trends in fatty acid distributions with temperature or pH are evident, likely reflecting overprinting due to population influences

Are Marine Group II Euryarchaeota significant contributors to tetraether lipids in the ocean?

The first line of evidence is the presence of GDGTs, including crenarchaeol, in suspended particulate matter (SPM) at 83 m, the archaeal community of which is nearly exclusively composed of MG-II (>94% of archaeal reads) (table 1 in ref. 1) as determined by pyrosequencing. However, according to Lincoln et al.’s definition, all SPM samples <100 m do not contain sufficient archaeal reads (i.e., <1,000) (figure S6 and table S2 in ref. 1) to draw any conclusion. This low abundance of archaeal DNA is also evident from the absence of detectable MG-I 16S rRNA gene copies (figure 2 in ref. 1). It is, however, not surprising that GDGTs were detected in the 83-m SPM sample because the lipid tracers used are core lipids. Core lipids do not occur as such in living cells, where they contain polar sugar and phospho head groups (e.g., ref. 2). Thus, by definition core lipid GDGTs are derived from dead material. The second line of evidence is based upon relating the presence of monohexose GDGTs in two SPM samples (although not the crucial 83-m sample) with archaeal diversity data. Although this approach uses intact polar lipids, it has been shown that monohexose GDGTs are also poor tracers of living archaeal cells (3) because they have a turnover time in the order of thousands of years (4), de facto also representing dead material.This dominance of dead lipid material readily explains the absence of any correlation of total MG-I+MG-II DNA abundance with total GDGT abundance (r2 = 0.06 and 0.04 for 0.3- to 3-µm and 3- to 57-µm fractions, respectively). Furthermore, it explains the much higher abundance of GDGTs in the large particle fraction compared to the small fraction (16–490 vs. 1–20 pg/L), contrasting its lower total archaeal abundance (0.3–1.8 × 105 vs. 1–7 × 105 cells/L) (figure 2 in ref. 1). We conclude that both lines of evidence are based on a comparison of minute amounts of archaeal DNA (often below detection limit) with unsuitable lipid tracers.The dominance of dead material and low abundance of archaeal cells make it impossible to infer the lipid composition of uncultivated MG-II from these samples, let alone to extrapolate this to the global ocean. In contrast, other studies, using abundant archaeal DNA and more suitable phospholipid GDGTs, do show a good match between MG-I DNA abundance and crenarchaeol concentration and not with MG-II (3, 5). Nevertheless, members of the Marine Group III Euryarchaeota have been suggested to contribute to GDGTs 0–3 (3); thus, members of the MG-II may potentially contribute to this pool of GDGTs as well. However, based on the data and arguments of Lincoln et al. (1) this is impossible to infer. The jury is, therefore, still out

Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea)

Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria

Spatial distribution of intact polar lipids in North Sea surface waters: Relationship with environmental conditions and microbial community composition

We characterized and quantified the intact polar lipid (IPL) composition of the surface waters of the North Sea and investigated its relationships with environmental conditions, microbial abundances, and community composition. The total IPL pool comprised at least 600 different IPL species in seven main classes: the glycerophospholipids phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE); the sulfur-bearing glycerolipid sulfoquinovosyldiacylglycerol (SQDG); and the nitrogen-bearing betaine lipids diacylglyceryl-trimethylhomoserine (DGTS), diacylglyceryl-hydroxymethyltrimethylalanine (DGTA), and diacylglyceryl-carboxy-hydroxymethylcholine (DGCC). Although no significant relationships were found between the IPL composition and environmental parameters, such as nutrient concentrations, distance-based ordination yielded distinct clusters of IPL species, which could in turn be tentatively correlated with the predominant microbial groups. SQDGs and PGs, as well as PC species containing saturated fatty acid moieties, were related to picoeukaryote abundances and PC species with polyunsaturated fatty acid (PUFA) moieties to nanoeukaryote abundances. The PEs were likely of mixed cyanobacterial-bacterial origin, whereas DGTA and DGCC species were mainly associated with cyanobacteria. DGTSs were likely derived from either pico-or nanoeukaryotes, although the DGTS species with PUFAs also showed some relationship with cyanobacterial abundances. Concentrations of the algal-derived IPLs showed strong positive correlations with chlorophyll a concentrations, indicating they may be used as biomarkers for living photosynthetic microbes. However, direct relationships between the IPLs and microbial groups were relatively weak, implying that the predominant IPLs in marine surface waters are not derived from single microbial groups and that direct inferences of microbial community compositions from IPL compositions should be considered with care

In situ produced branched glycerol dialkyl glycerol tetraethers in suspended particulate matter from the Yenisei River, Eastern Siberia

Soil-derived branched glycerol dialkyl glycerol tetraethers (brGDGTs) in marine river fan sediments have a potential use for determining changes in the mean annual temperature (MAT) and pH of the river watershed soils. Prior to their incorporation in marine sediments, the compounds are transported to the marine system by rivers. However, emerging evidence suggests that the brGDGTs in freshwater systems can be derived from both soil run-off and in situ production. The production of brGDGTs in the river system can complicate the interpretation of the brGDGT signal delivered to the marine system. Therefore, we studied the distribution of brGDGT lipids in suspended particulate matter (SPM) of the Yenisei River. Chromatographic improvements allowed quantification of the recently described hexamethylated brGDGT isomer, characterized by having two methyl groups at the 6/6 ' instead of the 5/5 ' positions, in an environmental dataset for the first time. This novel compound was the most abundant brGDGT in SPM from the Yenisei. Its fractional abundance correlated well with that of the 6-methyl isomer of the hexamethylated brGDGT that contains one cyclopentane moiety. The Yenisei River watershed is characterized by large differences in MAT (>11 degrees C) as it spans a large latitudinal range (46-73 degrees N), which would be expected to be reflected in brGDGT distributions of its soils. However, the brGDGT distributions in its SPM show little variation. Furthermore, the reconstructed pH values are high compared to the watershed soil pH. We, therefore, hypothesize that the brGDGTs in the Yenisei River SPM are predominantly produced in situ and not primarily derived from erosion of soil. This accounts for the absence of a change in the temperature signal, as the river water temperature is more stable. Using a lake calibration, the reconstructed temperature values agree with the mean summer temperatures (MST) recorded. The brGDGTs delivered to the sea by the Yenisei River during this season are thus not soil-derived, possibly complicating the use of brGDGTs in marine sediments for palaeoclimate reconstructions

Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in <i>Sphagnum</i>-Dominated Northern Wetlands

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses.Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine(TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomyceteisolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) andmolecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) inorder to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout theprofiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundanceof planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliatedwith the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group.Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoyepeat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mossepeat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundantTMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest thatplanctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and thechange in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redoxconditions at the oxic/anoxic interface

Engineering quantum dots for electrical control of the fine structure splitting

We have studied the variation in fine-structure splitting (FSS) under application of vertical electric field in a range of quantum dots grown by different methods. In each sample we confirm that this energy splitting changes linearly over the field range we can access. We conclude that this linear tuning is a general feature of self-assembled quantum dots, observed under different growth conditions, emission wavelengths and in different material systems. Statistical measurements of characteristic parameters such as emission energy, Stark shift and FSS tuning are presented which may provide a guide for future attempts to increase the yield of quantum dots that can be tuned to a minimal value of FSS with vertical electric field

Drastic changes in the distribution of branched tetraether lipids in suspended matter and sediments from the Yenisei River and Kara Sea (Siberia): Implications for the use of brGDGT-based proxies in coastal marine sediment

The distribution of branched glycerol dialkyl glycerol tetraethers (brGDGTs) in soils has been shown to correlate with pH and mean annual air temperature. Because of this dependence brGDGTs have found an application as palaeoclimate proxies in coastal marine sediments, based on the assumption that their distribution is not altered during the transport from soils to marine systems by rivers. To study the processes acting on the brGDGT distributions, we analysed the full suite of brGDGTs, including the recently described 6-Me brGDGTs, in both the suspended particulate matter (SPM) of the Siberian Yenisei River and the SPM and sediments of its outflow in the Kara Sea. The brGDGT distribution in the SPM of the Yenisei River was fairly constant and characterized by high abundances of the 6-Me brGDGTs, reflecting their production at the neutral pH of the river water. However, the brGDGT distribution showed marked shifts in the marine system. Firstly, in the Yenisei River Mouth, the fractional abundance of the 6-Me brGDGTs decreases sharply. The brGDGT signature in the Yenisei River Mouth possibly reflects brGDGTs delivered during the spring floods that may carry a different distribution. Also, coastal cliffs were shown to contain brGDGTs and to influence especially those sites without major river inputs (e.g. Khalmyer Bay). Further removed from the river mouth, in-situ production of brGDGTs in the marine system influences the distribution. However, also the fractional abundance of the tetramethylated brGDGT Ia increases, resulting in a distribution that is distinct from in-situ produced signals at similar latitudes (Svalbard). We suggest that this shift may be caused by preferential degradation of labile (riverine in-situ produced) brGDGTs and the subsequent enrichment in less labile (soil) material. The offshore distribution indeed agrees with the brGDGT distribution encountered in a lowland peat. This implies that the offshore Kara Sea sediments possibly carry a soil-dominated signal, indicating potential for palaeoclimate reconstructions at this site.Both in the river system and coastal cliffs, brGDGTs were much more abundant than crenarchaeol, an archaeal isoprenoid GDGT, resulting in high (>0.93) Branched and Isoprenoid Tetraether (BIT) index values. Moving downstream in the marine sediments, a decrease in brGDGT concentrations, coeval with an increase in crenarchaeol, resulted in decreasing BIT index values. This decrease correlates with changes in bulk proxies for terrigenous input (d13Corg, C/N), confirming the use of the BIT index to trace the delivery of river-transported and coastal cliff-derived terrigenous organic matter