Anoxygenic phototrophic bacteria (green and purple sulfur bacteria) thrive in anoxic environments where light penetrates a sulfide-containing (euxinic) water column. Genomic data and photosynthetic bacterial carotenoid pigments should provide complementary information on the spatio-temporal dynamics of anoxygenic phototrophs in modern euxinic environments. In turn, these contemporary depositional settings often serve as analogues for ancient counterparts. However, in some modern environments, DNA-informed patterns of phototrophic sulfur bacteria occurrence do not match distributions of their carotenoid inventories. One possible explanation for these seemingly incompatible observations is that the rapid sulfurization of carotenoids and incorporation into macromolecules via multiple carbon-sulfur bonds prevents or confounds their detection by conventional means. Here, to evaluate this conundrum, we revisit some representative contemporary euxinic environments where anoxygenic phototrophic bacteria have mostly been detected based on genomic analyses. Although free intact carotenoids are sporadically detected in surface sediments, their distributions do not reveal a complete picture. Exogenously sourced fossil carotenoids (e.g., paleorenieratane) is an additional complication. Carotenoid inventories obtained by desulfurization with Raney nickel, on the other hand, stand in stark contrast to those present as free lipids. In particular, sulfur-linked carotenoids present in euxinic lake sediments provide a more complete picture of compositions of anoxygenic sulfur bacterial communities and account for discrepancies reported in previous studies. We observe a closer alignment between genomic data and patterns of sulfurized carotenoids and, importantly, our results highlight how sulfurization serves as a pathway for the rapid modification of highly functionalised lipids and their sequestration into the macromolecular component of sediment extracts.

Redox gradients in oceanic oxygen minimum zones are hotspots of diverse bacterial populations and metabo-lisms. Here, we test whether bacteriohopanepolyols (BHPs), a suite of membrane-regulating pentacyclic tri-terpenoid lipids, are suitable tracers of major bacterial metabolisms and whether their structural diversity (BHP lipidomics) allows tracing the bacterial ecology across the Black Sea chemocline. We analyzed suspended par-ticulate matter (SPM) sampled along depth-profiles across the redox/chemocline at two sites in the eastern and western gyres and underlying core-top sediments at the western gyre site. Our results show that BHPs abun-dances reflect the stratification of the Black Sea and capture ecological niches across the chemocline, being highest in the lower suboxic zone and in upper to deep sulfidic waters. BHP-inferred bacterial metabolisms in the lower suboxic zone are dominated by anammox and aerobic methane oxidizers (primarily by Type I/gammap-roteobacteria). Bacterial biomass production in the upper to deep sulfidic zone is mirrored by a range of BHPs that are normally associated with aerobic metabolisms, most likely explained by either survival in oxygenated micro-niches or production by anaerobic bacteria (which could possibly include sulfate reducers and nitrite -dependent methane oxidizers). Most surprisingly, this ecological niche harbors seemingly unknown anaerobic bacteria which produce abundant C-2 and C-3 methylated BHPs. Core-top sediments reflect the BHP structural diversity found in SPM, but with notable compositional differences. Most strikingly, the export dynamics seem to result in near-absence of C-2 methylated BHPs in surface sediments. Sedimentary BHP distributions therefore underestimate the importance of C-2 methylated BHPs in the water column, which has implications for the geological record.

[1] Abstract: Measurements of the U K 0 37 index and the absolute abundance of alkenones in marine sediments are increasingly used in paleoceanographic research as proxies of past sea surface temperature and haptophyte (mainly coccolith-bearing species) primary productivity, respectively. An important aspect of these studies is to be able to compare reliably data obtained by different laboratories from a wide variety of locations. Hence the intercomparability of data produced by the research community is essential. Here we report results from an anonymous interlaboratory comparison study involving 24 of the leading laboratories that carry out alkenone measurements worldwide. The majority of laboratories produce data that are intercomparable within the considered confidence limits. For the

Comparison of Type II photosensitized oxidation of lipids (the photodynamic effect) and photodegradation of chlorophyll (sensitizer photobleaching) in samples of particulate matter collected previously from locations representing a diverse range of latitudes reveals an enhancement of the photooxidation of lipids at the expense of chlorophyll photodegradation in the polar regions. The efficiency of the photodynamic effect appears to be particularly high in sinking particles collected under sea ice and is attributed to the rapid settling of highly aggregated sympagic algae to depths of low light transmission favouring the photodynamic effect at the expense of photobleaching of the sensitizer. Paradoxically, the low efficiency of Type II photosensitized oxidation of lipids observed in temperate and equatorial regions is associated with high solar irradiances in these regions. Type II photosensitized oxidation of lipids in senescent phytoplankton seems thus to be strongly dependent of the intensity of solar irradiance.

Marine oxygen minimum zones play a crucial role in the global oceanic carbon, nitrogen, and sulfur cycles as they harbor microbial communities that are adapted to the water column chemistry and redox zonation, and in turn control the water column chemistry and greenhouse gas release. These micro-organisms have metabolisms that rely on terminal electron acceptors other than O2 and often benefit from syntrophic relationships (metabolic coupling). Here, we study chemo(auto)trophy along the redoxcline in two stratified fjords on Vancouver Island (Canada) using bacterial bacteriohopanepolyols and archaeal ether lipids. We analyze the distribution of these lipid classes in suspended particulate matter (SPM) to trace ammonia oxidation, anaerobic ammonium oxidation (anammox), sulfate reduction/sulfur oxidation, methanogenesis, and methane oxidation, and investigate ecological niches to evaluate potential links between their respective bacterial and archaeal sources. Our results show an unparalleled BHP and ether lipid structural diversity that allows tracing the major redox-driven metabolic processes at the time of sampling: Both fjords are dominated by archaeal ammonia oxidation and anammox; sulfate-reducing bacteria may be present in Deer Bay, but absent from Effingham Inlet; methanogenic Euryarchaeota and archaeal and bacterial methanotrophs are detectable at low abundance. Correlation analysis reveals distinct biomarker clusters that provide constraints on the biogeochemical niches of some orphan BHP and ether lipids such as in situ-produced adenosyl-BHPs or unsaturated archaeols.

Bacteriohopanepolyols (BHPs) that are commonly associated with soil and peat environments ("soil marker" BHPs), were analyzed along redox gradients in marine oxygen deficient zones (ODZs). The latter included suspended particulate organic matter (POM) from two fjords on Vancouver Island (Canada) and the Black Sea, as well as sinking POM collected in sediment trap time-series deployed in the Cariaco Basin. Our results show that the so-called "soil marker" BHPs occur in all ODZ settings. They have distributions that are best explained by in situ chemotrophic production within the chemocline and in anoxic/ euxinic waters, rather than exclusive supply from soils. In particular, adenosylhopane, adenosylhopanetype 2 and 2Me-adenosylhopane-type 2, appear to be produced within a common biogeochemical niche in the water column, irrespective of setting. On the other hand, 2Me-adenosylhopane, adenosylhopanetype 3 and 2Me-adenosylhopane-type 3 may be supplied partly from the continent, as they are also abundant in surface water suspended POM on Vancouver Island and accumulate almost exclusively in the shallower (upper chemocline) trap in the Cariaco Basin. However, their water column suspended POM distributions and time-series sinking POM fluxes also indicate additional chemotrophic sources that have spatially and temporally diverse origins. Our study suggests that caution is warranted when using "soil marker" BHPs and their associated soil input proxies in ODZ settings, as the diverse microbial community in these settings produces BHP signatures similar to those found in soils. (C) 2020 Elsevier Ltd. All rights reserved.

Advances in sampling tools, analytical methods, and data handling capabilities have been fundamental to the growth of marine organic biogeochemistry over the past four decades. There has always been a strong feedback between analytical advances and scientific advances. However, whereas advances in analytical technology were often the driving force that made possible progress in elucidating the sources and fate of organic matter in the ocean in the first decades of marine organic biogeochemistry, today process-based scientific questions should drive analytical developments. Several paradigm shifts and challenges for the future are related to the intersection between analytical progress and scientific evolution. Untargeted “molecular headhunting” for its own sake is now being subsumed into process-driven targeted investigations that ask new questions and thus require new analytical capabilities. However, there are still major gaps in characterizing the chemical composition and biochemical behavior of macromolecules, as well as in generating reference standards for relevant types of organic matter. Field-based measurements are now routinely complemented by controlled laboratory experiments and in situ rate measurements of key biogeochemical processes. And finally, the multidisciplinary investigations that are becoming more common generate large and diverse datasets, requiring innovative computational tools to integrate often disparate data sets, including better global coverage and mapping. Here, we compile examples of developments in analytical methods that have enabled transformative scientific advances since 2004, and we project some challenges and opportunities in the near future. We believe that addressing these challenges and capitalizing on these opportunities will ensure continued progress in understanding the cycling of organic carbon in the ocean.

Oceanic oxygen-deficient zones (ODZs) encompass open ocean and coastal oxygen minimum zones and euxinic marine basins. A primary goal of this review is to demonstrate how new approaches involving lipidomics and genomics are informing how we think about ODZs. There are five parts to the review. First, a brief overview of early investigations of organic geochemistry in ODZs sets the stage for follow-on work. Second, linkages between organic biomarkers and microbial and geochemical processes are described for three key biogeochemical processes that are characteristic of ODZs: (i) oxidation of ammonium by archaea and anammox bacteria; (ii) redox cycles of metals and sulfur; (iii) the methane cycle. Third, three different approaches are presented that make possible comprehensive, integrated views of the biogeochemistry of the Black Sea, as a case study. Fourth, examples of organic biogeochemical results for ODZs in the modern ocean are projected back into the geological past to show that the same processes have been in play for eons. The final section summarizes how chemistry and biology have been combined in investigations in ODZs and concludes with some challenges for future research. (C) 2020 Elsevier Ltd. All rights reserved.

We investigated the origin of sedimentary bacteriohopanepolyols (BHPs) in low-density (<1.6 g cm(-3)), mesodensity (1.6-2.0 and 2.0-2.5 g cm(-3)) and high-density fractions (>2.5 g cm(-3)) as well as unfractionated bulk samples in a highly dynamic coastal setting along a transect spanning from the Mississippi Delta into the Gulf of Mexico (GOM). We observe selective partitioning of BHPs among density fractions both in total abundance and structural diversity. BHPs primarily accumulate in the low-density fraction at all sites. Good correlation with other particle properties [surface area-normalized organic carbon loadings (OC/SA), C/N ratios, Delta C-14 values, and lignin phenol abundances] and the spatial distribution of absolute and relative BHP abundances suggests that a significant fraction of BHPs are terrestrially sourced and entrained in the OC pool that is stabilized on clay particles or associated with plant fragments. Only a small subset of BHPs seems to have a significant autochthonous origin at the station furthest offshore and they are associated with the low and mesodensity fractions. While provenance and hydrodynamic sorting of particles across the shelf seem to primarily determine BHP inventories along the transect, the samples also harbor an unusual diversity of amino-functionalized BHPs. A subset of these BHPs appears to derive from aerobic methane oxidizing bacteria and are likely exported with particles from the coastal swamps in the Mississippi Delta. Other amino-functionalized BHPs seem to derive from aerobic ammonia oxidizing bacteria thriving in the nutrient-rich Mississippi River plume. We find no evidence for anaerobic ammonium oxidizing bacteria related to recurring seasonal hypoxia on the Louisiana Shelf.

The advent of new sampling tools, analytical methods, and data handling capabilities that have been applied to marine chemistry since the 1970s along with coordinated, international and interdisciplinary research programs has led to explosive growth of marine organic biogeochemistry. Here we briefly summarize the history of stepwise growth as illustrated by community-wide workshop reports and symposia, highlighting evolving recommendations for future research put forth in those reports. Following that, we present examples of four frontiers that have been explored recently, focusing as much as possible at the molecular level and on marine water columns: (i) how analytical advances and informatics tools provide new insight into the chemical nature and cycling of dissolved organic matter; (ii) how evolving studies of suspended and sinking particles play an important role in understanding ocean biogeochemistry; (iii) the new symbiosis between marine microbiology, analytical chemistry and organic geochemistry as illustrated by the archaea, their habitats, lipid biomarkers, and influence on geochemical cycles; and (iv) how advances in compound-specific measurements of carbon, nitrogen, hydrogen, and sulfur isotopes shed new light on sources and behavior of marine organic matter. We cite selected recent (primarily the past two decades) research examples as a basis for further reading and to project into the future some aspects of these research areas that could be further developed. Throughout, we highlight how new analytical and sampling methods allowed these fields to progress.

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In this study we analyzed sediment trap time series from five tropical sites to assess seasonal variations in concentrations and fluxes of long-chain diols (LCDs) and associated proxies with emphasis on the long-chain diol index (LDI) temperature proxy. For the tropical Atlantic, we observe that generally less than 2 % of LCDs settling from the water column are preserved in the sediment. The Atlantic and Mozambique Channel traps reveal minimal seasonal variations in the LDI, similar to the two other lipid-based temperature proxies TEX86 and U37K′. In addition, annual mean LDI-derived temperatures are in good agreement with the annual mean satellite-derived sea surface temperatures (SSTs). In contrast, the LDI in the Cariaco Basin shows larger seasonal variation, as do the TEX86 and U37K′. Here, the LDI underestimates SST during the warmest months, which is possibly due to summer stratification and the habitat depth of the diol producers deepening to around 20–30 m. Surface sediment LDI temperatures in the Atlantic and Mozambique Channel compare well with the average LDI-derived temperatures from the overlying sediment traps, as well as with decadal annual mean SST. Lastly, we observed large seasonal variations in the diol index, as an indicator of upwelling conditions, at three sites: in the eastern Atlantic, potentially linked to Guinea Dome upwelling; in the Cariaco Basin, likely caused by seasonal upwelling; and in the Mozambique Channel, where diol index variations may be driven by upwelling from favorable winds and/or eddy migration.

Abstract. Intact polar lipids (IPLs) are the main building blocks of cellular membranes and contain chemotaxonomic, ecophysiologic and metabolic information, which makes them valuable biomarkers in microbial ecology and biogeochemistry. This study investigates the IPL distribution in suspended particulate matter (SPM) in the water column of the Eastern Tropical North Pacific Ocean (ETNP), an area characterized by one of the most extensive open ocean oxygen minimum zones (OMZ) in the world with strong gradients of nutrients, temperature and redox conditions. A wide structural variety in polar lipid head group composition and core structures exists along physical and geochemical gradients within the OMZ. Our goal is to use this structural diversity in IPLs to evaluate the microbial ecology and ecophysiological adaptations that affect organisms inhabiting the OMZ in the context of biogeochemical cycles. Diacylglycerol phospholipids are present at all depths, but exhibit highest relative abundance and compositional variety (including mixed acyl/ether core structures) in the upper and core OMZ where prokaryotic biomass was enriched. Surface ocean SPM is dominated by diacylglycerol glycolipids that are typical lipid components of photosynthetic membranes. These and other glycolipids with varying core structures composed of ceramides and hydroxylated fatty acids are also detected with varying relative abundances in the OMZ and deep oxycline, signifying additional non-phototrophic bacterial sources for these lipids. Similarly, betaine lipids (with none or multiple hydroxylations in the core structures) that are typically assigned to microalgae are found throughout the water column down to the deep oxycline but do not show a depth-related trend in relative abundance. Archaeal IPLs comprised of glycosidic and mixed glycosidic-phosphatidic glycerol dibiphytanyl glycerol tetraethers (GDGTs) are most abundant in the upper OMZ where nitrate maxima point to ammonium oxidation, but increase in relative abundance in the core OMZ and deep oxycline. The presence of abundant non-phosphorus lipids within the OMZ suggests that the indigenous microbes might be phosphorus limited at phosphate concentrations of 1 to 3.5 µM. It remains unclear if the detected amino and glycolipids indeed function as substitutes for phospholipid in these oxygen-depleted environments as microbial sources for many of these lipids still remain unknown.

Absolute concentrations of pigments detected in surface waters of the Eastern Tropical North Pacific at stations 1, 5 and 8.

Intact polar lipids (IPLs) are the main building blocks of cellular membranes and contain chemotaxonomic, ecophysiological and metabolic information, making them valuable biomarkers in microbial ecology and biogeochemistry. This study investigates IPLs in suspended particulate matter (SPM) in the water column of the eastern tropical North Pacific Ocean (ETNP), one of the most extensive open-ocean oxygen minimum zones (OMZs) in the world, with strong gradients of nutrients, temperature and redox conditions. A wide structural variety in polar lipid head-group composition and core structures exists along physical and geochemical gradients within the water column, from the oxygenated photic zone to the aphotic OMZ. We use this structural diversity in IPLs to evaluate the ecology and ecophysiological adaptations that affect organisms inhabiting the water column, especially the mid-depth OMZ in the context of biogeochemical cycles. Diacylglycerol phospholipids are present at all depths, but exhibit the highest relative abundance and compositional variety (including mixed acyl/ether core structures) in the upper and core OMZ where prokaryotic biomass was enriched. Surface ocean SPM is dominated by diacylglycerol glycolipids that are found in photosynthetic membranes. These and other glycolipids with varying core structures composed of ceramides and hydroxylated fatty acids are also detected with varying relative abundances in the OMZ and deep oxycline, signifying additional non-phototrophic bacterial sources for these lipids. Betaine lipids (with zero or multiple hydroxylations in the core structures) that are typically assigned to microalgae are found throughout the water column down to the deep oxycline but do not show a depth-related trend in relative abundance. Archaeal IPLs comprised of glycosidic and mixed glycosidic-phosphatidic glycerol dibiphytanyl glycerol tetraethers (GDGTs) are most abundant in the upper OMZ, where nitrate maxima point to ammonium oxidation but increase in relative abundance in the core OMZ and deep oxycline. The presence of non-phosphorus substitute lipids within the OMZ suggest that the indigenous microbes might be phosphorus limited (P starved) at ambient phosphate concentrations of 1 to 3.5 µM, although specific microbial sources for many of these lipids still remain unknown.

Membrane lipids of marine planktonic archaea have provided unique insights into archaeal ecology and paleoceanography. However, past studies of archaeal lipids in suspended particulate matter (SPM) and sediments mainly focused on a small class of fully saturated glycerol dibiphytanyl glycerol tetraether (GDGT) homologues identified decades ago. The apparent low structural diversity of GDGTs is in strong contrast to the high diversity of metabolism and taxonomy among planktonic archaea. Furthermore, adaptation of archaeal lipids in the deep ocean remains poorly constrained. We report the archaeal lipidome in SPM from diverse oceanic regimes. We extend the known inventory of planktonic archaeal lipids to include numerous unsaturated archaeal ether lipids (uns-AELs). We further reveal (i) different thermal regulations and polar headgroup compositions of membrane lipids between the epipelagic (≤ 100 m) and deep (>100 m) populations of archaea, (ii) stratification of unsaturated GDGTs with varying redox conditions, and (iii) enrichment of tetra-unsaturated archaeol and fully saturated GDGTs in epipelagic and deep oxygenated waters, respectively. Such stratified lipid patterns are consistent with the typical distribution of archaeal phylotypes in marine environments. We, thus, provide an ecological context for GDGT-based paleoclimatology and bring about the potential use of uns-AELs as biomarkers for planktonic Euryarchaeota.

Rivers are the primary means by which sediments and carbon are transported from the terrestrial biosphere to the oceans but gaps remain in our understanding of carbon associations from source to sink. Bed sediments from the Sacramento-San Joaquin River Delta (CA) were fractionated according to density and analyzed for sediment mass distribution, elemental (C and N) composition, mineral surface area, and stable carbon and radiocarbon isotope compositions of organic carbon (OC) and fatty acids to evaluate the nature of organic carbon in river sediments. OC was unevenly distributed among density fractions. Mass and OC were in general concentrated in mesodensity (1.6–2.0 and 2.0–2.5 g cm−3) fractions, comprising 84.0 ± 1.3 % of total sediment mass and 80.8 ± 13.3 % of total OC (TOC). Low-density (< 1.6 g cm−3) material, although rich in OC (34.0 ± 2.0 % OC) due to woody debris, constituted only 17.3 ± 12.8 % of TOC. High-density (> 2.5 g cm−3) organic-poor, mineral-rich material made-up 13.7 ± 1.4 % of sediment mass and 2.0 ± 0.9 % of TOC. Stable carbon isotope compositions of sedimentary OC were relatively uniform across bulk and density fractions (δ13C −27.4 ± 0.5 ‰). Radiocarbon content varied from Δ14C values of −382 (radiocarbon age 3800 yr BP) to +94 ‰ (modern) indicating a mix of young and old OC. Fatty acids were used to further constrain the origins of sedimentary OC. Short-chain n-C14–n-C18 fatty acids of algal origin were depleted in 13C (δ13C −37.5 to −35.2 ‰) but were enriched in 14C (Δ14C > 0) compared to long-chain n-C24–n-C28 acids of vascular plant origins with higher δ13C (−33.0 to −31.0 ‰) but variable Δ14C values (−180 and 61 ‰). These data demonstrate the potentially complex source and age distributions found within river sediments and provide insights about sediment and organic matter supply to the Delta.

Branched and isoprenoid glycerol dialkyl glycerol tetraethers (brGDGTs and isoGDGTs, respectively) are used to reconstruct carbon flow from terrestrial landscapes to the ocean in a proxy called the branched vs. isoprenoid tetraether index, or BIT index. The index is based on analysis of core GDGTs (C-GDGTs), that are produced from intact GDGTs (I-GDGTs) upon cell death. GDGTs are a component of the cell membranes of bacteria in soils (br) and archaea (iso) primarily in the marine environment. However, uncertainty as to the identity of the organisms that biosynthesize brGDGTs, the variation in the extent to which GDGTs represent end member carbon pools and the suspected production of brGDGTs and isoGDGTs in both marine and terrigenous environments hinders interpretation of the BIT index. Since brGDGTs remain our only tool for measuring the presence of unknown brGDGT producing organisms, it is particularly important to use the intact form of brGDGTs in living cells (rather than C-brGDGTs in relict biomass) to infer the distributions of the likely source organisms. In situ production within riverine, lacustrine and marine environments is currently thought to be possible, yet few measures of I-brGDGTs are available in these environments to support these claims. Here we assess the spatial distribution of core and intact GDGTs in the Columbia River Basin and nearby Willapa Bay (Washington and Oregon) in order to elucidate source environments and behavior of I-GDGTs vs. C-GDGTs. The presence of I-BrGDGTs throughout the studied soils, rivers and estuaries suggests in situ production across the continuum from soil to marine environments. Likewise, intact crenarchaeol, the marine end member isoGDGT used in the BIT index, was present in all samples. Widespread production of each GDGT class along terrigenous carbon transport paths likely alters the BIT index along this continuum. Core to intact ratios and the weak correlation between I-GDGT derived BIT values and carbon isotope signatures suggest a mixture of allochthonous and autochthonous sources of GDGTs in riverine and marine environments. Our findings highlight the need for further work into the provenance and behavior of GDGTs in order to improve interpretation of the BIT index and other environmental proxies that rely on them. (C) 2015 Elsevier Ltd. All rights reserved.