Identification of the bacterial community that degrades phenanthrene sorbed to polystyrene nanoplastics using DNA-based stable isotope probing.

In the Anthropocene, plastic pollution has become a new environmental biotope, the so-called plastisphere. In the oceans, nano- and micro-sized plastics are omnipresent and found in huge quantities throughout the water column and sediment, and their large surface area-to-volume ratio offers an excellent surface to which hydrophobic chemical pollutants (e.g. petrochemicals and POPs) can readily sorb to. Our understanding of the microbial communities that breakdown plastic-sorbed chemical pollutants, however, remains poor. Here, we investigated the formation of 500 nm and 1000 nm polystyrene (PS) agglomerations in natural seawater from a coastal environment, and we applied DNA-based stable isotope probing (DNA-SIP) with the 500 nm PS sorbed with isotopically-labelled phenanthrene to identify the bacterial members in the seawater community capable of degrading the hydrocarbon. Whilst we observed no significant impact of nanoplastic size on the microbial communities associated with agglomerates that formed in these experiments, these communities were, however, significantly different to those in the surrounding seawater. By DNA-SIP, we identified Arcobacteraceae, Brevundimonas, Comamonas, uncultured Comamonadaceae, Delftia, Sphingomonas and Staphylococcus, as well as the first member of the genera Acidiphilum and Pelomonas to degrade phenanthrene, and of the genera Aquabacterium, Paracoccus and Polymorphobacter to degrade a hydrocarbon. This work provides new information that feeds into our growing understanding on the fate of co-pollutants associated with nano- and microplastics in the ocean.

Organic geochemical evidence of human-controlled fires at Acheulean site of Valdocarros II (Spain, 245 kya).

Among the outstanding questions about the emergence of human-controlled fire is the systematic recurrence between the geochemical remains of fire and its preservation in the archaeological record, as the use of fire is considered a technological landmark, especially for its importance in food cooking, defensive strategies, and heating. Here we report fossil lipid biomarkers associated with incomplete combustion of organic matter at the Valdocarros II site, one of the largest European Acheulean sites in Spain dated to marine isotopic stage (MIS) 8/7 (~ 245 kya) allowing a multiproxy analysis of human-controlled fire use. Our results reveal isolated cases of highly concentrated and diverse polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs (APAHs), along with diagnostic conifer-derived triterpenoids in two hearth-like archaeological structures. The presence of combustion byproducts suggests the presence of anthropogenic (controlled) fires at Valdocarros-one of the oldest evidence of fire use in Europe-in association with Acheulean tools and bones. Hominins possibly used fire for two main activities, as a means of defense against predators and cooking. Our results help to better delineate major gaps in our current knowledge of human-controlled fire in the context of the Middle-Pleistocene in Europe and suggest that human ancestors were able to control fire before at least 250 kya.

New site at Olduvai Gorge (AGS, Bed I, 1.84 Mya) widens the range of locations where hominins engaged in butchery.

Outstanding questions about human evolution include systematic connections between critical landscape resources-such as water and food-and how these shaped the competitive and biodiverse environment(s) that our ancestors inhabited. Here, we report fossil n-alkyl lipid biomarkers and their associated δ13C values across a newly discovered Olduvai Gorge site (AGS) dated to 1.84 million years ago, enabling a multiproxy analysis of the distributions of critical local landscape resources across an explicit locus of hominin activity. Our results reveal that AGS was a seasonally waterlogged, largely unvegetated lakeside site situated near an ephemeral freshwater river surrounded by arid-adapted C4 grasses. The sparse vegetation at AGS contrasts with reconstructed (micro)habitats at the other anthropogenic sites at Olduvai Gorge, suggesting that central-provisioning places depended more heavily on water access than vegetation viz. woody plants as is often observed for modern hunter-gatherers. As hominins at AGS performed similar butchering activities as at other Bed I sites, our results suggest they did not need the shelter of trees and thus occupied a competitive position within the predatory guild.

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants.

BACKGROUND: Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52. RESULTS: Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment. CONCLUSION: Overall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills. Video abstract.

Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench.

BACKGROUND: The Mariana Trench is the deepest known site in the Earth's oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood. RESULTS: Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter, Thalassolituus, and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n-alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n-alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 µg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 µg/gdw). The δ2H values of n-C16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from - 79 to - 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source. CONCLUSIONS: These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment.

Radiocarbon Age Offsets Between Two Surface Dwelling Planktonic Foraminifera Species During Abrupt Climate Events in the SW Iberian Margin.

This study identifies temporal biases in the radiocarbon ages of the planktonic foraminifera species Globigerina bulloides and Globigerinoides ruber (white) in a sediment core from the SW Iberian margin (so-called Shackleton site). Leaching of the outer shell and measurement of the radiocarbon content of both the leachate and leached sample enabled us to identify surface contamination of the tests and its impact on their 14C ages. Incorporation of younger radiocarbon on the outer shell affected both species and had a larger impact downcore. Interspecies comparison of the 14C ages of the leached samples reveal systematic offsets with 14C ages for G. ruber being younger than G. bulloides ages during the last deglaciation and part of the Early and mid-Holocene. The greatest offsets (up to 1,030 years) were found during Heinrich Stadial 1, the Younger Dryas, and part of the Holocene. The potential factors differentially affecting these two planktonic species were assessed by complementary 14C, oxygen and carbon isotopes, and species abundance determinations. The coupled effect of bioturbation with changes in the abundance of G. ruber is invoked to account for the large age offsets. Our results highlight that 14C ages of planktonic foraminifera might be largely compromised even in settings characterized by high sediment accumulation rates. Thus, a careful assessment of potential temporal biases must be performed prior to using 14C ages for paleoclimate investigations or radiocarbon calibrations (e.g., marine calibration curve Marine13, Reimer et al., 2013, https://doi.org/10.2458/azu_js_rc.55.16947).

Isotopic variance among plant lipid homologues correlates with biodiversity patterns of their source communities.

Plant diversity is important to human welfare worldwide, and this importance is exemplified in subtropical and tropical [(sub)tropical] African savannahs where regional biodiversity enhances the sustaining provision of basic ecosystem services available to millions of residents. Yet, there is a critical lack of knowledge about how savannahs respond to climate change. Here, we report the relationships between savannah vegetation structure, species richness, and bioclimatic variables as recorded by plant biochemical fossils, called biomarkers. Our analyses reveal that the stable carbon isotope composition (δ13C) of discrete sedimentary plant biomarkers reflects vegetation structure, but the isotopic range among plant biomarkers-which we call LEaf Wax Isotopic Spread (LEWIS)-reflects species richness. Analyses of individual biomarker δ13C values and LEWIS for downcore sediments recovered from southeast Africa reveal that the region's species richness mirrored trends in atmospheric carbon dioxide concentration (pCO2) throughout the last 25,000 years. This suggests that increasing pCO2 levels during post-industrialization may prompt future declines in regional biodiversity (1-10 species per unit CO2 p.p.m.v.) through imminent habitat loss or extinction.

Transient hydrodynamic effects influence organic carbon signatures in marine sediments.

Ocean dynamics served an important role during past dramatic climate changes via impacts on deep-ocean carbon storage. Such changes are recorded in sedimentary proxies of hydrographic change on continental margins, which lie at the ocean-atmosphere-earth interface. However, interpretations of these records are challenging, given complex interplays among processes delivering particulate material to and from ocean margins. Here we report radiocarbon (14C) signatures measured for organic carbon in differing grain-size sediment fractions and foraminifera in a sediment core retrieved from the southwest Iberian margin, spanning the last ~25,000 yr. Variable differences of 0-5000 yr in radiocarbon age are apparent between organic carbon in differing grain-sizes and foraminifera of the same sediment layer. The magnitude of 14C differences co-varies with key paleoceanographic indices (e.g., proximal bottom-current density gradients), which we interpret as evidence of Atlantic-Mediterranean seawater exchange influencing grain-size specific carbon accumulation and translocation. These findings underscore an important link between regional hydrodynamics and interpretations of down-core sedimentary proxies.

Fatty acid specific δ13C values reveal earliest Mediterranean cheese production 7,200 years ago.

The earliest evidence for cheese production in the Mediterranean is revealed by stable carbon isotope analyses of individual fatty acids in pottery residues from the Dalmatian coast of Croatia. Lipid residue data indicate the presence of milk in the earliest pottery, Impressed Ware, by 5700 cal. BCE (7700 BP). In contrast, by 5200 cal BCE (7200 BP), milk was common in refined Figulina pottery, meat was mostly associated with Danilo ware, cheese occurred in Rhyta, and sieves contained fermented dairy, representing strong links between specific function and stylistically distinctive pottery vessels. Genetic data indicate the prevalence of lactose intolerance among early farming populations. However, young children are lactase persistent until after weaning and could consume milk as a relatively pathogen-free and nutrient rich food source, enhancing their chances of survival into adulthood. Fermentation of milk into yogurt and cheese decreases lactose content. The evidence for fermented dairy products by 5200 cal BCE indicates a larger proportion of the population was able to consume dairy products and benefit from their significant nutritional advantages. We suggest that milk and cheese production among Europe's early farmers reduced infant mortality and helped stimulate demographic shifts that propelled farming communities to expand to northern latitudes.

Dietary options and behavior suggested by plant biomarker evidence in an early human habitat.

The availability of plants and freshwater shapes the diets and social behavior of chimpanzees, our closest living relative. However, limited evidence about the spatial relationships shared between ancestral human (hominin) remains, edible resources, refuge, and freshwater leaves the influence of local resources on our species' evolution open to debate. Exceptionally well-preserved organic geochemical fossils--biomarkers--preserved in a soil horizon resolve different plant communities at meter scales across a contiguous 25,000 m(2) archaeological land surface at Olduvai Gorge from about 2 Ma. Biomarkers reveal hominins had access to aquatic plants and protective woods in a patchwork landscape, which included a spring-fed wetland near a woodland that both were surrounded by open grassland. Numerous cut-marked animal bones are located within the wooded area, and within meters of wetland vegetation delineated by biomarkers for ferns and sedges. Taken together, plant biomarkers, clustered bone debris, and hominin remains define a clear spatial pattern that places animal butchery amid the refuge of an isolated forest patch and near freshwater with diverse edible resources.

Ecosystem variability and early human habitats in eastern Africa.

The role of savannas during the course of early human evolution has been debated for nearly a century, in part because of difficulties in characterizing local ecosystems from fossil and sediment records. Here, we present high-resolution lipid biomarker and isotopic signatures for organic matter preserved in lake sediments at Olduvai Gorge during a key juncture in human evolution about 2.0 Ma--the emergence and dispersal of Homo erectus (sensu lato). Using published data for modern plants and soils, we construct a framework for ecological interpretations of stable carbon-isotope compositions (expressed as δ(13)C values) of lipid biomarkers from ancient plants. Within this framework, δ(13)C values for sedimentary leaf lipids and total organic carbon from Olduvai Gorge indicate recurrent ecosystem variations, where open C(4) grasslands abruptly transitioned to closed C(3) forests within several hundreds to thousands of years. Carbon-isotopic signatures correlate most strongly with Earth's orbital geometry (precession), and tropical sea-surface temperatures are significant secondary predictors in partial regression analyses. The scale and pace of repeated ecosystem variations at Olduvai Gorge contrast with long-held views of directional or stepwise aridification and grassland expansion in eastern Africa during the early Pleistocene and provide a local perspective on environmental hypotheses of human evolution.

Water, plants, and early human habitats in eastern Africa.

Water and its influence on plants likely exerted strong adaptive pressures in human evolution. Understanding relationships among water, plants, and early humans is limited both by incomplete terrestrial records of environmental change and by indirect proxy data for water availability. Here we present a continuous record of stable hydrogen-isotope compositions (expressed as δD values) for lipid biomarkers preserved in lake sediments from an early Pleistocene archaeological site in eastern Africa--Olduvai Gorge. We convert sedimentary leaf- and algal-lipid δD values into estimates for ancient source-water δD values by accounting for biochemical, physiological, and environmental influences on isotopic fractionation via published water-lipid enrichment factors for living plants, algae, and recent sediments. Reconstructed precipitation and lake-water δD values, respectively, are consistent with modern isotopic hydrology and reveal that dramatic fluctuations in water availability accompanied ecosystem changes. Drier conditions, indicated by less negative δD values, occur in association with stable carbon-isotopic evidence for open, C(4)-dominated grassland ecosystems. Wetter conditions, indicated by lower δD values, are associated with expanded woody cover across the ancient landscape. Estimates for ancient precipitation amounts, based on reconstructed precipitation δD values, range between approximately 250 and 700 mm · y(-1) and are consistent with modern precipitation data for eastern Africa. We conclude that freshwater availability exerted a substantial influence on eastern African ecosystems and, by extension, was central to early human proliferation during periods of rapid climate change.