A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia).

Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.

Deep subsurface microbial life in impact-altered Late Paleozoic granitoid rocks from the Chicxulub impact crater.

In 2016, IODP-ICDP Expedition 364 recovered an 829-meter-long core within the peak ring of the Chicxulub impact crater (Yucatán, Mexico), allowing us to investigate the post-impact recovery of the heat-sterilized deep continental microbial biosphere at the impact site. We recently reported increased cell biomass in the impact suevite, which was deposited within the first few hours of the Cenozoic, and that the overall microbial communities differed significantly between the suevite and the other main core lithologies (i.e., the granitic basement and the overlying Early Eocene marine sediments; Cockell et al., 2021). However, only seven rock intervals were previously analyzed from the geologically heterogenic and impact-deformed 587-m-long granitic core section below the suevite interval. Here, we used 16S rRNA gene profiling to study the microbial community composition in 45 intervals including (a) 31 impact-shocked granites, (b) 7 non-granitic rocks (i.e., consisting of suevite and impact melt rocks intercalated into the granites during crater formation and strongly serpentinized pre-impact sub-volcanic, ultramafic basanite/dolerite), and (c) 7 cross-cut mineral veins of anhydride and silica. Most recovered microbial taxa resemble those found in hydrothermal systems. Spearman correlation analysis confirmed that the borehole temperature, which gradually increased from 47 to 69°C with core depth, significantly shaped a subset of the vertically stratified modern microbial community composition in the granitic basement rocks. However, bacterial communities differed significantly between the impoverished shattered granites and nutrient-enriched non-granite rocks, even though both lithologies were at similar depths and temperatures. Furthermore, Spearman analysis revealed a strong correlation between the microbial communities and bioavailable chemical compounds and suggests the presence of chemolithoautotrophs, which most likely still play an active role in metal and sulfur cycling. These results indicate that post-impact microbial niche separation has also occurred in the granitic basement lithologies, as previously shown for the newly formed lithologies. Moreover, our data suggest that the impact-induced geochemical boundaries continue to shape the modern-day deep biosphere in the granitic basement underlying the Chicxulub crater.

Do distributions of diamondoid hydrocarbons accumulated in oil-contaminated fish tissues help to identify the sources of oil?

Identifying the sources of environmental oil contamination can be challenging, especially for oil in motile organisms such as fish. Lipophilic hydrocarbons from oil can bioaccumulate in fish adipose tissue and potentially provide a forensic "fingerprint" of the original oil. Herein, diamondoid hydrocarbon distributions were employed to provide such fingerprints. Indices produced from diamondoids were used to compare extracts from fish adipose tissues and the crude and fuel oils to which the fish were exposed under laboratory conditions. A suite of 20 diamondoids was found to have bioaccumulated in the dietary-exposed fish. Cross-plots of indices between fish and exposure oils were close to the ideal 1:1 relationship. Comparisons with diamondoid distributions of non-exposure oils produced overall, but not exclusively, weaker correlations. Linear Discriminatory Analysis on a combined set of 15 diamondoid and bicyclane molecular ratios was able to identify the exposure oils, so a use of both compound classes is preferable.

Polycyclic aromatic hydrocarbons in samples of Ryugu formed in the interstellar medium.

Polycyclic aromatic hydrocarbons (PAHs) contain ≲20% of the carbon in the interstellar medium. They are potentially produced in circumstellar environments (at temperatures ≳1000 kelvin), by reactions within cold (~10 kelvin) interstellar clouds, or by processing of carbon-rich dust grains. We report isotopic properties of PAHs extracted from samples of the asteroid Ryugu and the meteorite Murchison. The doubly-13C substituted compositions (Δ2×13C values) of the PAHs naphthalene, fluoranthene, and pyrene are 9 to 51‰ higher than values expected for a stochastic distribution of isotopes. The Δ2×13C values are higher than expected if the PAHs formed in a circumstellar environment, but consistent with formation in the interstellar medium. By contrast, the PAHs phenanthrene and anthracene in Ryugu samples have Δ2×13C values consistent with formation by higher-temperature reactions.

Rapid encapsulation of true ferns and arborane/fernane compounds fossilised in siderite concretions supports analytical distinction of plant fossils.

Fossilised true ferns (Pecopteris sp.) preserved in siderite concretions from the Mazon Creek Lagerstätte (Illinois) presented a unique opportunity to characterise the organic signatures of these late Carboniferous plants. Localised analyses of true fern fossils showed several highly abundant phytohopanoids and fernane/arborane derived aromatic products, which were present only negligibly within their siderite matrix, as well as from other types of fossilised plants. These terpenoids had been recognised in some extant ferns, but scarcely in sedimentary organic matter and their exact source remained ambiguous. The present fossil biomarker data confirms an ancient true fern origin. Furthermore, the excellent concretion preservation of a series of related terpenoid products provided a rare insight into their diagenetic formation. The benign properties of carbonate concretions could be exploited further for biomarker evidence of other fossilised organisms, with one important caveat being that biomarker signals attributed to isolated fossils be significantly distinct from background organic matter pervading the concretion matrix. For instance, hydrocarbon profiles of seed ferns (pteridosperms) and articulates (horsetails) also preserved in Mazon Creek concretions were indistinguishable from separate analysis of their concretion matrix, preventing biomarker recognition.

Microbially mediated fossil concretions and their characterization by the latest methodologies: a review.

The study of well-preserved organic matter (OM) within mineral concretions has provided key insights into depositional and environmental conditions in deep time. Concretions of varied compositions, including carbonate, phosphate, and iron-based minerals, have been found to host exceptionally preserved fossils. Organic geochemical characterization of concretion-encapsulated OM promises valuable new information of fossil preservation, paleoenvironments, and even direct taxonomic information to further illuminate the evolutionary dynamics of our planet and its biota. Full exploitation of this largely untapped geochemical archive, however, requires a sophisticated understanding of the prevalence, formation controls and OM sequestration properties of mineral concretions. Past research has led to the proposal of different models of concretion formation and OM preservation. Nevertheless, the formation mechanisms and controls on OM preservation in concretions remain poorly understood. Here we provide a detailed review of the main types of concretions and formation pathways with a focus on the role of microbes and their metabolic activities. In addition, we provide a comprehensive account of organic geochemical, and complimentary inorganic geochemical, morphological, microbial and paleontological, analytical methods, including recent advancements, relevant to the characterization of concretions and sequestered OM. The application and outcome of several early organic geochemical studies of concretion-impregnated OM are included to demonstrate how this underexploited geo-biological record can provide new insights into the Earth's evolutionary record. This paper also attempts to shed light on the current status of this research and major challenges that lie ahead in the further application of geo-paleo-microbial and organic geochemical research of concretions and their host fossils. Recent efforts to bridge the knowledge and communication gaps in this multidisciplinary research area are also discussed, with particular emphasis on research with significance for interpreting the molecular record in extraordinarily preserved fossils.

Fish Fingerprinting: Identifying Crude Oil Pollutants using Bicyclic Sesquiterpanes (Bicyclanes) in the Tissues of Exposed Fish.

In the present study, we investigated the possibility of identifying the source oils of exposed fish using ratios of bicyclic sesquiterpane (bicyclane) chemical biomarkers. In the event of an oil spill, identification of source oil(s) for assessment, or for litigation purposes, typically uses diagnostic ratios of chemical biomarkers to produce characteristic oil "fingerprints." Although this has been applied in identifying oil residues in sediments, water, and sessile filtering organisms, so far as we are aware this has never been successfully demonstrated for oil-exposed fish. In a 35-day laboratory trial, juvenile Lates calcarifer (barramundi or Asian seabass) were exposed, via the diet (1% w/w), to either a heavy fuel oil or to Montara, an Australian medium crude oil. Two-dimensional gas chromatography with high-resolution mass spectrometry and gas chromatography-mass spectrometry were then used to measure selected ratios of the bicyclanes to examine whether the ratios were statistically reproducibly conserved in the fish tissues. Six diagnostic bicyclane ratios showed high correlation (r2 > 0.98) with those of each of the two source oils. A linear discriminatory analysis model showed that nine different petroleum products could be reproducibly discriminated using these bicyclane ratios. The model was then used to correctly identify the bicyclane profiles of each of the two exposure oils in the adipose tissue extracts of each of the 18 fish fed oil-enriched diets. From our initial study, bicyclane biomarkers appear to show good potential for providing reliable forensic fingerprints of the sources of oil contamination of exposed fish. Further research is needed to investigate the minimum exposure times required for bicyclane bioaccumulation to achieve detectable concentrations in fish adipose tissues and to determine bicyclane depuration rates once exposure to oil has ceased. Environ Toxicol Chem 2023;42:7-18. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Salinity-driven ecology and diversity changes of heterocytous cyanobacteria in Australian freshwater and coastal-marine microbial mats.

N2 -fixing heterocytous cyanobacteria are considered to play a minor role in sustaining coastal microbial mat communities developing under normal marine to hypersaline conditions. Here, we investigated microbial mats growing under different salinities from freshwater mats of Giblin River (Tasmania) to metahaline and hypersaline mats of Shark Bay (Western Australia). Analyses of genetic (rRNA and mRNA) and biological markers (heterocyte glycolipids) revealed an unexpectedly large diversity of heterocytous cyanobacteria in all the studied microbial mat communities. It was observed that the taxonomic distribution as well as abundance of cyanobacteria is strongly affected by salinity. Low salinity favoured the presence of heterocytous cyanobacteria in freshwater mats, while mats thriving in higher salinities mainly supported the growth unicellular and filamentous non-heterocytous genera. However, even though mRNA transcripts derived from heterocytous cyanobacteria were lower in Shark Bay (<6%) microbial mats, functional analyses revealed that these diazotrophs were transcribing a substantial proportion of the genes involved in biofilm formation and nitrogen fixation. Overall, our data reveal an unexpectedly high diversity of heterocytous cyanobacteria (e.g. Calothrix, Scytonema, Nodularia, Gloeotrichia, Stigonema, Fischerella and Chlorogloeopsis) that had yet to be described in metahaline and hypersaline microbial mats from Shark Bay and that they play a vital role in sustaining the ecosystem functioning of coastal-marine microbial mat systems.

Fossil Biomarkers and Biosignatures Preserved in Coprolites Reveal Carnivorous Diets in the Carboniferous Mazon Creek Ecosystem.

The reconstruction of ancient trophic networks is pivotal to our understanding of ecosystem function and change through time. However, inferring dietary relationships in enigmatic ecosystems dominated by organisms without modern analogues, such as the Carboniferous Mazon Creek fauna, has previously been considered challenging: preserved coprolites often do not retain sufficient morphology to identify the dietary composition. Here, we analysed n = 3 Mazon Creek coprolites in concretions for dietary signals in preserved biomarkers, stable carbon isotope data, and macromolecular composition. Cholesteroids, metazoan markers of cholesterol, show an increased abundance in the sampled coprolites (86 to 99% of the total steranes) compared to the surrounding sediment, indicating an endogenous nature of preserved organics. Presence of unaltered 5α-cholestan-3ß-ol and coprostanol underline the exceptional molecular preservation of the coprolites, and reveal a carnivorous diet for the coprolite producer. Statistical analyses of in situ Raman spectra targeting coprolite carbonaceous remains support a metazoan affinity of the digested fossil remains, and suggest a high trophic level for the coprolite producer. These currently oldest, intact dietary stanols, combined with exquisitely preserved macromolecular biosignatures in Carboniferous fossils offer a novel source of trophic information. Molecular and biosignature preservation is facilitated by rapid sedimentary encapsulation of the coprolites within days to months after egestion.

Characterizations and comparison of low sulfur fuel oils compliant with 2020 global sulfur cap regulation for international shipping.

The International Marine Organization 2020 Global Sulfur Cap requires ships to burn fuels with <0.50% S and some countries require <0.10% S in certain Sulfur Emission Control Areas but little is known about these new types of fuels. Using both traditional GC-MS and more advanced chromatographic and mass spectrometry techniques, plus stable isotopic, δ13C and δ2H, analyses of pristane, phytane and n-alkanes, the organic components of a suite of three 0.50% S and three 0.10% S compliant fuels were characterized. Two oils were found to be near identical but all of the remaining oils could be forensically distinguished by comparison of their molecular biomarkers and by the profiles of the heterocyclic parent and alkylated homologues. Oils could also be differentiated by their δ13C and δ2H of n-alkanes and isoprenoids. This study provides important forensic data that may prove invaluable in the event of future oil spills.

Preservation of Terrestrial Microorganisms and Organics Within Alteration Products of Chondritic Meteorites from the Nullarbor Plain, Australia.

Meteorites that fall to Earth quickly become contaminated with terrestrial microorganisms. These meteorites are out of chemical equilibrium in the environments where they fall, and equilibration promotes formation of low-temperature alteration minerals that can entomb contaminant microorganisms and thus preserve them as microfossils. Given the well-understood chemistry of meteorites and their recent discovery on Mars by rovers, a similarly weathered meteorite on Mars could preserve organic and fossil evidence of a putative past biosphere at the martian surface. Here, we used several techniques to assess the potential of alteration minerals to preserve microfossils and biogenic organics in terrestrially weathered ordinary chondrites from the Nullarbor Plain, Australia. We used acid etching of ordinary chondrites to reveal entombed fungal hyphae, modern biofilms, and diatoms within alteration minerals. We employed synchrotron X-ray fluorescence microscopy of alteration mineral veins to map the distribution of redox-sensitive elements of relevance to chemolithotrophic organisms, such as Mn-cycling bacteria. We assessed the biogenicity of fungal hyphae within alteration veins using a combination of Fourier-transform infrared spectroscopy and pyrolysis gas chromatography-mass spectrometry, which showed that alteration minerals sequester and preserve organic molecules at various levels of decomposition. Our combined analyses results show that fossil microorganisms and the organic molecules they produce are preserved within calcite-gypsum admixtures in meteorites. Furthermore, the distributions of redox-sensitive elements (e.g., Mn) within alteration minerals are localized, which qualitatively suggests that climatically or microbially facilitated element mobilization occurred during the meteorite's residency on Earth. If returned as part of a sample suite from the martian surface, ordinary chondrites could preserve similar, recognizable evidence of putative past life and/or environmental change.

Multivariate analysis of otolith microchemistry can discriminate the source of oil contamination in exposed fish.

The uptake of metals into the aragonite lattice of the fish otolith (ear-bone) has been used for decades as a historical record of exposure to metals in polluted environments. The relative abundance of two metals in particular, Ni and V, are used in forensic chemical analysis of crude oils to assist in confirming its origin. In this study we investigate the potential for metal accumulation in otoliths to act as a biomarker of exposure to crude oil. Using a 33-day static-renewal laboratory trial design, 56 juvenile Lates calcarifer (commonly known as Asian seabass or barramundi) were fed diets enriched with V (20 mg/kg), Ni (500 mg/kg), Fe (500 mg/kg), and two crude oils with distinctly different metals profiles: a heavy fuel oil (1% w/w) and a typical Australian medium crude (1% w/w). Fish exposed to crude oils showed Ba and Al retained in otoliths in a dose-dependent manner, but fish fed V-, Ni- and Fe-enriched diets showed no metal increase in otoliths, indicating that V, Ni and Fe are not incorporated into the otolith of L. calcarifer via dietary exposure. For crude oils, incorporation into otolith for many metals is likely limited due to porphyrin casing reducing their bioavailability. Principal components analysis (PCA) and subsequent linear discriminatory analysis (LDA) of selected otolith metals demonstrated that, even despite large variability in the metal abundances detected in otolith between individuals within the test groups (cv = 1.00), it is possible to discriminate between fish exposed to different crude oils using multivariate analysis of their otolith microchemistry.

MV Wakashio grounding incident in Mauritius 2020: The world's first major spillage of Very Low Sulfur Fuel Oil.

Very Low Sulfur Fuel Oils (VSLFO, <0.5% S) are a new class of marine fuel oils, introduced to meet recent International Maritime Organization regulations. The MV Wakashio was reported to have released 1000 t of VLSFO when it grounded on a reef in Mauritius on 25th July 2020. A field sample of oily residue contaminating the Mauritian coast was collected on 16th August 2020 and compared with the Wakashio fuel oil. Both oils were analyzed for organic and elemental content, and stable isotope ratios δ13C and δ2H measured. Comprehensive two-dimensional gas chromatography with high-resolution mass spectrometry was used to identify and compare biomarkers resistant to weathering. The aromatic content in the VLSFO was relatively low suggesting that the potential for ecosystem harm arising from exposure to toxic components may be less than with traditional fuel oil spills. The Wakashio oil spill is, to our knowledge, the first documented spill involving VLSFO.

Discriminating source of oil contamination in teleost fish, Lates calcarifer, using multivariate analysis of a suite of physiological and behavioral biomarkers.

The release of petroleum hydrocarbons into the environment from natural seeps, well blowouts, pipeline leaks, shipping accidents and deliberate tank washing poses an ongoing threat to marine ecosystems. Distinguishing the source of oil contamination in exposed biota can be relatively straightforward if samples of the oil are available but, in their absence, such discrimination in fish poses a major challenge. The use of physiological and behavioral biomarker analysis provides a useful tool to describe sub-lethal effects of toxicant exposure. In this study we describe the responses of 12 biomarkers in Lates calcarifer (Asian seabass) following a 33-day dietary exposure (1%w/w) to heavy fuel oil (HFO) and to Montara, a typical Australian medium crude oil (MCO). Principal components analysis was used to differentiate between fish exposed to HFO from those exposed to MCO. Inferences can be made about the composition of an oil from the biomarker profiles produced in exposed fish.

Natural attenuation of legacy hydrocarbon spills in pristine soils is feasible despite difficult environmental conditions in the monsoon tropics.

The Kimberley region of Western Australia is a National Heritage listed region that is internationally recognised for its environmental and cultural significance. However, petroleum spills have been reported at a number of sites across the region, representing an environmental concern. The region is also characterised as having low soil nutrients, high temperatures and monsoonal rain - all of which may limit the potential for natural biodegradation of petroleum. Therefore, this work evaluated the effect of legacy petroleum hydrocarbons on the indigenous soil microbial community (across the domains Archaea, Bacteria and Fungi) at three sites in the Kimberley region. At each site, soil cores were removed from contaminated and control areas and analysed for total petroleum hydrocarbons, soil nutrients, pH and microbial community profiling (using16S rRNA and ITS sequencing on the Illumina MiSeq Platform). The presence of petroleum hydrocarbons decreased microbial diversity across all kingdoms, altered the structure of microbial communities and increased the abundance of putative hydrocarbon degraders (e.g. Mycobacterium, Acremonium, Penicillium, Bjerkandera and Candida). Microbial community shifts from contaminated soils were also associated with an increase in soil nutrients (notably Colwell P and S). Our study highlights the long-term effect of legacy hydrocarbon spills on soil microbial communities and their diversity in remote, infertile monsoonal soils, but also highlights the potential for natural attenuation to occur in these environments.

Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous.

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

Structure and function of Shark Bay microbial communities following tropical cyclone Olwyn: A metatranscriptomic and organic geochemical perspective.

Shark Bay, Western Australia, is episodically impacted by tropical cyclones. During 2015, the region was hit by a category 3 cyclone, "severe tropical cyclone Olywn," leading to the formation of a black sludge in an intertidal zone harboring microbial mats and microbialites. Upon returning to the impacted site 12 months later, the black sludge deposit was still recognizable between the microbialite columns and mucilaginous cobbles near the shoreline in the impacted area. Metatranscriptomic and organic geochemical analyses were carried out on the cyclone-derived materials and impacted microbial mat communities to unravel the structure, function, and potential preservation of these deposits following a tropical cyclone. It was found that samples derived from the black sludge contained low relative abundances of cyanobacteria but had higher proportions of heterotrophic and anaerobic microorganisms (e.g., methanogens and sulfate-reducing bacteria). Increased metabolic activity by these microorganisms (e.g., sulfate reduction and organic matter degradation) is thought to drive calcium carbonate precipitation and helps in mat preservation. Comparison of the aliphatic biomarker by gas chromatography-mass spectrometry (GC-MS) analyses showed that C25  highly branched isoprenoid (HBI) alkenes were significantly higher in the cyclone-derived materials attributed to the relocation of subtidal sediments containing HBI-producing diatom communities by the tropical cyclone. Raney nickel desulfurization of the polar fraction extracted from a mucilaginous cobble revealed sulfur-bound hopanoids and a series of benzohopanes. The presence of these compounds could be indicative of microbial matter that has been influenced by the tropical cyclone which may have caused elevated levels of water column anoxia promoting increased sulfurization of the organic matter to occur.

Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem.

Groundwaters host vital resources playing a key role in the near future. Subterranean fauna and microbes are crucial in regulating organic cycles in environments characterized by low energy and scarce carbon availability. However, our knowledge about the functioning of groundwater ecosystems is limited, despite being increasingly exposed to anthropic impacts and climate change-related processes. In this work we apply novel biochemical and genetic techniques to investigate the ecological dynamics of an Australian calcrete under two contrasting rainfall periods (LR-low rainfall and HR-high rainfall). Our results indicate that the microbial gut community of copepods and amphipods experienced a shift in taxonomic diversity and predicted organic functional metabolic pathways during HR. The HR regime triggered a cascade effect driven by microbes (OM processors) and exploited by copepods and amphipods (primary and secondary consumers), which was finally transferred to the aquatic beetles (top predators). Our findings highlight that rainfall triggers ecological shifts towards more deterministic dynamics, revealing a complex web of interactions in seemingly simple environmental settings. Here we show how a combined isotopic-molecular approach can untangle the mechanisms shaping a calcrete community. This design will help manage and preserve one of the most vital but underrated ecosystems worldwide.

Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea.

The vertical distribution of subseafloor archaeal communities is thought to be primarily controlled by in situ conditions in sediments such as the availability of electron acceptors and donors, although sharp community shifts have also been observed at lithological boundaries suggesting that at least a subset of vertically stratified Archaea form a long-term genetic record of coinciding environmental conditions that occurred at the time of sediment deposition. To substantiate this possibility, we performed a highly resolved 16S rRNA gene survey of vertically stratified archaeal communities paired with paleo-oceanographic proxies in a sedimentary record from the northern Red Sea spanning the last glacial-interglacial cycle (i.e., marine isotope stages 1-6; MIS1-6). Our results show a strong significant correlation between subseafloor archaeal communities and drastic paleodepositional changes associated with glacial low vs. interglacial high stands (ANOSIM; R = .73; p = .001) and only a moderately strong correlation with lithological changes. Bathyarchaeota, Lokiarchaeota, MBGA, and DHVEG-1 were the most abundant identified archaeal groups. Whether they represented ancient cell lines from the time of deposition or migrated to the specific sedimentary horizons after deposition remains speculative. However, we show that the majority of sedimentary archaeal tetraether membrane lipids were of allochthonous origin and not produced in situ. Slow post-burial growth under energy-limited conditions would explain why the downcore distribution of these dominant archaeal groups still indirectly reflect changes in the paleodepositional environment that prevailed during the analyzed marine isotope stages. In addition, archaea seeded from the overlying water column such as Thaumarchaeota and group II and III Euryarchaeota, which were likely not have been able to subsist after burial, were identified from a lower abundance of preserved sedimentary DNA signatures, and represented direct markers of paleoenvironmental changes in the Red Sea spanning the last six marine isotope stages.

Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses.

Microbial mat communities possess extensive taxonomic and functional diversity, which drive high metabolic rates and rapid cycling of major elements. Modern microbial mats occurring in hypersaline environments are considered as analogs to extinct geobiological formations dating back to ∼ 3.5 Gyr ago. Despite efforts to understand the diversity and metabolic potential of hypersaline microbial mats in Shark Bay, Western Australia, there has yet to be molecular analyses at the transcriptional level in these microbial communities. In this study, we generated metatranscriptomes for the first time from actively growing mats comparing the type of mat, as well as the influence of diel and seasonal cycles. We observed that the overall gene transcription is strongly influenced by microbial community structure and seasonality. The most transcribed genes were associated with tackling the low nutrient conditions by the uptake of fatty acids, phosphorus, iron, and nickel from the environment as well as with protective mechanisms against elevated salinity conditions and to prevent build-up of ammonium produced by nitrate reducing microorganisms. A range of pathways involved in carbon, nitrogen, and sulfur cycles were identified in mat metatranscriptomes, with anoxygenic photosynthesis and chemoautotrophy using the Arnon-Buchanan cycle inferred as major pathways involved in the carbon cycle. Furthermore, enrichment of active anaerobic pathways (e.g., sulfate reduction, methanogenesis, Wood-Ljungdahl) in smooth mats corroborates previous metagenomic studies and further advocates the potential of these communities as modern analogs of ancient microbialites.