Phytohormones,Rhizobium mutants,and nodulation in legumes. IV. Auxin metabolites in pea root nodules

High specific activity [³H]indole-3-acetic acid (IAA) was applied directly to root nodules of intact pea plants. After 24 h, radioactivity was detected in all plant tissues. In nodule and root tissue, only 2–3% of³H remained as IAA, and analysis by thin layer chromatography suggested that indole-3-acetyl-L-aspartic acid (IAAsp) was a major metabolite. The occurrence of IAAsp in pea root and nodule tissue was confirmed unequivocally by gas chromatography-mass spectrometry (GC-MS). The following endogenous indole compounds were also unequivocally identified in pea root nodules by GC-MS: IAA, indole-3-pyruvic acid, indole-3-lactic acid, indole-3-propionic acid, indole-3-butyric acid, and indole-3-carboxylic acid. Evidence of the occurrence of indole-3-methanol was also obtained. With the exception of IAA and indole-3-propionic acid, these compounds have not previously been unequivocally identified in a higher plant tissue.     

Phytohormones,Rhizobium mutants, and nodulation in legumes. IV. Auxin metabolites in pea root nodules

High specific activity [³H]indole-3-acetic acid (IAA) was applied directly to root nodules of intact pea plants. After 24 h, radioactivity was detected in all plant tissues. In nodule and root tissue, only 2–3% of³H remained as IAA, and analysis by thin layer chromatography suggested that indole-3-acetyl-L-aspartic acid (IAAsp) was a major metabolite. The occurrence of IAAsp in pea root and nodule tissue was confirmed unequivocally by gas chromatography-mass spectrometry (GC-MS). The following endogenous indole compounds were also unequivocally identified in pea root nodules by GC-MS: IAA, indole-3-pyruvic acid, indole-3-lactic acid, indole-3-propionic acid, indole-3-butyric acid, and indole-3-carboxylic acid. Evidence of the occurrence of indole-3-methanol was also obtained. With the exception of IAA and indole-3-propionic acid, these compounds have not previously been unequivocally identified in a higher plant tissue.     

Bacteriohopanepolyols across environmental gradients in Lake Vanda,Antarctica

Bacteriohopanepolyols (BHPs) are bacterial membrane lipids that may be used as biological or environmental biomarkers. Previous studies have described the diversity, distribution, and abundance of BHPs in a variety of modern environments. However, the regulation of BHP production in polar settings is not well understood. Benthic microbial mats from ice‐covered lakes of the McMurdo Dry Valleys, Antarctica provide an opportunity to investigate the sources, physiological roles, and preservation of BHPs in high‐latitude environments. Lake Vanda is one of the most stable lakes on Earth, with microbial communities occupying specific niches along environmental gradients. We describe the influence of mat morphology and local environmental conditions on the diversity and distribution of BHPs and their biological sources in benthic microbial mats from Lake Vanda. The abundance and diversity of C‐2 methylated hopanoids (2‐MeBHP) are of particular interest, given that their stable degradation products, 2‐methylhopanes, are among the oldest and most prevalent taxonomically informative biomarkers preserved in sedimentary rocks. Furthermore, the interpretation of sedimentary 2‐methylhopanes is of great interest to the geobiology community. We identify cyanobacteria as the sole source of 2‐MeBHP in benthic microbial mats from Lake Vanda and assess the hypothesis that 2‐MeBHP are regulated in response to a particular environmental variable, namely solar irradiance.     

Carbon and sulfur isotopic signatures of ancient life and environment at the microbial scale: Neoarchean shales and carbonates

An approach to coordinated, spatially resolved, in situ carbon isotope analysis of organic matter and carbonate minerals, and sulfur three‐ and four‐isotope analysis of pyrite with an unprecedented combination of spatial resolution, precision, and accuracy is described. Organic matter and pyrite from eleven rock samples of Neoarchean drill core express nearly the entire range of δ¹³C, δ³⁴S, Δ³³S, and Δ³⁶S known from the geologic record, commonly in correlation with morphology, mineralogy, and elemental composition. A new analytical approach (including a set of organic calibration standards) to account for a strong correlation between H/C and instrumental bias in SIMS δ¹³C measurement of organic matter is identified. Small (2–3 μm) organic domains in carbonate matrices are analyzed with sub‐permil accuracy and precision. Separate 20‐ to 50‐μm domains of kerogen in a single ~0.5 cm³ sample of the ~2.7 Ga Tumbiana Formation have δ¹³C = ?52.3 ± 0.1‰ and ?34.4 ± 0.1‰, likely preserving distinct signatures of methanotrophy and photoautotrophy. Pyrobitumen in the ~2.6 Ga Jeerinah Formation and the ~2.5 Ga Mount McRae Shale is systematically ¹³C‐enriched relative to co‐occurring kerogen, and associations with uraniferous mineral grains suggest radiolytic alteration. A large range in sulfur isotopic compositions (including higher Δ³³S and more extreme spatial gradients in Δ³³S and Δ³⁶S than any previously reported) are observed in correlation with morphology and associated mineralogy. Changing systematics of δ³⁴S, Δ³³S, and Δ³⁶S, previously investigated at the millimeter to centimeter scale using bulk analysis, are shown to occur at the micrometer scale of individual pyrite grains. These results support the emerging view that the dampened signature of mass‐independent sulfur isotope fractionation (S‐MIF) associated with the Mesoarchean continued into the early Neoarchean, and that the connections between methane and sulfur metabolism affected the production and preservation of S‐MIF during the first half of the planet's history.     

Lipid biomarker and carbon isotopic signatures for stromatolite-forming, microbial mat communities and Phormidium cultures from Yellowstone National Park

The molecular and isotopic compositions of lipid biomarkers from cultured filamentous cyanobacteria (Phormidium, also known as Leptolyngbya) have been used to investigate the community and trophic structure of photosynthetic mats from alkaline hot springs of the Lower Geyser Basin at Yellowstone National Park. We studied a shallow‐water coniform mat from Octopus Spring (OS) and a submerged, tufted mat from Fountain Paint Pots (FPP) and found that 2‐methylhopanepolyols and mid‐chain branched methylalkanes were diagnostic for cyanobacteria, whereas abundant wax esters were representative of the green non‐sulphur bacterial population. The biomarker composition of cultured Phormidium‐isolates varied, but was generally representative of the bulk mat composition. The carbon isotopic fractionation for biomass relative to dissolved inorganic carbon (DIC; ?_CO2) for cultures grown with 1% CO₂ ranged from 21.4 to 26.1 and was attenuated by diffusion limitation associated with filament aggregation (i.e. cell clumping). Isotopic differences between biomass and lipid biomarkers, and between lipid classes, depended on the cyanobacterial strain, but was positively correlated with overall fractionation. Acetogenic lipids (alkanes and fatty acids) were generally more depleted than isoprenoids (phytol and hopanoids). The δ¹³C_TOC for OS and FPP mats were somewhat heavier than for cultures (?16.9 and ?23.6, respectively), which presumably reflects the lower availability of DIC in the natural environment. The isotopic dispersions among cyanobacterial biomarkers, biomass and DIC reflected those established for culture experiments. The 7‐methyl‐ and 7,11‐dimethylheptadecanes were from 9 to 11 depleted relative to the bulk organic carbon, whereas 2‐methylhopanols derived from the oxidation‐reduction of bacteriohopanepolyol were enriched relative to branched alkanes by approximately 5–7. These isotopic relationships survived with depth and indicated that the relatively heavy isotopic composition of the OS mat resulted from diffusion limitation. This study supports the suggestion that culture studies can establish valid isotopic relationships for interpretation of trophic structure in modern and ancient microbial ecosystems.     

The “Dirty Ice” of the McMurdo Ice Shelf: Analogues for biological oases during the Cryogenian

The Cryogenian (~717–636 Ma) is characterized by widespread glaciation and dramatic fluctuations in biogeochemical cycling during the Sturtian and Marinoan glaciations. The Snowball Earth hypothesis posits that during this period, ice‐covered oceans of more or less global extent shut down or greatly diminished photosynthesis in the marine realm. However, rather than suffering a catastrophic loss of biodiversity, fossil evidence suggests that major eukaryotic lineages survived and, indeed, the end of the Cryogenian marks the onset of a rapid diversification of eukaryotic life. Persistence of diverse life forms through glaciations is thought to have occurred in supraglacial refugia although the exact nature and full extent of such habitats remain uncertain. We present further evidence for the diversity and characteristics of supraglacial ecosystems on the McMurdo Ice Shelf in Antarctica and suggest that refugia analogous to “dirty ice,” that is debris‐covered ice shelf ecosystems, potentially provided nutrient‐rich and long‐lasting biological Cryogenian oases. We also discuss how features of the McMurdo Ice Shelf indicate that mechanisms exist whereby material can be exchanged between the shallow sea floor and the surfaces of ice shelves along continental margins, providing vectors whereby ice shelf ecosystems can nourish underlying seafloor communities and vice versa.     

Active eukaryotes in microbialites from Highborne Cay,Bahamas, and Hamelin Pool (Shark Bay), Australia

Microbialites are organosedimentary structures that are formed through the interaction of benthic microbial communities and sediments and include mineral precipitation. These lithifying microbial mat structures include stromatolites and thrombolites. Exuma Sound in the Bahamas, and Hamelin Pool in Shark Bay, Western Australia, are two locations where significant stands of modern microbialites exist. Although prokaryotic diversity in these structures is reasonably well documented, little is known about the eukaryotic component of these communities and their potential to influence sedimentary fabrics through grazing, binding and burrowing activities. Accordingly, comparisons of eukaryotic communities in modern stromatolitic and thrombolitic mats can potentially provide insight into the coexistence of both laminated and clotted mat structures in close proximity to one another. Here we examine this possibility by comparing eukaryotic diversity based on Sanger and high-throughput pyrosequencing of small subunit ribosomal RNA (18S rRNA) genes. Analyses were based on total RNA extracts as template to minimize input from inactive or deceased organisms. Results identified diverse eukaryotic communities particularly stramenopiles, Alveolata, Metazoa, Amoebozoa and Rhizaria within different mat types at both locations, as well as abundant and diverse signatures of eukaryotes with <80% sequence similarity to sequences in GenBank. This suggests the presence of significant novel eukaryotic diversity, particularly in hypersaline Hamelin Pool. There was evidence of vertical structuring of protist populations and foraminiferal diversity was highest in bioturbated/clotted thrombolite mats of Highborne Cay.     

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche

Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (P-value<10⁻⁶); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.     

New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces

Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets.