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We compared the microbial community composition in soils from the Brazilian Amazon with two contrasting histories; anthrosols and their adjacent non-anthrosol soils of the same mineralogy. The anthrosols, also known as the Amazonian Dark Earths or terra preta, were managed by the indigenous pre-Colombian Indians between 500 and 8,700 years before present and are characterized by unusually high cation exchange capacity, phosphorus (P), and calcium (Ca) contents, and soil carbon pools that contain a high proportion of incompletely combusted biomass as biochar or black carbon (BC). We sampled paired anthrosol and unmodified soils from four locations in the Manaus, Brazil, region that differed in their current land use and soil type. Community DNA was extracted from sampled soils and characterized by use of denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism. DNA bands of interest from Bacteria and Archaea DGGE gels were cloned and sequenced. In cluster analyses of the DNA fingerprints, microbial communities from the anthrosols grouped together regardless of current land use or soil type and were distinct from those in their respective, paired adjacent soils. For the Archaea, the anthrosol communities diverged from the adjacent soils by over 90%. A greater overall richness was observed for Bacteria sequences as compared with those of the Archaea. Most of the sequences obtained were novel and matched those in databases at less than 98% similarity. Several sequences obtained only from the anthrosols grouped at 93% similarity with the Verrucomicrobia, a genus commonly found in rice paddies in the tropics. Sequences closely related to Proteobacteria and Cyanobacteria sp. were recovered only from adjacent soil samples. Sequences related to Pseudomonas, Acidobacteria, and Flexibacter sp. were recovered from both anthrosols and adjacent soils. The strong similarities among the microbial communities present in the anthrosols for both the Bacteria and Archaea suggests that the microbial community composition in these soils is controlled more strongly by their historical soil management than by soil type or current land use. The anthrosols had consistently higher concentrations of incompletely combusted organic black carbon material (BC), higher soil pH, and higher concentrations of P and Ca compared to their respective adjacent soils. Such characteristics may help to explain the longevity and distinctiveness of the anthrosols in the Amazonian landscape and guide us in recreating soils with sustained high fertility in otherwise nutrient-poor soils in modern times.

Conical stromatolites are thought to be robust indicators of the presence of photosynthetic and phototactic microbes in aquatic environments as early as 3.5 billion years ago. However, phototaxis alone cannot explain the ubiquity of disrupted, curled, and contorted laminae in the crests of many Mesoproterozoic, Paleoproterozoic, and some Archean conical stromatolites. Here, we demonstrate that cyanobacterial production of oxygen in the tips of modern conical aggregates creates contorted laminae and submillimeter-to-millimeter-scale enmeshed bubbles. Similarly sized fossil bubbles and contorted laminae may be present only in the crestal zones of some conical stromatolites 2.7 billion years old or younger. This implies not only that cyanobacteria built Proterozoic conical stromatolites but also that fossil bubbles may constrain the timing of the evolution of oxygenic photosynthesis.

Natural organic matter (NOM) is a highly active component of soils and sediments, and plays an important role in global C cycling. However, NOM has defied molecular-level structural characterization, owing to variations along the decomposition continuum and its existence as highly functionalized polyelectrolytes. We conducted a comprehensive systematic overview of spectral signatures and peak positions of major organic molecules that occur as part of NOM using near-edge x-ray absorption fine structure (NEXAFS) spectroscopy. The spectra of carbohydrates and amino sugars show resonances between 289.10 and 289.59 eV, attributed to 1s-3p/sigma* transitions of O-alkyl (C-OH) moieties. They also exhibited distinct peaks between 288.42 and 288.74 eV, representing C 1s–pi*(C = O) transition from COOH functionalities. Amino acids produced a strong signal around 288.70 eV, which can be identified as a C 1s–pi*(C=O) transition of carboxyl/carbonyl (COOH/COO-) structures. Spectral features near 285.29 eV were ascribed to C 1s–pi*C=C transition of ring structure of aromatic amino acids, while spectra between 287.14 and 287.86 eV were attributed to C 1s–pi*(C-H) and C 1s–sigma*(C-H)/3p Rydberg-like excitations from CH and CH2 groups. Phenols and benzoquinone produced strong resonances between 285.08 and 285.37 eV, attributed to the pi* orbital of C (C 1s–pi*(C=C)) atoms connected to either C or H (C–H) in the aromatic ring. The next higher excitation common to both phenols and quinone appeared between 286.05 and 286.35 eV, and could be associated with C 1s–pi*(C=C) transitions of aromatic C bonded to O atom in phenols, and to C 1s–pi*(C=O) transitions from aromatic C connected to O atom (C-OH) in phenols or to a C=O in p-benzoquinone and some phenols with carbonyl structures, respectively. Nucleobases exhibited complex spectral features with pronounced resonances between 286.02 and 286.84 eV and between 288.01 and 288.70 eV. Molecular markers for black C (benzenecarboxylic acid and biphenyl-4,4'-dicarboxylic acid) exhibit sharp absorption bands between 285.01 and at 285.43 eV, possibly from C 1s–pi*(C=C) transition characteristic of C-H sites or unsaturated C (C=C) on aromatic ring structures. These aromatic carboxylic acids also exhibit broad peaks between 288.35 and 288.48 eV, reflecting C 1s–pi*(C=O) transition of carboxyl functional groups bonded to unsaturated C. This investigation provides a more comprehensive NEXAFS spectral library of biogeochemically relevant organic C compounds. The spectra of these reference organic compounds reveal distinct spectral features and peak positions at the C K-edge that are characteristic of the molecular orbitals bonding C atoms. Detailed structural information can be derived from these distinctive spectral features that could be used to build robust peak assignment criteria to exploit the chemical sensitivity of NEXAFS spectroscopy for in situ molecular-level spatial investigation and fingerprinting of complex organic C compounds in environmental samples.

SmcR family proteins were discovered in the 1990s as central regulators of quorum-sensing gene expression and later discovered to be conserved in all studied Vibrio species. SmcR homologs regulate a wide range of genes involved in pathogenesis, including but not limited to genes involved in biofilm production and toxin secretion. As archetypal members of the broad class of TetR-type transcription factors, each SmcR-type protein has a predicted ligand-binding pocket. However, no native ligand has been identified for these proteins that control their function as regulators. Here, we used SmcR-specific chemical inhibitors to determine that ligand binding drives proteolytic degradation in vivo , providing the first demonstration of SmcR function connected to ligand binding for this historical protein family.

X-ray 3D tomographic techniques are powerful tools for investigating the morphology and internal structures of specimens. A common strategy for obtaining 3D tomography is to capture a series of 2D projections from different X-ray illumination angles of specimens mounted on a finely calibrated rotational stage. However, the reconstruction quality of 3D tomography relies on the precision and stability of the rotational stage, i.e. the accurate alignment of the 2D projections in the correct three-dimensional positions. This is a crucial problem for nano-tomographic techniques due to the non-negligible mechanical imperfection of the rotational stages at the nanometer level which significantly degrades the spatial resolution of reconstructed 3-D tomography. Even when using an X-ray micro-CT with a highly stabilized rotational stage, thermal effects caused by the CT system are not negligible and may cause sample drift. Here, we propose a markerless image auto-alignment algorithm based on an iterative method. This algorithm reduces the traditional projection matching method into two simplified matching problems and it is much faster and more reliable than traditional methods. This algorithm can greatly decrease hardware requirements for both nano-tomography and data processing and can be easily applied to other tomographic techniques, such as X-ray micro-CT and electron tomography.

Soil organic matter (SOM) is a fundamental component of soil and the global C cycle. We used C (1s) near-edge x-ray absorption fine structure (NEXAFS) and synchrotron-based Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy to speciate C and investigate the influence of land use on the composition of SOM in the humic substances extracted from clay and silt fractions. Soil samples were collected from natural forest, tea and Cupressus plantations and cultivated fields in Ethiopia. Carbon K-edge spectra revealed multiple C (1s) electron transitions in the fine structure of C NEXAFS region (284-290 eV) indicating the presence of aromatic-C, phenolic-C, aliphatic-C, carboxylic-C, and O-alkyl-C in the humic substances. It also exhibited good selectivity, where specific energy regions correspond to C in discrete functional groups. However, regions of slight overlap between 1s-3p/sigma* transition of aliphatic-C and 1s-pi* transition of carboxylic-C may not be excluded. Fourier transform infrared-attenuated total reflectance spectroscopy showed larger proportions of aromatic-C (25.5%, 21.9%) and asymmetric and symmetric aliphatic-C (19.7%, 15.2%) groups in the silt than in clay, respectively. However, smaller proportion of polysaccharides (19.3%, 11.5%) was obtained from the silt compared with clay. The proportions of phenols (20.7%, 20.4%), aliphatic deformation of CH2 or CH3 (13.1%, 14.5%), and carboxylic (9.8%, 8.3%) groups were of similar magnitude in both fractions. The proportion of polysaccharides decreased in the order: natural forests > plantations > cultivated fields, while recalcitrant aromatic-C increased in the order: natural forest < plantation < cultivation. Therefore, C (1s) NEXAFS and synchrotron-based FTIR-ATR spectroscopy are powerful, nondestructive techniques that can potentially be used not only to identify and fingerprint complex structural characteristics of organic C macromolecules but also to investigate the impact of long-term anthropogenic management on the composition and biogeochemical cycling of organic C in terrestrial ecosystems.

Methodological constraints limit the extent to which existing soil aggregation models explain carbon (C) stabilization in soil. We hypothesize that the physical infrastructure of microaggregates plays a major role in determining the chemistry of the occluded C and intimate associations between particulate C, chemically stabilized C and the soil mineral matrix. We employed synchrotron-based scanning transmission X-ray microscopy (STXM) coupled with near-edge X-ray absorption fine structure (C 1s-NEXAFS) spectroscopy to investigate the nanoscale physical assemblage and C chemistry of 150-micrometer microaggregates from a Kenyan Oxisol. Ultra-thin sections were obtained after embedding microaggregates in a sulfur block and sectioning on a cryo-microtome at -55°C. Principal component and cluster analyses revealed four spatially distinct features: pore surfaces, mineral matter, organic matter, and their mixtures. The occurrence of these features did not vary between exterior and interior locations; however, the degree of oxidation decreased while the complexity and occurrence of aliphatic C forms increased from exterior to interior regions of the microaggregate. At both locations, compositional mapping rendered a nanoscale distribution of oxidized C clogging pores and coating pore cavities on mineral surface. Hydrophobic organic matter of aromatic and aliphatic nature, representing particulate C forms appeared physically occluded in 2- to 5-micrometer pore spaces. Our findings demonstrate that organic matter in microaggregates may be found as either oxidized C associated with mineral surfaces or aromatic and aliphatic C in particulate form. Using STXM and C 1s-NEXAFS we are for the first time able to resolve the nanoscale biogeocomplexity of unaltered soil microaggregates.

Thin, filamentous, non-heterocystous, benthic cyanobacteria (Subsection III) from some marine, lacustrine and thermal environments aggregate into macroscopic cones and conical stromatolites. We investigate the uptake and storage of inorganic carbon by cone-forming cyanobacteria from Yellowstone National Park using high-resolution stable isotope mapping of labeled carbon (H(13)CO3 (-)) and immunoassays. Observations and incubation experiments in actively photosynthesizing enrichment cultures and field samples reveal the presence of abundant cyanophycin granules in the active growth layer of cones. These ultrastructurally heterogeneous granules rapidly accumulate newly fixed carbon and store 18% of the total particulate labeled carbon after 120 mins of incubation. The intracellular distribution of labeled carbon during the incubation experiment demonstrates an unexpectedly large contribution of PEP carboxylase to carbon fixation, and a large flow of carbon and nitrogen toward cyanophycin in thin filamentous, non-heterocystous cyanobacteria. This pattern does not occur in obvious response to a changing N or C status. Instead, it may suggest an unusual interplay between the regulation of carbon concentration mechanisms and accumulation of photorespiratory products that facilitates uptake of inorganic C and reduces photorespiration in the dense, surface-attached communities of cyanobacteria from Subsection III.

We investigated speciation, oxidative state changes, and long‐ and short‐term molecular‐level dynamics of organic S after 365 d of aerobic incubation with and without the addition of sugarcane residue using XANES spectroscopy. Soil samples were collected from the upper 15 cm of undisturbed grasslands since 1880, from undisturbed grasslands since 1931, and from cultivated fields since 1880 in the western United States. We found three distinct groups of organosulfur compounds in these grassland‐derived soils: (i) strongly reduced (S0 to S1+) organic S that encompasses thiols, monosulfides, disulfides, polysulfides, and thiophenes; (ii) organic S in intermediate oxidation (S2+ to S5+) states, which include sulfoxides and sulfonates; and (iii) strongly oxidized (S6+) organic S, which comprises ester–SO4–S. The first two groups represent S directly linked to C and accounted for 80% of the total organic S detected by XANES from the undisturbed soils. Aerobic incubation without the addition of sugarcane residue led to a 21% decline in organanosulfur compounds directly linked to C and to up to an 82% increase inorganic S directly bonded to O. Among the C‐bonded S compounds, low‐valence thiols, sulfides, thiophenic S, and intermediate‐valence sulfoxide S seem to be highly susceptible to microbial attack and may represent the most reactive components of organic S pool in these grassland soils. Sulfonate S exhibited a much lower short‐term reactivity. The incorporation of sugarcane residue resulted in an increase in organosulfur compounds directly bonded to C at the early stage of incubation. However, similar to soils incubated without residue addition, the proportion of organic S directly linked to C continued to decline with increasing duration of aerobic incubation, whereas the proportion of organic S directly bonded to O showed a steady rise.

Some modern filamentous oxygenic photosynthetic bacteria (cyanobacteria) form macroscopic tufts, laminated cones and ridges that are very similar to some Archean and Proterozoic stromatolites. However, it remains unclear whether microbes that constructed Archean clumps, tufts, cones and ridges also produced oxygen. Here, we address this question by examining the physiology of cyanobacterial clumps, aggregates ~0.5 mm in diameter that initiate the growth of modern mm- and cm-scale cones. Clumps contain more particulate organic carbon in the form of denser, bowed and bent cyanobacterial filaments, abandoned sheaths and non-cyanobacterial cells relative to the surrounding areas. Increasing concentrations of oxygen in the solution enhance the bending of filaments and the persistence of clumps by reducing the lateral migration of filaments away from clumps. Clumped mats in oxic media also release less glycolate, a soluble photorespiration product, and retain a larger pool of carbon in the mat. Clumping thus benefits filamentous mat builders whose incorporation of inorganic carbon is sensitive to oxygen. The morphogenetic sequence of mm-scale clumps, reticulate ridges and conical stromatolites from the 2.7 Ga Tumbiana Formation likely records similar O2-dependent behaviors, preserving currently the oldest morphological signature of oxygenated environments on Early Earth.