Review of Soils in Archaeological Research by Vance T. Holliday

When I teach geoarchaeology, I tell students on the first day of class that "soils are the canvas for much of the archaeological record." Just as an artist's canvas holds and affects the paint, soils hold archaeological materials, and soil-forming processes strongly influence the preservation and spatial pattern of cultural deposits. Given this close relationship between soils and the material remains of humans, we have long needed a treatise that addresses all aspects of soils from an archaeological perspective. Vance Holliday's latest book, Soils in Archaeological Research, does this and more.

Amazonian Anthrosols Support Similar Microbial Communities that Differ Distinctly from Those Extant in Adjacent, Unmodified Soils of the Same Mineralogy

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.

Biogenic calcium phosphate transformation in soils over millennial time scales

Changes in bioavailability of phosphorus (P) during pedogenesis and ecosystem development have been shown for geogenic calcium phosphate (Ca-P). However, very little is known about long-term changes of biogenic Ca-P in soil. Long-term transformation characteristics of biogenic Ca-P were examined using anthropogenic soils along a chronosequence from centennial to millennial time scales. Phosphorus fractionation of Anthrosols resulted in overall consistency with the Walker and Syers model of geogenic Ca-P transformation during pedogenesis. The biogenic Ca-P (e.g., animal and fish bones) disappeared to 3% of total P within the first ca. 2,000 years of soil development. This change concurred with increases in P adsorbed on metal-oxides surfaces, organic P, and occluded P at different pedogenic time. Phosphorus K-edge X-ray absorption near-edge structure (XANES) spectroscopy revealed that the crystalline and therefore thermodynamically most stable biogenic Ca-P was transformed into more soluble forms of Ca-P over time. While crystalline hydroxyapatite (34% of total P) dominated Ca-P species after about 600-1,000 years, beta-tricalcium phosphate increased to 16% of total P after 900-1,100 years, after which both Ca-P species disappeared. Iron-associated P was observable concurrently with Ca-P disappearance. Soluble P and organic P determined by XANES maintained relatively constant (58-65%) across the time scale studied. Disappearance of crystalline biogenic Ca-P on a time scale of a few thousand years appears to be ten times faster than that of geogenic Ca-P.

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal beta-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal b-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

Metals and semi-metals in street soils of So Paulo city, Brazil

So Paulo is the largest city in Brazil and South America with about 20 million inhabitants in the metropolitan area, more than nine million motor vehicles and intense industrial activity, which are responsible for increasing pollution in the region. Nevertheless, little is known concerning metal and semi-metal content in the soils of this metropolitan region. This type of information could be extremely useful as a fingerprint of environmental pollution. The present study determined the elements As, Ba, Co, Cr, Sb, and Zn concentrations in soils adjacent to avenues of highly dense traffic in So Paulo city to assess their levels and possible sources. The analytical technique employed was Instrumental neutron activation analysis. The results showed, except for Co, concentration levels higher than the reference values for soils of So Paulo, according to the Environmental Protection Agency of the State of So Paulo guidelines. When compared to similar studies in other cities around the world, So Paulo soils presented higher levels, probably due to its high density traffic and industrial activity. The concentrations obtained for As and Cr indicate anthropogenic origin. The high levels of the traffic-related elements Ba, Sb, and Zn in soils nearby high density traffic avenues indicate they may originate from vehicular exhausts.

Lufaxin, a Novel Factor Xa Inhibitor From the Salivary Gland of the Sand Fly Lutzomyia longipalpis Blocks Protease-Activated Receptor 2 Activation and Inhibits Inflammation and Thrombosis In Vivo

Objective-Blood-sucking arthropods' salivary glands contain a remarkable diversity of antihemostatics. The aim of the present study was to identify the unique salivary anticoagulant of the sand fly Lutzomyia longipalpis, which remained elusive for decades. Methods and Results-Several L. longipalpis salivary proteins were expressed in human embryonic kidney 293 cells and screened for inhibition of blood coagulation. A novel 32.4-kDa molecule, named Lufaxin, was identified as a slow, tight, noncompetitive, and reversible inhibitor of factor Xa (FXa). Notably, Lufaxin's primary sequence does not share similarity to any physiological or salivary inhibitors of coagulation reported to date. Lufaxin is specific for FXa and does not interact with FX, Dansyl-Glu-Gly-Arg-FXa, or 15 other enzymes. In addition, Lufaxin blocks prothrombinase and increases both prothrombin time and activated partial thromboplastin time. Surface plasmon resonance experiments revealed that FXa binds Lufaxin with an equilibrium constant approximate to 3 nM, and isothermal titration calorimetry determined a stoichiometry of 1:1. Lufaxin also prevents protease-activated receptor 2 activation by FXa in the MDA-MB-231 cell line and abrogates edema formation triggered by injection of FXa in the paw of mice. Moreover, Lufaxin prevents FeCl3-induced carotid artery thrombus formation and prolongs activated partial thromboplastin time ex vivo, implying that it works as an anticoagulant in vivo. Finally, salivary gland of sand flies was found to inhibit FXa and to interact with the enzyme. Conclusion-Lufaxin belongs to a novel family of slow-tight FXa inhibitors, which display antithrombotic and anti-inflammatory activities. It is a useful tool to understand FXa structural features and its role in prohemostatic and proinflammatory events. (Arterioscler Thromb Vasc Biol. 2012;32:2185-2196.)

PHOSPHITE AS PHOSPHORUS SOURCE TO GRAIN YIELD OF COMMON BEAN PLANTS GROWN IN SOILS UNDER LOW OR ADEQUATE PHOSPHATE AVAILABILITY

The effects of foliar and soil applied phosphite on grain yield in common bean (Phaseolus vulgaris L.) grown in a weathered soil under low and adequate phosphate availability were evaluated. In the first experiment, treatments were composed of a 2 x 7 + 2 factorial scheme, with 2 soil P levels supplied as phosphate (40 e 200 mg P dm(-3) soil), 7 soil P levels supplied as phosphite (0-100 mg P dm(-3) soil), and 2 additional treatments (without P supply in soil, and all P supplied as phosphite). In the second experiment, treatments were composed of a 2 x 3 x 2 factorial scheme, with 2 soil phosphate levels (40 e 200 mg P dm(-3) soil), combined with 3 nutrient sources applied via foliar sprays (potassium phosphite, potassium phosphate, and potassium chloride as a control), and 2 foliar application numbers (single and two application). Additional treatments showed that phosphite is not P source for common bean nutrition. Phosphite supply in soil increased the P content in shoot (at full physiological maturity stage) and grains, but at the same time considerably decreased grain yield, regardless of the soil phosphate availability. Foliar sprays of phosphite decreased grain yield in plants grown under low soil phosphate availability, but no effect was observed in plants grown under adequate soil phosphate availability. In general, foliar sprays of phosphate did not satisfactorily improve grain yield of the common bean plants grown under low soil phosphate availability.

Convergent Adaptations: Bitter Manioc Cultivation Systems in Fertile Anthropogenic Dark Earths and Floodplain Soils in Central Amazonia

Shifting cultivation in the humid tropics is incredibly diverse, yet research tends to focus on one type: long-fallow shifting cultivation. While it is a typical adaptation to the highly-weathered nutrient-poor soils of the Amazonian terra firme, fertile environments in the region offer opportunities for agricultural intensification. We hypothesized that Amazonian people have developed divergent bitter manioc cultivation systems as adaptations to the properties of different soils. We compared bitter manioc cultivation in two nutrient-rich and two nutrient-poor soils, along the middle Madeira River in Central Amazonia. We interviewed 249 farmers in 6 localities, sampled their manioc fields, and carried out genetic analysis of bitter manioc landraces. While cultivation in the two richer soils at different localities was characterized by fast-maturing, low-starch manioc landraces, with shorter cropping periods and shorter fallows, the predominant manioc landraces in these soils were generally not genetically similar. Rather, predominant landraces in each of these two fertile soils have emerged from separate selective trajectories which produced landraces that converged for fast-maturing low-starch traits adapted to intensified swidden systems in fertile soils. This contrasts with the more extensive cultivation systems found in the two poorer soils at different localities, characterized by the prevalence of slow-maturing high-starch landraces, longer cropping periods and longer fallows, typical of previous studies. Farmers plant different assemblages of bitter manioc landraces in different soils and the most popular landraces were shown to exhibit significantly different yields when planted in different soils. Farmers have selected different sets of landraces with different perceived agronomic characteristics, along with different fallow lengths, as adaptations to the specific properties of each agroecological micro-environment. These findings open up new avenues for research and debate concerning the origins, evolution, history and contemporary cultivation of bitter manioc in Amazonia and beyond.

Additional scaled solutions to Richards' equation for infiltration and drainage

Warrick and Hussen developed in the nineties of the last century a method to scale Richards' equation (RE) for similar soils. In this paper, new scaled solutions are added to the method of Warrick and Hussen considering a wider range of soils regardless of their dissimilarity. Gardner-Kozeny hydraulic functions are adopted instead of Brooks-Corey functions used originally by Warrick and Hussen. These functions allow to reduce the dependence of the scaled RE on the soil properties. To evaluate the proposed method (PM), the scaled RE was solved numerically using a finite difference method with a fully implicit scheme. Three cases were considered: constant-head infiltration, constant-flux infiltration, and drainage of an initially uniform wet soil. The results for five texturally different soils ranging from sand to clay (adopted from the literature) showed that the scaled solutions were invariant to a satisfactory degree. However, slight deviations were observed mainly for the sandy soil. Moreover, the scaled solutions deviated when the soil profile was initially wet in the infiltration case or when deeply wet in the drainage condition. Based on the PM, a Philip-type model was also developed to approximate RE solutions for the constant-head infiltration. The model showed a good agreement with the scaled RE for the same range of soils and conditions, however only for Gardner-Kozeny soils. Such a procedure reduces numerical calculations and provides additional opportunities for solving the highly nonlinear RE for unsaturated water flow in soils. (C) 2011 Elsevier B.V. All rights reserved.

CHEMICAL AND BIOCHEMICAL PROPERTIES OF ARAUCARIA ANGUSTIFOLIA (BERT.) KTZE. FOREST SOILS IN THE STATE OF SAO PAULO

Araucaria angustifolia, commonly named Araucaria, is a Brazilian native species that is intensively exploited due to its timber quality. Therefore, Araucaria is on the list of species threatened by extinction. Despite the importance of soil for forest production, little is known about the soil properties of the highly fragmented Araucaria forests. This study was designed to investigate the use of chemical and biological properties as indicators of conservation and anthropogenic disturbance of Araucaria forests in different sampling periods. The research was carried out in two State parks of Sao Paulo: Parque Estadual Turistico do Alto do Ribeira and Parque Estadual de Campos de Jordao. The biochemical properties carbon and nitrogen in microbial biomass (MB-C and MB-N), basal respiration (BR), the metabolic quotient (qCO(2)) and the following enzyme activities: beta-glucosidase, urease, and fluorescein diacetate hydrolysis (FDA) were evaluated. The sampling period (dry or rainy season) influenced the results of mainly MB-C, MB-N, BR, and qCO(2). The chemical and biochemical properties, except K content, were sensitive indicators of differences in the conservation and anthropogenic disturbance stages of Araucaria forests. Although these forests differ in biochemical and chemical properties, they are efficient in energy use and conservation, which is shown by their low qCO(2), suggesting an advanced stage of succession.

Abundant and Stable Char Residues in Soils: Implications for Soil Fertility and Carbon Sequestration

Large-scale soil application of biochar may enhance soil fertility, increasing crop production for the growing human population, while also sequestering atmospheric carbon. But reaching these beneficial outcomes requires an understanding of the relationships among biochar's structure, stability, and contribution to soil fertility. Using quantitative C-13 nuclear magnetic resonance (NMR) spectroscopy, we show that Terra Preta soils (fertile anthropogenic dark earths in Amazonia that were enriched with char >800 years ago) consist predominantly of char residues composed of similar to 6 fused aromatic rings substituted by COO- groups that significantly increase the soils' cation-exchange capacity and thus the retention of plant nutrients. We also show that highly productive, grassland-derived soils in the U.S, (Mollisols) contain char (generated by presettlement fires) that is structurally comparable to char in the Terra Preta soils and much more abundant than previously thought (similar to 40-50% of organic C). Our findings indicate that these oxidized char residues represent a particularly stable, abundant, and fertility-enhancing form of soil organic matter.

Unconfined shear strength of compacted unsaturated plastic soils

A central goal in unsaturated soil mechanics research is to create a smooth transition between traditional soil mechanics approaches and an approach that is applicable to unsaturated soils. Undrained shear strength and the liquidity index of reconstituted or remoulded saturated soils are consistently correlated, which has been demonstrated by many studies. In the liquidity index range from 1 (at w(l)) to 0 (at w(p)), the shear strength ranges from approximately 2 kPa to 200 kPa. Similarly, for compacted soil, the shear strength at the plastic limit ranges from 150 kPa to 250 kPa. When compacted at their optimum water content, most soils have a suction that ranges from 20 kPa to 500 kPa; however, in the field, compacted materials are subjected to drying and wetting, which affect their initial suction and as a consequence their shear strength. Unconfined shear tests were performed on five compacted tropical soils and kaolin. Specimens were tested in the as-compacted condition, and also after undergoing drying or wetting. The test results and data from prior literature were examined, taking into account the roles of void ratio, suction, and relative water content. An interpretation of the phenomena that are involved in the development of the undrained shear strength of unsaturated soils in the contexts of soil water retention and Atterberg limits is presented, providing a practical view of the behaviour of compacted soil based on the concept of unsaturated soil. Finally, an empirical correlation is presented that relates the unsaturated state of compacted soils to the unconfined shear strength.

Description of Two New Sand Fly Species Related to Nyssomyia antunesi (Diptera, Psychodidae, Phlebotominae)

Both sexes of two new Brazilian phlebotomine sand flies of the genus Nyssomyia Barretto 1962 [= Lutzomyia (Nyssomyia) sensu Barretto], Nyssomyia delsionatali n. sp. and Nyssomyia urbinattii n. sp., presenting close affinity with Nyssomyia antunesi (Coutinho), are described and illustrated. N. delsionatali n. sp was captured on the edge of a riparian Amazonian forest on the Juruena river in the northwest of Mato Grosso state and N. urbinattii n. sp in a riparian Amazonian forest on the Teles Pires river between Mato Grosso and Para states. Some measurements of both sexes of N. antunesi and illustration of the male genitalia and the female spermathecae as well as an identi_cation key for males and females of the genus Nyssomyia are provided.

Cutting Edge: Brazilian Pemphigus Foliaceus Anti-Desmoglein 1 Autoantibodies Cross-React with Sand Fly Salivary LJM11 Antigen

The environmental factors that contribute to the development of autoimmune diseases are largely unknown. Endemic pemphigus foliaceus in humans, known as Fogo Selvagem (FS) in Brazil, is mediated by pathogenic IgG4 autoantibodies against desmoglein 1 (Dsg1). Clusters of FS overlap with those of leishmaniasis, a disease transmitted by sand fly (Lutzomyia longipalpis) bites. In this study, we show that salivary Ags from the sand fly, and specifically the LJM11 salivary protein, are recognized by FS Abs. Anti-Dsg1 monoclonal autoantibodies derived from FS patients also cross-react with LJM11. Mice immunized with LJM11 generate anti-Dsg1 Abs. Thus, insect bites may deliver salivary Ags that initiate a cross-reactive IgG4 Ab response in genetically susceptible individuals and lead to subsequent FS. Our findings establish a clear relationship between an environmental, noninfectious Ag and the development of potentially pathogenic autoantibodies in an autoimmune disease. The Journal of Immunology, 2012, 189: 1535-1539.