Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.     

Population dynamics of the lichen genus Bulbothrix Hale as potential bioindicators of 'time-since-last-fire' in the cerrado of the Distrito Federal, central Brazil

This paper investigates the potential use of the corticolous lichen genus Bulbothrix Hale as a bioindicator of ‘time-since-last-fire’ in the cerrado (savannas) of central Brazil. Work was carried out at the Reserva Ecológica do IBGE and the Jardim Botãnico de Brasilia, 33 km outside Brasilia D.F., in plots of cerrado denso with known fire histories within the ‘Fire Project’ area. Measurements of abundance and thallus size were taken of all Bulbothrix individuals encountered up to 2 m on the trunks of three phorophyte species. The results show that abundances and thalli sizes of the Bulbothrix populations can be correlated with the ‘time-since-last-fire’ that had occurred in each of the plots. This study shows that is is possible to use characteristics of specific lichen populations as bioindicators of fire history.     

Effects of abandoned Eucalyptus plantations on lizard communities in the Brazilian Cerrado

The rapid expansion of human altered landscapes affects biodiversity on every continent. A fundamental goal of conservation biologists is to understand why certain species are at risk of extinction while others are able to persist in human altered landscapes. Afforestation, the conversion of unforested lands to planted forest, is rapidly altering many natural landscapes worldwide. In the Cerrado (Brazilian savanna), a global biodiversity hotspot, a shortage of government incentives has the landscape riddled with abandoned plantation forests that are not subject to active restoration projects. Studies investigating the impacts of abandoned plantations on biodiversity are strikingly limited. We examine the effects of abandoned Eucalyptus plantations on the structure of Cerrado lizard communities. We assessed changes in lizard capture, richness and equitability along cerrado sensu stricto—Eucalyptus transects. Our results indicate abandoned Eucalyptus plantations have subsets of Cerrado species persisting with a great loss of endemic species. The cerrado sensu stricto—Eucalyptus linear transect analysis demonstrated distance from native habitat is positively correlated with loss of biodiversity. We performed correspondence analyses to summarize the variation in species captures across different sites, habitats and pitfall array positions. These analyses depicted strong species associations between habitats and their pitfall array positions. This study is the first to show the negative impacts of abandoned Eucalyptus plantations on Cerrado lizard communities, serving as a cautionary tale of Cerrado biodiversity non-resilience in abandoned Eucalyptus plantations. Mitigation requires that abandoned Eucalyptus plantations are made more suitable to Cerrado lizards by implementing targeted habitat heterogeneity restoration.     

The root to shoot ratio of trees from open- and closed-canopy cerrado in south-eastern Brazil

Background: The Brazilian savanna, or Cerrado, has been described as an ‘upside-down forest’, with higher below-ground than above-ground biomass. The cerrado vegetation, ranging from open grasslands to forests, comprises a wide range of ecological conditions and plant biomass.

Aims: To determine if and how root:shoot ratio in 102 trees differed between open- (cerrado sensu stricto) and closed-canopy cerrado (cerradão) within the same region in south-eastern Brazil.

Methods: Differences in root:shoot ratios and environmental conditions between the two cerrado types were examined, by uprooting and weighing trees from different species and functional groups.

Results: Root:shoot ratio was higher in the open than in the closed cerrado, especially among deciduous species. Root:shoot ratio in the open cerrado was lower than reported for the same cerrado type in central Brazil. Soil fertility did not differ between cerrado types, but soil water was lower and light availability was higher in the open cerrado.

Conclusions: The lower root:shoot ratio in closed than in open cerrado is probably a response to lower light and higher soil water availability, and/or to less frequent fires. Estimates of above-ground carbon storage alone significantly underestimate the carbon stock in open relative to closed cerrado.     

Molecular phylogenetic diversity of bacteria associated with soil of the savanna-like Cerrado vegetation

The Brazilian savanna-like vegetation of Cerrado is rapidly being converted to pasture and agricultural fields. A 16S rDNA-based approach was taken to study the bacterial community associated with the soil of a native cerrado area (sensu stricto) and an area that has been converted to pasture. The bacterial group most abundantly identified in cerrado sensu stricto soil was the alpha-Proteobacteria while in cerrado converted to pasture the Actinobacteria were the most abundant. Rarefaction curves indicate that the species richness of cerrado sensu stricto is greater than that of cerrado converted to pasture. Furthermore, lineage-through-time plots show that the expected richness of species present in cerrado sensu stricto soil is approximately 10 times greater than that of cerrado converted to pasture.     

Novel Euryarchaeotal Lineages Detected on Rice Roots and in the Anoxic Bulk Soil of Flooded Rice Microcosms

Because excised, washed roots of rice (Oryza sativa) immediately produce CH₄ when they are incubated under anoxic conditions (P. Frenzel and U. Bosse, FEMS Microbiol. Ecol. 21:25–36, 1996), we employed a culture-independent molecular approach to identify the methanogenic microbial community present on roots of rice plants. Archaeal small-subunit rRNA-encoding genes were amplified directly from total root DNA by PCR and then cloned. Thirty-two archaeal rice root (ARR) gene clones were randomly selected, and the amplified primary structures of ca. 750 nucleotide sequence positions were compared. Only 10 of the environmental sequences were affiliated with known methanogens; 5 were affiliated with Methanosarcina spp., and 5 were affiliated with Methanobacterium spp. The remaining 22 ARR gene clones formed four distinct lineages (rice clusters I through IV) which were not closely related to any known cultured member of the Archaea. Rice clusters I and II formed distinct clades within the phylogenetic radiation of the orders “Methanosarcinales” and Methanomicrobiales. Rice cluster I was novel, and rice cluster II was closely affiliated with environmental sequences obtained from bog peat in northern England. Rice cluster III occurred on the same branch as Thermoplasma acidophilum and marine group II but was only distantly related to these taxa. Rice cluster IV was a deep-branching crenarchaeotal assemblage that was closely related to clone pGrfC26, an environmental sequence recovered from a temperate marsh environment. The use of a domain-specific oligonucleotide probe in a fluorescent in situ hybridization analysis revealed that viable members of the Archaea were present on the surfaces of rice roots. In addition, we describe a novel euryarchaeotal main line of descent, designated rice cluster V, which was detected in anoxic rice paddy soil. These results indicate that there is an astonishing richness of archaeal diversity present on rice roots and in the surrounding paddy soil.     

Diversity of soil fungal communities of Cerrado and its closely surrounding agriculture fields

Cerrado is a savanna-like region that covers a large area of Brazil. Despite its biological importance, the Cerrado has been the focus of few microbial diversity studies. A molecular approach was chosen to characterize the soil fungal communities in four areas of the Cerrado biome: a native Cerrado, a riverbank forest, an area converted to a soybean plantation, and an area converted to pasture. Global diversity of fungal communities in each area was assessed through Ribosomal intergenic spacer analysis which revealed remarkable differences among the areas studied. Sequencing of approximately 200 clones containing 18S rDNA sequences from each library was performed and, according to the genetic distance between sequences, these were assigned to operational taxonomic units (OTUs). A total of 75, 85, 85, and 70 OTUs were identified for the native Cerrado, riverbank forest, pasture, and soybean plantation, respectively. Analysis of sequences using a similarity cutoff value of 1% showed that the number of OTUs for the native Cerrado area was reduced by 35%; for the soybean plantation, a reduction by more than 50% was observed, indicating a reduction in fungal biodiversity associated with anthropogenic activity. This is the first study demonstrating the anthropogenic impact on Cerrado soil fungal diversity.     

Trait diversity on the phylogeny of cerrado woody species

During the Neogene, the Brazilian cerrado became established as a large‐scale vegetation type. Cerrado lineages started to diversify less than 10 million years ago, coinciding with the rise to dominance of flammable C₄ grasses and the expansion of the savanna biome. Cerrado lineages are strongly associated with adaptations to fire and have sister groups in fire‐free nearby forests, implying that the cerrado formed in situ via adaptive shifts to resist fire. By including phylogeny into the analysis of biological traits, we investigated trait diversity of cerrado woody species in a phylogenetic context, sampling a cerrado site in central Brazil. Decomposing trait diversity along the nodes of a phylogenetic tree of cerrado woody species, we found that the rate of trait diversification was higher in the past, coinciding with the major species diversification of angiosperms in mid‐Cretaceous, long before the cerrado originated. Some more recent adaptive shifts to resist fire, however, must have occurred during the origin and expansion of the cerrado woody flora. Analysing values of each trait separately at the tips of the phylogenetic tree, we found that most trait values were randomly distributed, probably because we analysed only species that had already been filtered by drought, fire, and soil. Analysing values of all traits simultaneously at the tips, we found close to root events and broad, macro‐evolutionary patterns, called ‘global structures’, opposing some lineages, especially Fabaceae and Myrtaceae, with different ecological strategies. Fabaceae presented compound, large, tender leaves, with high nitrogen content due to symbiosis with nitrogen‐fixing bacteria, and Myrtaceae presented simple, small, tough leaves, with low nitrogen and high potassium content. We also found relatively recent events that induced divergence of the evolutionary strategies close to the tips, called ‘local structures’, involving more recent changes in most lineages.     

Biological functioning of Brazilian Cerrado soils under different vegetation types

Aims

Over a 2?year period, we compared the soil biological functioning (SBF) of Cerrado physiognomies ranging from grassland-savannic to forest formations, sampling in the middle of the dry and rainy seasons.

Methods

Soil samples were collected at two depths (0 to 5?cm and 5 to 20?cm) under the following physiognomies: Campo Sujo, Cerrado Ralo, Cerrado sensu stricto, Cerrad?o and Mata de Galeria. The SBF was represented by the simultaneous analyses of microbial biomass carbon, soil basal respiration and the activity of enzymes linked to the C, P and S cycles (β-glucosidase, acid phosphatase and arylsulfatase, respectively).

Results

The results demonstrated that Cerrado physiognomies are a major determinant of SBF patterns. The forest-like physiognomies (Mata de Galeria and Cerrad?o) presented the highest biomass and activity compared to the grassland (Campo Sujo) and savanna physiognomies (Cerrado Ralo and Cerrado sensu stricto). These differences were more evident in the topsoil layer (0 to 5?cm), and the seasonal effect on the SBF of the Mata de Galeria and Cerrad?o was more pronounced than on the other physiognomies.

Conclusions

These results provide a benchmark for evaluating changes in SBF and related processes in Cerrado areas due to shifts toward agriculture and cattle production.     

Priming and microbial nutrient limitation in lowland tropical forest soils of contrasting fertility

Priming is an increase in soil organic carbon decomposition following input of labile organic carbon. In temperate soils where biological activity is limited commonly by nitrogen availability, priming is expected to occur through microbial acquisition of nitrogen from organic matter or stimulated activity of recalcitrant-carbon degrading microorganisms. However, these priming mechanisms have not yet been assessed in strongly weathered tropical forest soils where biological activity is often limited by the availability of phosphorus. We examined whether microbial nutrient limitation or community dynamics drive priming in three lowland tropical forest soils of contrasting fertility (‘low’, ‘mid’ and ‘high’) by applying C₄-sucrose (alone or in combination with nutrients; nitrogen, phosphorus and potassium) and measuring (1) the δ¹³C-signatures in respired CO₂ and in phospholipid fatty acid (PLFA) biomarkers, and (2) the activities of enzymes involved in nitrogen (N-acetyl β-glucosaminidase), phosphorus (phosphomonoesterase) and carbon (β-glucosidase, cellobiohydrolase, xylanase, phenol oxidase) acquisition from organic compounds. Priming was constrained in part by nutrient availability, because priming was greater when sucrose was added alone compared to when added with nutrients. However, the greatest priming with sucrose addition alone was detected in the medium fertility soil. Priming occurred in parallel with stimulated activity of phosphomonoesterase and phenol oxidase (but not N-acetyl β-glucosaminidase); when sucrose was added with nutrients there were lower activities of phosphomonoesterase and phenol oxidase. There was no evidence according to PLFA δ¹³C-incorporation that priming was caused by specific groups of recalcitrant-carbon degrading microorganisms. We conclude that priming occurred in the intermediate fertility soil following microbial mineralization of organic nutrients (phosphorus in particular) and suggest that priming was constrained in the high fertility soil by high nutrient availability and in the low fertility soil by the low concentration of soil organic matter amenable to priming. This first study of priming mechanisms in tropical forest soils indicates that input of labile carbon can result in priming by microbial mineralization of organic nutrients, which has important implications for understanding the fate of organic carbon in tropical forest soils.     

Water availability determines physiognomic gradient in an area of low-fertility soils under Cerrado vegetation

Soil is one of the environmental elements to influence Cerrado vegetation. Aluminum toxicity of Cerrado soils is well known, but the importance of water availability is still to be understood, especially in Cerrado under wetter climates. We studied the association between Cerrado physiognomies (cerrado sensu stricto and cerradão) and morphological, chemical, physical, and physical–hydrical soil attributes at southwestern São Paulo State, Brazil. Characterization of soil morphology, classification and sample collection for particle-size distribution, and chemical and water-retention analyses were carried out in 15 permanent plots, where vegetation was characterized floristically and structurally. Simple correlation and canonical correspondence analyses were performed with soil data. Classification of soils (U.S. Soil Taxonomy) with very low clay contents was not able to separate soils under cerradão—forestry physiognomy—from those under cerrado sensu stricto—savannic physiognomy, even though it tends to distinguish soils under greater biomass from those under lower biomass physiognomies. High soil acidity of all studied soils and increased at the sites with greater contents of organic matter, mainly with the cerradão physiognomy, precluded Al toxicity as a cause of the physiognomic gradient within Cerrado. Clay content, microporosity, and residual and saturation moisture were the most significant soil attributes to correlate directly with the cerradão physiognomy, indicating that water availability is the main factor explaining the physiognomic gradient of Cerrado vegetation in a local scale, where climate and soil fertility do not vary spatially.     

Open vegetation formations (grasslands and savannahs) support a higher diversity of Cetoniidae (Insecta: Coleoptera) than forest formations in the brazilian Cerrado

Brazil has 22 genera and 75 species of Cetoniidae, with the Cerrado hosting the greatest diversity among Brazilian biomes. However, the diversity of groups among the different phytophysiognomies of the biome is not known. The objectives of this study are to assess Cetoniidae diversity and to verify the seasonality of these beetles in three Cerrado phytophysiognomies (gallery forest, cerrado sensu stricto, and campo sujo) located in three conservation units in Brasilia, Distrito Federal, Brazil. We collected adults monthly (October/2016 to September/2018) using 180 traps baited with bananas fermented with sugarcane juice, totaling 1,574 specimens, 8 genera, and 17 species. Cetoniidae diversity was higher in the phytophysiognomies with lower tree density (campo sujo and cerrado sensu stricto) than in gallery forests (forest formation), confirming our hypothesis that more open areas favor the dispersal of these insects due to their diurnal long-flying behavior. The seasonality of Cetoniidae was directly related to the precipitation, with higher numbers of individuals and species in the rainy season. However, the distribution varies among the phytophysiognomies, with aggregated distribution in campo sujo and gallery forest and dispersed in cerrado sensu stricto. Our results suggest that the Cetoniidae take advantage of the open Cerrado physiognomies to locate resources faster and with less energy expenditure, presenting higher diversity in these environments, despite the more ephemeral and dispersed food resources.

     

Assessment of microbial diversity bias associated with soil heterogeneity and sequencing resolution in pyrosequencing analyses

It is important to estimate the true microbial diversities accurately for a comparative microbial diversity analysis among various ecological settings in ecological models. Despite drastically increasing amounts of 16S rRNA gene targeting pyrosequencing data, sampling and data interpretation for comparative analysis have not yet been standardized. For more accurate bacterial diversity analyses, the influences of soil heterogeneity and sequence resolution on bacterial diversity estimates were investigated using pyrosequencing data of oak and pine forest soils with focus on the bacterial 16SrRNA gene. Soil bacterial community sets were phylogenetically clustered into two separate groups by forest type. Rarefaction curves showed that bacterial communities sequenced from the DNA mixtures and the DNAs of the soil mixtures hadmidsize richness compared with other samples. Richness and diversity estimates were highly variable depending on the sequence read numbers. Bacterial richness estimates (ACE, Chao 1 and Jack) of the forest soils had positive linear relationships with the sequence read number. Bacterial diversity estimates (NPShannon, Shannon and the inverse Simpson) of the forest soils were also positively correlated with the sequence read number. One-way ANOVA shows that sequence resolution significantly affected the a-diversity indices (P<0.05), but the soil heterogeneity did not (P>0.05). For an unbiased evaluation, richness and diversity estimates should be calculated and compared from subsets of the same size.     

Comparison of Diversities and Compositions of Bacterial Populations Inhabiting Natural Forest Soils

The diversity and composition of soil bacterial communities were compared among six Austrian natural forests, including oak-hornbeam, spruce-fir-beech, and Austrian pine forests, using terminal restriction fragment length polymorphism (T-RFLP, or TRF) analysis and sequence analysis of 16S rRNA genes. The forests studied differ greatly in soil chemical characteristics, microbial biomass, and nutrient turnover rates. The aim of this study was to relate these differences to the composition of the bacterial communities inhabiting the individual forest soils. Both TRF profiling and clone sequence analysis revealed that the bacterial communities in soils under Austrian pine forests, representing azonal forest types, were distinct from those in soils under zonal oak-hornbeam and spruce-fir-beech forests, which were more similar in community composition. Clones derived from an Austrian pine forest soil were mostly affiliated with high-G+C gram-positive bacteria (49%), followed by members of the α-Proteobacteria (20%) and the Holophaga/Acidobacterium group (12%). Clones in libraries from oak-hornbeam and spruce-fir-beech forest soils were mainly related to the Holophaga/Acidobacterium group (28 and 35%), followed by members of the Verrucomicrobia (24%) and the α-Proteobacteria (27%), respectively. The soil bacterial communities in forests with distinct vegetational and soil chemical properties appeared to be well differentiated based on 16S rRNA gene phylogeny. In particular, the outstanding position of the Austrian pine forests, which are determined by specific soil conditions, was reflected in the bacterial community composition.     

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. ‘Cerrado stricto sensu’ and ‘Cerradao’ share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while ‘Floresta decidual’ and ‘Campo graminoide’ show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.     

Regeneration patterns of <Emphasis Type="Italic">Polylepis subtusalbida</Emphasis> growing with the exotic trees <Emphasis Type="Italic">Pinus radiata</Emphasis> and <Emphasis Type="Italic">Eucalyptus globulus</Emphasis> at Parque Nacional Tunari,Bolivia

Dry semideciduous and deciduous forests occur only on calcium-rich soils and occupy almost 20% of the 200 million ha of the cerrado region of central Brazil. Other savanna physiognomies of woodlands and grasslands, and gallery forests generally occur on acid soils with low calcium levels. The literature on phytosociological aspects of such cerrado physiognomies is quite abundant whereas there is very little information on deciduous forests. Also lacking is information on soil fertility and its influence on species distribution. The objective of the present study was to study the distribution of native species within a dry deciduous forest in the Araguari river valley, Uberlândia, Minas Gerais as related to soil properties. A 1-ha sampling area, with no apparent difference in physiognomy, was divided into fifty 10 m × 20 m plots arrayed in 10 × 5 grid and all trees with a minimum circumference of 15 cm at 1.30 m height were surveyed. A composite soil sample was collected from 0 to 10 cm depth in each plot and soil pH, organic C and nutrient availability were determined. Cluster analysis based on soil chemical properties showed the existence of two distinct groups of plots. Further field examinations revealed that the forest was situated in an area of transition between mica schist and basalt parent materials, without any apparent difference in the forest physiognomy. The basalt-derived soil in 23 plots had significantly higher availability of Ca (47.0 cmol(+) kg^?1 soil), Mg (2.59), and K (0.96) than the mica schist derived soil (Ca—18.4, Mg—1.29, and K—0.66) in the remaining 27 plots, though both soils would be classified as eutrophic. A total of 59 species belonging to 27 families were encountered in the area as a whole, of which 36 were common to both soils. In total, 16 species occurred exclusively on the mica schist soil and 7 on the basaltic soil. Myracrodruon urundeuva Allem. (Anacardiaceae) and Tabebuia roseo-alba (Ridl.) Sandwith (Bignoniaceae) were species with high importance values in the forest as a whole. Though there was no significant difference in the diversity index between the two soils, the importance values of these species was larger in the basalt-derived soil with higher nutrient availability.     

Vertical profiles of microbial communities in perfluoroalkyl substance-contaminated soils

Poly- and perfluoroalkyl compounds (PFASs) are ubiquitous in the environment, but their influences on microbial community remain poorly known. The present study investigated the depth-related changes of archaeal and bacterial communities in PFAS-contaminated soils. The abundance and structure of microbial community were characterized using quantitative PCR and high-throughput sequencing, respectively. Microbial abundance changed considerably with soil depth. The richness and diversity of both bacterial and archaeal communities increased with soil depth. At each depth, bacterial community was more abundant and had higher richness and diversity than archaeal community. The structure of either bacterial or archaeal community displayed distinct vertical variations. Moreover, a higher content of perfluorooctane sulfonate (PFOS) could have a negative impact on bacterial richness and diversity. The rise of soil organic carbon content could increase bacterial abundance but lower the richness and diversity of both bacterial and archaeal communities. In addition, Proteobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Acidobacteria were the major bacterial groups, while Thaumarchaeota, Euryarchaeota, and unclassified Archaea dominated in soil archaeal communities. PFASs could influence soil microbial community.     

Spatial Heterogeneity of Crenarchaeal Assemblages within Mesophilic Soil Ecosystems as Revealed by PCR-Single-Stranded Conformation Polymorphism Profiling

Microbial ecologists have discovered novel rRNA genes (rDNA) in mesophilic soil habitats worldwide, including sequences that affiliate phylogenetically within the division Crenarchaeota (domain Archaea). To characterize the spatial distribution of crenarchaeal assemblages in mesophilic soil habitats, we profiled amplified crenarchaeal 16S rDNA sequences from diverse soil ecosystems by using PCR-single-stranded-conformation polymorphism (PCR-SSCP) analysis. PCR-SSCP profiles provide a measure of relative microbial diversity in terms of richness (number of different phylotypes as estimated from the number of unique PCR-SSCP peaks) and evenness (abundance of each phylotype as estimated from the relative area under a peak). Crenarchaeal assemblages inhabiting prairie, forest, turf, and agricultural soils were characterized at six sampling locations in southern and central Wisconsin. Phylotype richness was found to be more stable than evenness among triplicate samples collected within 30 cm at each sampling location. Transformation of the PCR-SSCP data by principal-component analysis, followed by statistical testing (analysis of variance [P < 0.0001] and least-significant-difference analysis [α = 0.5]), supported the conclusion that each location exhibited a unique profile. To further characterize the spatial distribution of crenarchaeal assemblages at one location, additional soil samples (a total of 30) were collected from agricultural field plots at the Hancock Agricultural Research Station. PCR-SSCP revealed a patchy spatial distribution of crenarchaeal assemblages within and between these plots. This mosaic of crenarchaeal assemblages was characterized by differences in phylotype evenness that could not be correlated with horizontal distance (15 to 30 m) or with depth (0 to 20 cm below the surface). Crenarchaeal 16S rDNA clone libraries were produced and screened for unique SSCP peaks. Clones representing the dominant phylotypes at each location were identified, sequenced, and found to group phylogenetically with sequences in crenarchaeal clade C1b.     

Phylogenetic Composition of Arctic Ocean Archaeal Assemblages and Comparison with Antarctic Assemblages

Archaea assemblages from the Arctic Ocean and Antarctic waters were compared by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified using the Archaea-specific primers 344f and 517r. Inspection of the DGGE fingerprints of 33 samples from the Arctic Ocean (from SCICEX submarine cruises in 1995, 1996, and 1997) and 7 Antarctic samples from Gerlache Strait and Dallman Bay revealed that the richness of Archaea assemblages was greater in samples from deep water than in those from the upper water column in both polar oceans. DGGE banding patterns suggested that most of the Archaea ribotypes were common to both the Arctic Ocean and the Antarctic Ocean. However, some of the Euryarchaeota ribotypes were unique to each system. Cluster analysis of DGGE fingerprints revealed no seasonal variation but supported depth-related differences in the composition of the Arctic Ocean Archaea assemblage. The phylogenetic composition of the Archaea assemblage was determined by cloning and then sequencing amplicons obtained from the Archaea-specific primers 21f and 958r. Sequences of 198 clones from nine samples covering three seasons and all depths grouped with marine group I Crenarchaeota (111 clones), marine group II Euryarchaeota (86 clones), and group IV Euryarchaeota (1 clone). A sequence obtained only from a DGGE band was similar to those of the marine group III Euryarchaeota.     

Quantifying the effects of nutrient addition on community diversity of serpentine vegetation using parametric entropy of type α

A desirable property of a diversity index is the so-called sum property. For a diversity index that possesses the sum property, such as species richness N, Shannon’s entropy H or Simpson’s index 1/D, the community diversity is decomposable into species-level patterns and the sum of single species diversities gives the pooled diversity of the species collection. In this paper, parametric diversity of type α is used to quantify how fertilizer applied to soil affects the relative contribution of species endemic or preferential to serpentine soils within a garigue plant community in Tuscany (Italy). Soil fertilizer significantly improved the biomass production of the original species pool without any significant colonization by alien species. However, the major biomass increments were experienced by species that are not exclusive to serpentine soils. In this view, the reduced abundance of species endemic or preferential to serpentine soils can be interpreted as a loss of ‘ecological quality’ of the analyzed community.