Carbon Stocks in Compartments of Soil Organic Matter 31 Years after Substitution of Native Cerrado Vegetation by Agroecosystems

ABSTRACT Changes in carbon stocks in different compartments of soil organic matter of a clayey Latossolo Vermelho Distrófico (Typic Haplustox), caused by the substitution of native savanna vegetation (cerrado sensu stricto) by agroecosystems, were assessed after 31 years of cultivation. Under native vegetation, a stock of 164.5 Mg ha-1 C was estimated in the 0.00-1.00 m layer. After 31 years of cultivation, these changes in soil C stocks were detected to a depth of 0.60 m. In the case of substitution of cerrado sensu stricto by no-tillage soybean-corn rotation, a reduction of at least 11 % of the soil C pools was observed. However, the adoption of no-tillage as an alternative to tillage with a moldboard plow (conventional system) reduced CO2 emissions by up to 12 %.

Community-wide plasmid gene mobilization and selection.

Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.

Abundance and diversity of soil mites of fragmented habitats in a biosphere reserve in Southern Nigeria

Soil samples were collected from the top 7.5 cm of soil in a Strict Natural Reserve (SNR), a surrounding buffer zone, a cassava farm and matured plantations of Gmelina, teak, and pine, so as to determine if plantation establishment and intensive cultivation affect the density and diversity of soil mites. Altogether, 41 taxonomic groups of mites were identified. The diversity and densities of mites in within the SNR, the buffer zone and the Gmelina were more than the diversity and densities in the cassava farm, teak and pine plantations. Each plantation had its own unique community structure which was different from the community structure in the SNR plot. The SNR plot and Gmelina were dominated by detritivorous cryptostigmatid mites unlike teak and pine which were dominated by predatory mesostigmatid and prostigmatid mites respectively. Low cryptostigmatid mite densities in the plantations and cassava farm were seen as a consequence of low fertility status of the soil, the evidence of which was revealed by soil pH and organic matter data.

Influence of repeated applications of glyphosate on its persistence and soil bioactivity

Pesticide degradation studies are essential to evaluate its impact in the environment and on non-target organisms. The effect of repeated soil applications of the herbicide glyphosate on its dissipation and on soil microorganisms was studied by radiometric and microbial techniques. Results indicated fast dissipation of the [14C]-glyphosate or [14C]metabolites extractable residues (half-life of 0.92±0.29 month), but increasing half-lives of total mineralization ranging from 2.2 to 3.4 months as the number of applications increased from 1 to 4. No significant correlation was found between 14CO2 production and dehydrogenase activity.

Effect of Bacillus thuringiensis on microbial functional groups in sorghum rhizosphere

The objective of this work was to assess the effect of two strains of Bacillus thuringiensis var. kurstaki on sorghum rhizosphere microorganisms. The strains were HD1, that produces the bioinsecticidal protein, and 407, that is a mutant non-producer. The strains do not influence microbial population, but reduce plant growth and improve mycorrhizal colonization and free living fixing N2 community.

Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis

Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity. From the NFA soil 134 clones were analyzed, while 116 clones were analyzed from the EAA soil samples. The sequences were compared with those online at the GenBank. Phylogenetic analyses revealed differences between the soil types and high diversity in both communities. Soil from the Eucalyptus spp. arboretum was found to have a greater bacterial diversity than the soil investigated from the native forest area.

Temporal changes of an alfalfa succession and related soil physical properties on the Loess Plateau, China

The objective of this work was to investigate the relationship between changes in the plant community and changes in soil physical properties and water availability, during a succession from alfalfa (Medicago sativa L.) to natural vegetation on the Loess Plateau, China. Data from a succession sere spanning 32 years were collated, and vegetative indexes were compared to changes related to soil bulk density and soil water storage. The alfalfa yield increased for approximately 7 years, then it declined and the alfalfa was replaced by a natural community dominated by Stipa bungeana that began to thrive about 10 years after alfalfa seeding. Soil bulk density increased over time, but the deterioration of the alfalfa was mainly ascribed to a severe reduction in soil water storage, which was lowest around the time when degradation commenced. The results indicated that water consumption by alfalfa could be reduced by reducing plant density. The analysis of the data also suggested that soil water recharge could be facilitated by rotating the alfalfa with other crops, natural vegetation, or bare soil.

DNA barcodes for soil animal taxonomy

The biodiversity of soil communities remains very poorly known and understood. Soil biological sciences are strongly affected by the taxonomic crisis, and most groups of animals in that biota suffer from a strong taxonomic impediment. The objective of this work was to investigate how DNA barcoding - a novel method using a microgenomic tag for species identification and discrimination - permits better evaluation of the taxonomy of soil biota. A total of 1,152 barcode sequences were analyzed for two major groups of animals, collembolans and earthworms, which presented broad taxonomic and geographic sampling. Besides strongly reflecting the taxonomic impediment for both groups, with a large number of species-level divergent lineages remaining unnamed so far, the results also highlight a high level (15%) of cryptic diversity within known species of both earthworms and collembolans. These results are supportive of recent local studies using a similar approach. Within an impeded taxonomic system for soil animals, DNA-assisted identification tools can facilitate and improve biodiversity exploration and description. DNA-barcoding campaigns are rapidly developing in soil animals and the community of soil biologists is urged to embrace these methods.

Why should we care about soil fauna?

The reasons why we care about soil fauna are related to their intrinsic, utilitarian and functional values. The intrinsic values embrace aesthetic or moral reasons for conserving below-ground biodiversity. Unfortunately, the protection of soil invertebrates has rarely been a criterion for avoiding changes in land use and management. Utilitarian, or direct use values, have been investigated more extensively for fungi, bacteria and marine invertebrates than for soil fauna. However, some traditional remedies, novel enzymes and pharmaceutical compounds have been derived from earthworms, termites and other groups, and gut symbionts may provide microbial strains with interesting properties for biotechnology. The functional importance of soil invertebrates in ecosystem processes has been a major focus of research in recent decades. It is suggested herein that it is rarely possible to identify the role of soil invertebrates as rate determinants of soil processes at plot and ecosystem scales of hectares and above because other biophysical controls override their effects. There are situations, however, where the activities of functional groups of soil animals, even of species, are synchronised in space or time by plant events, resource inputs, seasonality or other perturbations to the system, and their emergent effects are detectable as higher order controls.

A new method to simulate the hydrological state of soil under natural conditions

Micro, macro and mesofauna in the soil often respond to fluctuating environmental conditions, resulting in changes of abundance and community structure. Effects of changing soil parameters are normally determined with samples taken in the field and brought to the laboratory, i.e. where natural environmental conditions may not apply. We devised a method (STAFD - soil tubes for artificial flood and drought), which simulates the hydrological state of soil in situ using implanted cores. Control tubes were compared with treatment tubes in which floods of 15, 30, 60 and 90 days, and droughts of 60, 90 and 120 days were simulated in the field. Flooding and drought were found to reduce number of individuals in all soil faunal groups, but the response to drought was slower and not in proportion to the expected decrease of the water content. The results of the simulated floods in particular show the value of the STAFD method for the investigation of such extreme events in natural habitats.

Impact of direct seeding mulch-based cropping systems on soil nematodes in a long-term experiment in Madagascar

The objective of this work was to assess the effects of conventional tillage and of different direct seeding mulch-based cropping systems (DMC) on soil nematofauna characteristics. The long-term field experiment was carried out in the highlands of Madagascar on an andic Dystrustept soil. Soil samples were taken once a year during three successive years (14 to 16 years after installation of the treatments) from a 0-5-cm soil layer of a conventional tillage system and of three kinds of DMC: direct seeding on mulch from rotation soybean-maize residues; direct seeding of maize-maize rotation on living mulch of silverleaf (Desmodium uncinatum); direct seeding of bean (Phaseolus vulgaris)-soybean rotation on living mulch of kikuyu grass (Pennisetum clandestinum). The samples were compared with samples from natural fallows. The soil nematofauna, characterized by the abundance of different trophic groups and indices (MI, maturity index; EI and SI, enrichment and structure indices), allowed the discrimination of the different cropping systems. The different DMC treatments had a more complex soil food web than the tillage treatment: SI and MI were significantly greater in DMC systems. Moreover, DMC with dead mulch had a lower density of free-living nematodes than DMC with living mulch, which suggested a lower microbial activity.

Spatiotemporal dynamics of soil rotifers in a South-Bohemian beech forest

The objective of this work was to determine seasonal variation and vertical distribution of the soil rotifer assemblage in a climax beech forest in South Bohemia. During 2005, soil rotifer was investigated to the species level. Soil samples of 10 cm² and 10 cm in depth were divided into five layers, which were processed separately. Thirty one rotifer species were identified during the investigation. Dominant species significantly changed throughout the seasons. The most abundant species were Encentrum arvicola and Wierzejskiella vagneri among the monogononts, and Adineta steineri, Ceratotrocha cornigera, Habrotrocha filum, Habrotrocha ligula, Macrotrachela plicata, Mniobia tentans, Mniobia incrassata and Mniobia granulosa among the bdelloids. Mean Shannon diversity index varied from 1.99 to 2.63. Total rotifer abundance varied from 212±63 to 513±127 10³ individuals m-2 along the year, with the highest numbers found in May, and the lowest in July. The great part of the community was concentrated in the upper (fresh litter) and second (partially decomposed litter) layers and significantly decreased in the soil vertical profile on all sampling dates. The highest rotifer density of 43 individuals g-1 was found in the upper layer in May.

Soil biological attributes in pastures of different ages in a crop-livestock integrated system

The objective of this work was to evaluate the effect of the pasture (Urochloa brizantha) component age on soil biological properties, in a crop-livestock integrated system. The experiment was carried out in a Brazilian savannah (Cerrado) area with 92 ha, divided into six pens of approximately 15 ha. Each pen represented a different stage of the pasture component: formation, P0; one year, P1; two years, P2; three years, P3; and final with 3.5 years, Pf. Samples were taken in the 0-10 cm soil depth. The soil biological parameters - microbial biomass carbon (MBC), microbial biomass respiration (C-CO2), metabolic quotient (qCO2), microbial quotient (q mic), and total organic carbon (TOC) - were evaluated and compared among different stages of the pasture, and between an adjacent area under native Cerrado and another area under degraded pasture (PCD). The MBC, q mic and TOC increased and qCO2 reduced under the different pasture stages. Compared to PCD, the pasture stages had higher MBC, q mic and TOC, and lower qCO2. The crop-livestock integrated system improved soil microbiological parameters and immobilized carbon in the soil in comparison to the degraded pasture.

Microbiological and chemical attributes of a Hapludalf soil with swine manure fertilization

The objective of this work was to evaluate the microbiological and chemical attributes of a soil with a seven‑year history of urea and swine manure application. In the period from October 2008 to October 2009, soil samples were collected in the 0-10 cm layer and were subjected to the treatments: control, without application of urea or manure; and with the application of urea, pig slurry, and deep pig litter in two doses, in order to supply one or two times the recommended N doses for the maize (Zea mays)/black oat (Avena strigosa) crop succession. The carbon of the microbial biomass (MB‑C) and the basal respiration (C‑CO2) were analyzed, and the metabolic (qCO2) and microbial quotient (qmic) were calculated with the obtained data. Organic matter, pH in water, available P and K, and exchangeable Ca and Mg were also determined. The application of twice the dose of deep pig litter increases the MB‑C and C‑CO2 values. The qmic and qCO2 are little affected by the application of swine manure. The application of twice the dose of deep pig litter increases the values of pH in water and the contents of available P and of exchangeable Ca and Mg in the soil.

The role of community and population ecology in applying mycorrhizal fungi for improved food security.

The global human population is expected to reach ∼9 billion by 2050. Feeding this many people represents a major challenge requiring global crop yield increases of up to 100%. Microbial symbionts of plants such as arbuscular mycorrhizal fungi (AMF) represent a huge, but unrealized resource for improving yields of globally important crops, especially in the tropics. We argue that the application of AMF in agriculture is too simplistic and ignores basic ecological principals. To achieve this challenge, a community and population ecology approach can contribute greatly. First, ecologists could significantly improve our understanding of the determinants of the survival of introduced AMF, the role of adaptability and intraspecific diversity of AMF and whether inoculation has a direct or indirect effect on plant production. Second, we call for extensive metagenomics as well as population genomics studies that are crucial to assess the environmental impact that introduction of non-local AMF may have on native AMF communities and populations. Finally, we plead for an ecologically sound use of AMF in efforts to increase food security at a global scale in a sustainable manner.