Flávio Anastácio de Oliveira Camargo

Pyrosequencing enumerates and contrasts soil microbial diversity.

Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006). The highest estimate suggests that the number may be so large as to be impractical to test by amplification and sequencing of the highly conserved 16S rRNA gene from soil DNA (Gans et al., 2005). Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess bacterial diversity in four soils across a large transect of the western hemisphere. The number of bacterial 16S rRNA sequences obtained from each site varied from 26 140 to 53 533. The most abundant bacterial groups in all four soils were the Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Using three estimators of diversity, the maximum number of unique sequences (operational taxonomic units roughly corresponding to the species level) never exceeded 52 000 in these soils at the lowest level of dissimilarity. Furthermore, the bacterial diversity of the forest soil was phylum rich compared to the agricultural soils, which are species rich but phylum poor. The forest site also showed far less diversity of the Archaea with only 0.009% of all sequences from that site being from this group as opposed to 4%–12% of the sequences from the three agricultural sites. This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.

Biodegradation potential of oily sludge by pure and mixed bacterial cultures.

The biodegradation capacity of aliphatic and aromatic hydrocarbons of petrochemical oily sludge in liquid medium by a bacterial consortium and five pure bacterial cultures was analyzed. Three bacteria isolated from petrochemical oily sludge, identified as Stenotrophomonas acidaminiphila, Bacillus megaterium and Bacillus cibi, and two bacteria isolated from a soil contaminated by petrochemical waste, identified as Pseudomonas aeruginosa and Bacillus cereus demonstrated efficiency in oily sludge degradation when cultivated during 40 days. The bacterial consortium demonstrated an excellent oily sludge degradation capacity, reducing 90.7% of the aliphatic fraction and 51.8% of the aromatic fraction, as well as biosurfactant production capacity, achieving 39.4% reduction of surface tension of the culture medium and an emulsifying activity of 55.1%. The results indicated that the bacterial consortium has potential to be applied in bioremediation of petrochemical oily sludge contaminated environments, favoring the reduction of environmental passives and increasing industrial productivity.

Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment

The Park Grass experiment (PGE) in the UK has been ongoing since 1856. Its purpose is to study the response of biological communities to the long-term treatments and associated changes in soil parameters, particularly soil pH. In this study, soil samples were collected across pH gradient (pH 3.6–7) and a range of fertilizers (nitrogen as ammonium sulfate, nitrogen as sodium nitrate, phosphorous) to evaluate the effects nutrients have on soil parameters and microbial community structure. Illumina 16S ribosomal RNA (rRNA) amplicon sequencing was used to determine the relative abundances and diversity of bacterial and archaeal taxa. Relationships between treatments, measured soil parameters, and microbial communities were evaluated. Clostridium, Bacteroides, Bradyrhizobium, Mycobacterium, Ruminococcus, Paenibacillus, and Rhodoplanes were the most abundant genera found at the PGE. The main soil parameter that determined microbial composition, diversity, and biomass in the PGE soil was pH. The most probable mechanism of the pH impact on microbial community may include mediation of nutrient availability in the soil. Addition of nitrogen to the PGE plots as ammonium sulfate decreases soil pH through increased nitrification, which causes buildup of soil carbon, and hence increases C/N ratio. Plant species richness and plant productivity did not reveal significant relationships with microbial diversity; however, plant species richness was positively correlated with soil microbial biomass. Plants responded to the nitrogen treatments with an increase in productivity and a decrease in the species richness.

Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize

Recent studies suggest a high diversity of diazotrophic bacteria in maize. However, none of these works have been based on a sufficient number of samples to provide reasonable quantitative estimates of diazotrophic bacterial diversity. Here we present the use of molecular tools and statistical inference to assess diazotrophic bacterial diversity within rhizosphere soils, roots and stems of field grown maize. DNA was isolated from the latter collected from six maize growing regions within the southern most state in Brazil, Rio Grande do Sul. Using conserved primers, nifH Cluster I gene fragments were amplified from each of the three zones, and the products cloned and sequenced. The majority of the sequences were classified within the Proteobacteria with the α-proteobacteria and β-proteobacteria being the most abundant in the rhizosphere soil and stem samples. The γ-proteobacteria were most abundant in rhizosphere soils, less so in roots, and least in the stem samples. According to three different diversity measures, the rhizosphere soil samples possessed greater diazotrophic bacterial diversity than the roots and stems of the maize plants. Only two genera, Azospirillum and Azotobacter, were found in virtually all samples at an abundance of over 1% of the total nifH sequences obtained. Other genera were largely restricted to soil (Methylocystis, Beijerinckia, Geobacter, Rhodovulum, Methylobacterium, Gluconacetobacter, Methylocella, and Delftia), roots (Dechloromonas), or stems (Methylosinus, Raoultella, and Rhizobium). Three genera, Herbaspirillum, Ideonella, and Klebsiella, appeared to dominate in the interior of the plant but were much rarer in soil.

Drivers of archaeal ammonia-oxidizing communities in soil

Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.

Bioremediation of soil contaminated by diesel oil

Were evaluated natural attenuation, biostimulation and bioaugmentation on the degradation of total petroleum hydrocarbons (TPH) in soils contaminated with diesel oil. Bioaugmentation showed the greatest degradation in the light (C12 - C23) fractions (72.7%) and heavy (C23 - C40) fractions of TPH (75.2%) and natural attenuation was more effective than biostimulation. The greatest dehydrogenase activity was observed upon bioaugmentation of the Long Beach soil (3.3-fold) and the natural attenuation of the Hong Kong soil sample (4.0-fold). The number of diesel oil degrading microorganisms and heterotrophic population was not influenced by the bioremediation treatments. The best approach for bioremediation of soil contaminated with diesel oil is the inoculum of microorganisms pre-selected from their own environment.

Utilização de microondas na avaliação da biomassa microbiana do solo

The objective of this work was to determine carbon and nitrogen content in the soil microbial biomass by comparing microwave radiation and chloroform fumigation using the extraction and incubation methods. Two soil samples (Dark-Red Podzolic) were submitted to incubation and extraction after chloroform fumigation and microwave radiation during different periods (2, 5, 10, 15, 20, 30, 40 and 50 min). Two minutes under microwave radiation were sufficient to determine C and N content in the soil biomass using incubation and extraction procedures. These values were similar to those obtained by chloroform fumigation. The coefficients of variation in the soil samples submitted to microwave radiation extraction were reduced. Thus, this was considered the most adequate procedure for carbon and nitrogen quantification in soil biomass.

CHARACTERIZATION OF COPPER BIOREDUCTION AND BIOSORPTION BY A HIGHLY COPPER RESISTANT BACTERIUM ISOLATED FROM COPPER-CONTAMINATED VINEYARD SOIL

Copper is an essential but toxic heavy metal that negatively impacts living systems at high concentration. This study presents factors affecting copper bioremoval (bioreduction and biosorption) by a highly copper resistant monoculture of Pseudomonas sp. NA and copper bioremoval from soil. Seven bacteria resistant to high concentration of Cu(II) were isolated from enrichment cultures of vineyard soils and mining wastes. Culture parameters influencing copper bioreduction and biosorption by one monoculture isolate were studied. The isolate was identified by 16S rRNA gene sequence analysis as a Pseudomonas sp. NA (98% similarity to Pseudomonas putida, Pseudomonas plecoglossicida and other Pseudomonas sp.). The optimal temperature for growth was 30 degrees C and bioremoval of Cu(II) was maximal at 35 degrees C. Considerable growth of the isolate was observed between pH 5.0 and 8.0 with the highest growth and biosorption recorded at pH 6.0. Maximal bioreduction was observed at pH 5.0. Cu(II) bioremoval was directly proportional to Cu(II) concentration in media. Pseudomonas sp. NA removed more than 110mg L(-1) Cu(II) in water within 24h through bioreduction and biosorption at initial concentration of 300mg L(-1). In cultures amended with 100mg L(-1), 20.7mg L(-1) of Cu(II) was biologically reduced and more than 23mg L(-1) of Cu(II) was biologically removed in 12h. The isolate strongly promoted copper bioleaching in soil. Results indicate that Pseudomonas sp. NA has good potential as an agent for removing copper from water and soil.

Characterization of a Polycyclic Aromatic Hydrocarbon–Degrading Microbial Consortium from a Petrochemical Sludge Landfarming Site

ABSTRACT Anthracene, phenanthrene, and pyrene are polycyclic aromatic hydrocarbon (PAHs) that display both mutagenic and carcinogenic properties. They are recalcitrant to microbial degradation in soil and water due to their complex molecular structure and low solubility in water. This study presents the characterization of an efficient PAH (anthracene, phenanthrene, and pyrene)-degrading microbial consortium, isolated from a petrochemical sludge landfarming site. Soil samples collected at the landfarming area were used as inoculum in Warburg flasks containing soil spiked with 250 mg kg−1 of anthracene. The soil sample with the highest production of CO2-C in 176 days was used in liquid mineral medium for further enrichment of anthracene degraders. The microbial consortium degraded 48%, 67%, and 22% of the anthracene, phenanthrene, and pyrene in the mineral medium, respectively, after 30 days of incubation. Six bacteria, identified by 16S rRNA sequencing as Mycobacterium fortuitum, Bacillus cereus, Microbacterium sp., Gordonia polyisoprenivorans, two Microbacteriaceae bacteria, and a fungus identified as Fusarium oxysporum were isolated from the enrichment culture. The consortium and its monoculture isolates utilized a variety of hydrocarbons including PAHs (pyrene, anthracene, phenanthrene, and naftalene), monoaromatics hydrocarbons (benzene, ethylbenzene, toluene, and xylene), aliphatic hydrocarbons (1-decene, 1-octene, and hexane), hydrocarbon mixtures (gasoline and diesel oil), intermediary metabolites of PAHs degradation (catechol, gentisic acid, salicylic acid, and dihydroxybenzoic acid) and ethanol for growth. Biosurfactant production by the isolates was assessed by an emulsification index and reduction of the surface tension in the mineral medium. Significant emulsification was observed with the isolates, indicating production of high-molecular-weigh surfactants. The high PAH degradation rates, the wide spectrum of hydrocarbons utilization, and emulsification capacities of the microbial consortium and its member microbes indicate that they can be used for biotreatment and bioaugumentation of soils contaminated with PAHs.

Potencial de mineralização do nitrogênio em solos do Rio Grande do Sul

Nitrogen mineralization potential (No) for ten Rio Grande do Sul, Brazil, soils was studied with corn grown on 20 kg pots for 45 days, as compared with nitrogen mineralized in aerobic incubation for 32 weeks. No values ranged from 108.6 to 210.8 mg kg-1, being similar to the total nitrogen mineralized. Mineralization velocity was higher during the first four weeks, and overall mineralization rate varied from 0.2985 to 0.3181 week-1 among soils. The correlation coefficient between corn absorbed nitrogen and mineralization potential was significant (0.886), indicating that this can be used as an index for soil nitrogen availability to plants.