Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization.

Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.

Desulfobotulus mexicanus sp. nov., a novel sulfate-reducing bacterium isolated from the sediment of an alkaline crater lake in Mexico.

A novel Gram-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacterium, designated strain PAR22NT, was isolated from sediment samples collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR22NT grew at temperatures between 15 and 37 °C (optimum, 32 °C), at pH between pH 8.3 and 10.1 (optimum, pH 9.0-9.6), and in the presence of NaCl up to 10 %. Pyruvate, 2-methylbutyrate and fatty acids (4-18 carbon atoms) were used as electron donors in the presence of sulfate as a terminal electron acceptor and were incompletely oxidized to acetate and CO2. Besides sulfate, both sulfite and elemental sulfur were also used as terminal electron acceptors and were reduced to sulfide. The predominant fatty acids were summed feature 10 (C18 : 1 ω7c and/or C18 : 1 ω9t and/or C18 : 1 ω12t), C18 : 1 ω9c and C16 : 0. The genome size of strain PAR22NT was 3.8 Mb including 3391 predicted genes. The genomic DNA G+C content was 49.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that it belongs to the genus Desulfobotulus within the class Deltaproteobacteria. Its closest phylogenetic relatives are Desulfobotulus alkaliphilus (98.4 % similarity) and Desulfobotulus sapovorans (97.9 % similarity). Based on phylogenetic, phenotypic and chemotaxonomic characteristics, we propose that the isolate represents a novel species of the genus Desulfobotulus with the name Desulfobotulus mexicanus sp. nov. The type strain is PAR22NT (=DSM 105758T=JCM 32146T).

Fluoroquinolones in agricultural soils: Multi-temporal variation and risks in Rio de Janeiro upland region.

Our main goal was to investigate the potential accumulation of fluoroquinolones (FQs) in agricultural soils over extended periods of land use, predicting leaching and estimating risk quotients for soil microorganisms. Short to long-term of poultry litter fertilization (<1-30 years) were evaluated for enrofloxacin (ENR) and ciprofloxacin (CIP) input, in addition to the emergence of plasmid-mediated quinolone resistance (PMQR) genes. High FQs concentration (range 0.56-100 mg kg-1) were measured in poultry litter samples. In soils, FQs occurrence and risks have changed over the years. An accumulation trend was observed between short and medium-term fertilized soils (ST and MT soils), reaching a range of 330-6138 µg kg-1 ENR and 170-960 µg kg-1 CIP in MT soil, followed by decreased concentrations in long-term fertilized soils (LT soils). The environmental risk assessment showed a high ENR risk quotient (RQ ≥ 1) in ST and MT soils ranging (7-226) and high CIP risk (9-53) in LT soils. The detection of qnrS genes in the area with the lowest FQs concentration emphasizes the importance of a broader approach to environmental assessment, in which not only target compounds are considered. FQs soil-water migration model pointed out a high leaching risk in ST soil. To reduce risks, management measures to decrease antibiotic environmental load should be taken before poultry litter application. In addition, the high weathering of tropical soils contributing to possible fate of antibiotics to water resources through drainage basins should be considered.

Impact of hydrocarbons, PCBs and heavy metals on bacterial communities in Lerma River, Salamanca, Mexico: Investigation of hydrocarbon degradation potential.

Freshwater contamination usually comes from runoff water or direct wastewater discharges to the environment. This paper presents a case study which reveals the impact of these types of contamination on the sediment bacterial population. A small stretch of Lerma River Basin, heavily impacted by industrial activities and urban wastewater release, was studied. Due to industrial inputs, the sediments are characterized by strong hydrocarbon concentrations, ranging from 2 935 to 28 430µg·kg(-1) of total polyaromatic hydrocarbons (PAHs). These sediments are also impacted by heavy metals (e.g., 9.6µg·kg(-1) of Cd and 246µg·kg(-1) of Cu, about 8 times the maximum recommended values for environmental samples) and polychlorinated biphenyls (ranging from 54 to 123µg·kg(-1) of total PCBs). The bacterial diversity on 6 sediment samples, taken from upstream to downstream of the main industrial and urban contamination sources, was assessed through TRFLP. Even though the high PAH concentrations are hazardous to aquatic life, they are not the only factor driving bacterial community composition in this ecosystem. Urban discharges, leading to hypoxia and low pH, also strongly influenced bacterial community structure. The bacterial bioprospection of these samples, using PAH as unique carbon source, yielded 8 hydrocarbonoclastic strains. By sequencing the 16S rDNA gene, these were identified as similar to Mycobacterium goodii, Pseudomonas aeruginosa, Pseudomonas lundensis or Aeromonas veronii. These strains showed high capacity to degrade naphthalene (between 92 and 100% at 200mg·L(-1)), pyrene (up to 72% at 100mg·L(-1)) and/or fluoranthene (52% at 50mg·L(-1)) as their only carbon source on in vitro experiments. These hydrocarbonoclastic bacteria were detected even in the samples upstream of the city of Salamanca, suggesting chronical contamination, already in place longer before. Such microorganisms are clearly potential candidates for hydrocarbon degradation in the treatment of oil discharges.

Microbial diversity in Los Azufres geothermal field (Michoacán, Mexico) and isolation of representative sulfate and sulfur reducers.

Los Azufres spa consists of a hydrothermal spring system in the Mexican Volcanic Axis. Five samples (two microbial mats, two mud pools and one cenote water), characterized by high acidity (pH between 1 and 3) and temperatures varying from 27 to 87 °C, were investigated for their microbial diversity by Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and 16S rRNA gene library analyses. These data are the first to describe microbial diversity from Los Azufres geothermal belt. The data obtained from both approaches suggested a low bacterial diversity in all five samples. Despite their proximity, the sampling points differed by their physico-chemical conditions (mainly temperature and matrix type) and thus exhibited different dominant bacterial populations: anoxygenic phototrophs related to the genus Rhodobacter in the biomats, colorless sulfur oxidizers Acidithiobacillus sp. in the warm mud and water samples, and Lyzobacter sp.-related populations in the hot mud sample (87 °C). Molecular data also allowed the detection of sulfate and sulfur reducers related to Thermodesulfobium and Desulfurella genera. Several strains affiliated to both genera were enriched or isolated from the mesophilic mud sample. A feature common to all samples was the dominance of bacteria involved in sulfur and iron biogeochemical cycles (Rhodobacter, Acidithiobacillus, Thiomonas, Desulfurella and Thermodesulfobium genera).

Bacterial biodiversity from anthropogenic extreme environments: a hyper-alkaline and hyper-saline industrial residue contaminated by chromium and iron.

Anthropogenic extreme environments are among the most interesting sites for the bioprospection of extremophiles since the selection pressures may favor the presence of microorganisms of great interest for taxonomical and astrobiological research as well as for bioremediation technologies and industrial applications. In this work, T-RFLP and 16S rRNA gene library analyses were carried out to describe the autochthonous bacterial populations from an industrial waste characterized as hyper-alkaline (pH between 9 and 14), hyper-saline (around 100 PSU) and highly contaminated with metals, mainly chromium (from 5 to 18 g kg(-1)) and iron (from 2 to 108 g kg(-1)). Due to matrix interference with DNA extraction, a protocol optimization step was required in order to carry out molecular analyses. The most abundant populations, as evaluated by both T-RFLP and 16S rRNA gene library analyses, were affiliated to Bacillus and Lysobacter genera. Lysobacter related sequences were present in the three samples: solid residue and lixiviate sediments from both dry and wet seasons. Sequences related to Thiobacillus were also found; although strains affiliated to this genus are known to have tolerance to metals, they have not previously been detected in alkaline environments. Together with Bacillus (already described as a metal reducer), such organisms could be of use in bioremediation technologies for reducing chromium, as well as for the prospection of enzymes of biotechnological interest.

A case study of in situ oil contamination in a mangrove swamp (Rio De Janeiro, Brazil).

Mangroves are sensitive ecosystems of prominent ecological value that lamentably have lost much of their areas across the world. The vulnerability of mangroves grown in proximity to cities requires the development of new technologies for the remediation of acute oil spills and chronic contaminations. Studies on oil remediation are usually performed with in vitro microcosms whereas in situ experiments are rare. The aim of this work was to evaluate oil degradation on mangrove ecosystems using in situ microcosms seeded with an indigenous hydrocarbonoclastic bacterial consortium (HBC). Although the potential degradation of oil through HBC has been reported, their seeding directly on the sediment did not stimulate oil degradation during the experimental period. This is probably due to the availability of carbon sources that are easier to degrade than petroleum hydrocarbons. Our results emphasize the fragility of mangrove ecosystems during accidental oil spills and also the need for more efficient technologies for their remediation.