Draft genome sequence of <i>Bacillus thuringiensis</i> strain BrMgv02-JM63, a chitinolytic bacterium isolated from oil-contaminated mangrove soil in Brazil

Here, we report the draft genome sequence and the automatic annotation of Bacillus thuringiensis strain BrMgv02-JM63. This genome comprises a set of genes involved in the metabolism of chitin and N-acetylglucosamine utilization, thus suggesting the possible role of this strain in the cycling of organic matter in mangrove soils

A comprehensive study on diesel oil bioremediation under microcosm conditions using a combined microbiological, enzymatic, mass spectrometry, and metabarcoding approach

This study aims at the application of a marine fungal consortium (Aspergillus sclerotiorum CRM 348 and Cryptococcus laurentii CRM 707) for the bioremediation of diesel oil-contaminated soil under microcosm conditions. The impact of biostimulation (BS) and/or bioaugmentation (BA) treatments on diesel-oil biodegradation, soil quality, and the structure of the microbial community were studied. The use of the fungal consortium together with nutrients (BA/BS) resulted in a TPH (Total Petroleum Hydrocarbon) degradation 42% higher than that obtained by natural attenuation (NA) within 120 days. For the same period, a 72 to 92% removal of short-chain alkanes (C12 to C19) was obtained by BA/BS, while only 3 to 65% removal was achieved by NA. BA/BS also showed high degradation efficiency of long-chain alkanes (C20 to C24) at 120 days, reaching 90 and 92% of degradation of icosane and heneicosane, respectively. In contrast, an increase in the levels of cyclosiloxanes (characterized as bacterial bioemulsifiers and biosurfactants) was observed in the soil treated by the consortium. Conversely, the NA presented a maximum of 37% of degradation of these alkane fractions. The 5-ringed PAH benzo(a)pyrene, was removed significantly better with the BA/BS treatment than with the NA (48 vs. 38 % of biodegradation, respectively). Metabarcoding analysis revealed that BA/BS caused a decrease in the soil microbial diversity with a concomitant increase in the abundance of specific microbial groups, including hydrocarbon-degrading (bacteria and fungi) and also an enhancement in soil microbial activity. Our results highlight the great potential of this consortium for soil treatment after diesel spills, as well as the relevance of the massive sequencing, enzymatic, microbiological and GC-HRMS analyses for a better understanding of diesel bioremediation.This research was financially supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (grant #2016/07957-7) and by Conselho Nacional de Desenvolvimento Tecnológico (CNPq) (grant #407986/2018-6).Peer reviewe

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments

Genome sequence of Streptomyces caatingaensis CMAA 1322, a new abiotic stress-tolerant actinomycete isolated from dried lake bed sediment in the Brazilian Caatinga biome

The genome sequence of the first Streptomyces species isolated from the Brazilian Caatinga is reported here. Genes related to environmental stress tolerance were prevalent and included many secondary metabolic gene clusters

Use of molecular approach to verify the influence of a eutrophic lagoon in the nearby ocean's bacterioplankton communities Uso de metodologia molecular para verificar a influência de uma lagoa eutrófica na comunidade bacterioplanctônica do oceano adjacente

Rodrigo de Freitas lagoon is an eutrophic aquatic environment. The waters from the lagoon are released to the sea at Ipanema and Leblon beaches, through Jardim de Alah channel. In this work, the influence of these waters on the bacterial communities of these beaches was investigated. Eleven sampling stations were set between the lagoon and the beaches, and the samples were analyzed by molecular and microbiological parameters. PCR-DGGE of the DNA extracted from the samples was performed using rpoB primers. Preliminary results indicate that all used approaches could reveal the influence of the lagoon on the beaches bacterial communities.<br>A lagoa Rodrigo de Freitas é um ambiente aquático eutrofizado, cujas águas são lançadas ao mar nas praias de Ipanema e Leblon através do canal do Jardim de Alah. Nesse trabalho, foi estudada a influência desse aporte na comunidade bacteriana dessas praias. Para isso coletou-se água de onze estações distribuídas entre a lagoa e as praias. Essas amostras foram analisadas quanto a parâmetros moleculares e microbiológicos. Foi realizado também PCR-DGGE utilizando-se iniciadores para o gene rpoB, a partir de DNA extraído das amostras de água coletadas. Resultados preliminares mostram que a influência da lagoa na comunidade bacteriana das praias pode ser verificada por todas as abordagens

The seventeen most significant genera (p<0.05) with respect to the season.

<p>The seventeen most significant genera (p<0.05) with respect to the season.</p

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009) from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old), agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE) using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA) of Archaea (306 sequences), the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366), followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715), crops (H' = 1.4613; D = 0.3309) and secondary forest (H' = 0.8633; D = 0.5405). All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 %) previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils

Sampling in the Caatinga biome in the semi-arid region of northeast Brazil.

<p>A - Map of Brazil in detail showing the distribution of the sampling sites comprising five states (#1 - Bahia (BA), S09°13′24.8′′; W41°05′11.4′′; #2 - Piauí (PI), S08°50′01.6′′, W42°33′13.3′′; #3 - Ceará (CE), S06°27′37.1′′, W40°44′50.5′′; #4 - Paraíba (PB), S06°42′44.2′′, W38°15′08.2′′; #5 - Rio Grande do Norte (RN), S06°39′15.6′′, W37°29′33.4′′). B and C - Pictures of <i>Cereus jamacaru,</i> a cactus found in the Caatinga biome of Brazil, during rainy (B) and dry seasons (C). (Pictures taken by the first author, 2009 and 2010).</p

PCA of the 16S libraries based on taxonomic affiliation of reads determined by mothur.

<p>Samples are bulk soil during the rainy season (RSSL), bulk soil during the dry season (DSSL), rhizosphere during the rainy season (RSRZ) and rhizosphere during the dry season (DSRZ). The most common phyla are: Acidobacteria (Acidobac), Actinobacteria (Actinoba), Bacteroidetes (Bacteroi), Chloroflexi, Cyanobacteria (Cyanoba), Firmicutes (Firmicut), Gemmatimonadetes (Gemmati), Lentisphaerae (Lentisph), Nitrospirae (Nitro), Others, Proteobacteria (Proteoba), Tenericutes (Tener) and Verrucomicrobia (Verrucom).</p