Laboratory of Environmental Microbiology

Jaguariúna, Brazil

Laboratory of Environmental Microbiology

Jaguariúna, Brazil
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Kavamura V.N.,Laboratory of Environmental Microbiology | Santos S.N.,Laboratory of Environmental Microbiology | Taketani R.G.,Laboratory of Environmental Microbiology | Vasconcellos R.L.F.,Laboratory of Environmental Microbiology | Melo I.S.,Laboratory of Environmental Microbiology
Genome Announcements | Year: 2017

The strain of Bacillus sp. CMAA 1363 was isolated from the Brazilian Caatinga biome and showed plant growth-promoting traits and ability to promote maize growth under drought stress. Sequencing revealed genes involved in stress response and plant growth promotion. These genomic features might aid in the protection of plants against the negative effects imposed by drought. © 2017 Kavamura et al.


Mendes R.,Laboratory of Environmental Microbiology | Garbeva P.,Netherlands Institute of Ecology | Raaijmakers J.M.,Wageningen University
FEMS Microbiology Reviews | Year: 2013

Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health. In this review, we focus on the frequency, diversity and activities of beneficial ('the good'), plant pathogenic ('the bad') and human pathogenic ('the ugly') microorganisms in the rhizosphere and how they impact on health and disease. Specific attention is given to mechanisms involved in multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we discuss strategies to re-direct or re-shape the rhizosphere microbiome in favour of those microbes that are beneficial to plant growth and health. © 2013 Federation of European Microbiological Societies.


Dias A.C.F.,Laboratory of Environmental Microbiology | Dias A.C.F.,University of Sao Paulo | Dini-Andreote F.,Laboratory of Environmental Microbiology | Dini-Andreote F.,University of Sao Paulo | And 5 more authors.
Journal of Soils and Sediments | Year: 2011

Purpose: This study evaluates the presence and diversity of 16S rRNA (rrs) and amoA genes from archaea in three mangrove sediments under different stages of preservation (one pristine mangrove, one affected by anthropogenic activity, and another contaminated by an oil spill) in the state of São Paulo (Brazil). Materials and methods: A combination of DGGE, coupled with ordination analysis, and clone libraries of both targeted genes (rrs and amoA) was used to infer the diversity and phylogeny of archaeal communities in the mangrove analyzed samples. Results and discussion: The DGGE combined with multivariate analysis revealed, based on the ribosomal gene, differences in archaeal communities according to environmental parameters such as mangrove location, anthropogenic activity, and oil contamination. The profiles based on the amoA gene were more similar than those obtained for the gene rrs, with the only difference statistically observed for the community found in the mangrove under anthropogenic pressure. Furthermore, phylogenetic analysis revealed most archaeal groups affiliated to sequences belonging to the Thaumarchaeota (53. 1%, 24 OTUs) and Euryarchaeota (29. 6%, 14 OTUs) phyla, in addition to 14 sequences affiliated to an unclassified Archaea (16. 1%, 8 OTUs). Concerning the analysis of the amoA gene, mangroves harbored sequences affiliated with those previously described in water column and soil/sediment samples, besides two possible clusters specifically found in mangroves. Conclusions: The findings are that the mangroves act as a reservoir for archaeal diversity, are possibly involved in nitrogen transformation in this ecosystem, and are affected by distinct pressures caused by anthropogenic activities. © 2011 Springer-Verlag.


Dias A.C.F.,University of Sao Paulo | Andreote F.D.,Laboratory of Environmental Microbiology | Andreote F.D.,University of Sao Paulo | Rigonato J.,University of Sao Paulo | And 2 more authors.
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology | Year: 2010

The bacterial diversity present in sediments of a well-preserved mangrove in Ilha do Cardoso, located in the extreme south of São Paulo State coastline, Brazil, was assessed using culture-independent molecular approaches (denaturing gradient gel electrophoresis (DGGE) and analysis of 166 sequences from a clone library). The data revealed a bacterial community dominated by Alphaproteobacteria (40.36% of clones), Gammaproteobacteria (19.28% of clones) and Acidobacteria (27.71% of clones), while minor components of the assemblage were affiliated to Betaproteobacteria, Deltaproteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The clustering and redundancy analysis (RDA) based on DGGE were used to determine factors that modulate the diversity of bacterial communities in mangroves, such as depth, seasonal fluctuations, and locations over a transect area from the sea to the land. Profiles of specific DGGE gels showed that both dominant ('universal' Bacteria and Alphaproteobacteria) and low-density bacterial communities (Betaproteobacteria and Actinobacteria) are responsive to shifts in environmental factors. The location within the mangrove was determinant for all fractions of the community studied, whereas season was significant for Bacteria, Alphaproteobacteria, and Betaproteobacteria and sample depth determined the diversity of Alphaproteobacteria and Actinobacteria. © 2010 Springer Science+Business Media B.V.


Varon-Lopez M.,University of Sao Paulo | Varon-Lopez M.,Netherlands Institute of Ecology | Dias A.C.F.,University of Sao Paulo | Fasanella C.C.,University of Sao Paulo | And 4 more authors.
Environmental Microbiology | Year: 2014

Mangrove soils are anaerobic environments rich in sulphate and organic matter. Although the sulphur cycle is one of the major actors in this ecosystem, little is known regarding the sulphur bacteria communities in mangrove soils. We investigated the abundance, composition and diversity of sulphur-oxidizing (SOB) and sulphate-reducing (SRB) bacteria in sediments from three Brazilian mangrove communities: two contaminated, one with oil (OilMgv) and one with urban waste and sludge (AntMgv), and one pristine (PrsMgv). The community structures were assessed using quantitative real-time polymerase chain reaction (qPCR), polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and clone libraries, using genes for the enzymes adenosine-5′-phosphosulphate reductase (aprA) and sulphite reductase (Dsr) (dsrB). The abundance for qPCR showed the ratio dsrB/aprA to be variable among mangroves and higher according to the gradient observed for oil contamination in the OilMgv. The PCR-DGGE patterns analysed by Nonmetric Multidimensional Scaling revealed differences among the structures of the three mangrove communities. The clone libraries showed that Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria were the most abundant groups associated with sulphur cycling in mangrove sediments. We conclude that the microbial SOB and SRB communities in mangrove soils are different in each mangrove forest and that such microbial communities could possibly be used as a proxy for contamination in mangrove forests. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.


Nessner Kavamura V.,Laboratory of Environmental Microbiology | Nessner Kavamura V.,University of Sao Paulo | Taketani R.G.,Laboratory of Environmental Microbiology | Lanconi M.D.,Laboratory of Environmental Microbiology | And 4 more authors.
PLoS ONE | Year: 2013

We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes. © 2013 Nessner Kavamura et al.


Faria D.C.,Sapucai Valley University | Dias A.C.F.,University of Sao Paulo | Melo I.S.,Laboratory of Environmental Microbiology | de Carvalho Costa F.E.,National Institute of Communications of Brazil
World Journal of Microbiology and Biotechnology | Year: 2013

Twelve endophytic bacteria were isolated from the meristem of in vitro Cymbidium eburneum orchid, and screened according to indole yield quantified by colorimetric assay, in vitro phosphate solubilization, and potential for plant growth promotion under greenhouse conditions. Eight strains with positive results were classified into the genus Paenibacillus by FAME profile, and evaluated for their ability to increase survival and promote the growth of in vitro germinated Cattleya loddigesii seedlings during the acclimatization process. The obtained results showed that all strains produced detectable indole levels and did not exhibit potential for solubilizing inorganic phosphate. Particularly, an increase of the total biomass and number of leaves was observed. Two strains of Paenibacillus macerans promoted plant growth under greenhouse conditions. None of the treatments had a deleterious effect on growth of inoculated plants. These results suggest that these bacterial effects could be potentially useful to promote plant growth during seedling acclimatization in orchid species other than the species of origin. © 2012 Springer Science+Business Media Dordrecht.


van der Voort M.,Wageningen University | Kempenaar M.,The Netherlands Bioinformatics Center | van Driel M.,The Netherlands Bioinformatics Center | Raaijmakers J.M.,Netherlands Institute of Ecology | And 2 more authors.
Ecology Letters | Year: 2016

The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature-sensitive and slow-growing bacteria have a disadvantage. The results also pointed to a potential role of slow-growing, heat-tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression. © 2016 John Wiley & Sons Ltd/CNRS.


PubMed | Wageningen University, The Netherlands Bioinformatics Center, Netherlands Institute of Ecology and Laboratory of Environmental Microbiology
Type: Letter | Journal: Ecology letters | Year: 2016

The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature-sensitive and slow-growing bacteria have a disadvantage. The results also pointed to a potential role of slow-growing, heat-tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression.


PubMed | Laboratory of Environmental Microbiology
Type: Journal Article | Journal: Antonie van Leeuwenhoek | Year: 2015

The rumen is a complex ecosystem enriched for microorganisms able to degrade biomass during the animals digestion process. The recovery of new enzymes from naturally evolved biomass-degrading microbial communities is a promising strategy to overcome the inefficient enzymatic plant destruction in industrial production of biofuels. In this context, this study aimed to describe the bacterial composition and functions in the sheep rumen microbiome, focusing on carbohydrate-active enzymes (CAE). Here, we used phylogenetic profiling analysis (inventory of 16S rRNA genes) combined with metagenomics to access the rumen microbiome of four sheep and explore its potential to identify fibrolytic enzymes. The bacterial community was dominated by Bacteroidetes and Firmicutes, followed by Proteobacteria. As observed for other ruminants, Prevotella was the dominant genus in the microbiome, comprising more than 30 % of the total bacterial community. Multivariate analysis of the phylogenetic profiling data and chemical parameters showed a positive correlation between the abundance of Prevotellaceae (Bacteroidetes phylum) and organic matter degradability. A negative correlation was observed between Succinivibrionaceae (Proteobacteria phylum) and methane production. An average of 2 % of the shotgun metagenomic reads was assigned to putative CAE when considering nine protein databases. In addition, assembled contigs allowed recognition of 67 putative partial CAE (NCBI-Refseq) representing 12 glycosyl hydrolase families (Pfam database). Overall, we identified a total of 28 lignocellulases, 22 amylases and 9 other putative CAE, showing the sheep rumen microbiome as a promising source of new fibrolytic enzymes.

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