Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest

Souza, Felipe F.C.; Rissi, Daniel Vasconcelos; Pedrosa, Fábio O.; Souza, Emanuel Maltempi de; Baura, Valter A.; Monteiro, Rose A.; Balsanelli, Eduardo; Cruz, Leonardo M.; Souza, R. A. F. D.; Reis, Rodrigo Arantes; Godoi, Ricardo H. M.; Huergo, Luciano F.

doi:10.1016/j.scitotenv.2019.06.218

Cited by 17 publications

(11 citation statements)

References 17 publications

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“…Aeolian microbial metagenomes were rich in unique genes, with a yield of 30.9 × 10 6 predicted genes per Tera base-pair of DNA sequenced, resulting in a total of 2.37 million non-redundant coding DNA sequences contained in the GCAM. The aeolian communities were dominated with Actinobacteria , Proteobacteria , and Firmicutes of the prokaryotic genes and Ascomycota of the eukaryotes, which is in line with findings in other bioaerosols studies 47–50 . Moreover, these communities were variable, likely a consequence of the diverse sources of the microorganisms present, and highly enriched in eukaryotic genes compared to the underlying seawater surface microbiome.…”

Section: Discussionsupporting

confidence: 90%

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

Aalismail

Ngugi

Díaz‐Rúa

et al. 2019

Sci Rep

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Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.

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Section: Discussionsupporting

confidence: 90%

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

Aalismail

Ngugi

Díaz‐Rúa

et al. 2019

Sci Rep

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“…The genome size of Bacteria was defined as 4 Mb, as found in the NCBI data base for airborne Bacteria present in the Amazonian air microbiome (e.g. Proteobacteria, Actinobacteria, Souza et al, 2019). Archaeal genome size was defined as 4 Mb as well (Landenmark et al, 2015).…”

Section: Epifluorescent Microscopic Enumeration and Bioaerosol Projectionmentioning

confidence: 99%

Bioaerosols in the Amazon rain forest: Temporal variations and vertical profiles of Eukarya, Bacteria and Archaea

Prass¹,

Andreae²,

Araújo³

et al. 2021

Preprint

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Abstract. The Amazon rain forest plays a major role in global hydrological cycling and biogenic aerosols are likely to influence the formation of clouds and precipitation. Information about the sources and altitude profiles of primary biological aerosol particles, however, is sparse. We used fluorescence in situ hybridization (FISH), a molecular biological staining technique largely unexplored in aerosol research, to investigate the sources and spatiotemporal distribution of Amazonian bioaerosols on domain level. We found wet season bioaerosol number concentrations in the range of 1–5 · 105 m−3 accounting for > 70 % of the coarse mode aerosol. Eukaryotic and bacterial particles predominated, with fractions of ~56 % and ~26 % of the intact airborne cells. Archaea occurred at very low concentrations. Vertical profiles exhibit a steep decrease of bioaerosol numbers from the understory to 325 m height on the Amazon Tall Tower Observatory, with a stronger decrease of Eukarya compared to Bacteria. Considering earlier investigations, our results can be regarded as representative for near-pristine Amazonian wet season conditions. The observed concentrations and profiles provide unprecedented insights into the sources and dispersion of different types of Amazonian bioaerosols as a solid basis for model studies on biosphere-atmosphere interactions such as bioprecipitation cycling.

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“…Total DNA extraction from the three Sambaqui soil layers were performed using Power Soil DNA Kit (MOBIO). The DNA recovered from the kit was precipitated with ethanol 80%, dried and all the genetic material was used as template for PCR ampli cation as described previously (Souza et al, 2019). Brie y, the V4 region of the 16S gene was PCR ampli ed in 10 µl reactions using: all dried template DNA; 1 µM primer 515F; remove chimeras, join forward and reverse reads, and dereplicate sequences in amplicon sequence variants (ASV).…”

Section: Total Dna Extraction and 16s Rrna Gene Amplicon Illumina Sequencingmentioning

confidence: 99%

“…Still, most of the Brazilian biomes are only marginally explored in terms of microbiome composition (Pylro and Roesch, 2017). Our research group is combining metagenomics and traditional cell culture techniques to uncover the microbiome in yet to be explored Brazilian environments such as the pristine Amazon forest air (Souza et al, 2019) and the mangrove soil (Huergo et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

The Microbiome of a Shell Mound: Ancient Anthropogenic Waste as a Source of Streptomyces Degrading Recalcitrant Polysaccharides

Huergo

Conzentino

Gonçalves

et al. 2021

Preprint

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Metagenome amplicon DNA sequencing and traditional cell culture techniques are helping to uncover the diversity and the biotechnological potential of prokaryotes in different habitats around the world. It has also had a profound impact on microbial taxonomy in the last decades. Here we used metagenome 16S rDNA amplicon sequencing to reveal the microbiome composition of different layers of an anthropogenic soil collected at a shell mound Sambaqui archeological site. The Samabaqui soil microbiome is mainly composed by phyla Acidobacteria, Rokubacteria, Proteobacteria and Thaumarchaeota. Using culture-dependent analysis we isolated few Streptomyces strains from the Sambaqui soil. One of the isolates, named Streptomyces sp. S3, was able to grow in minimal medium containing recalcitrant polysaccharides including chitin, xylan, carboxymethylcellulose or microcrystalline cellulose as sole carbon sources. The activities of enzymes degrading these compounds were confirmed in cell free supernatants. The genome sequence revealed not only an arsenal of genes related to polysaccharides degradation but also biosynthetic gene clusters which may be involved in the production of biotechnologically interesting secondary metabolites.

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Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest

Cited by 17 publications

References 17 publications

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

Bioaerosols in the Amazon rain forest: Temporal variations and vertical profiles of Eukarya, Bacteria and Archaea

The Microbiome of a Shell Mound: Ancient Anthropogenic Waste as a Source of Streptomyces Degrading Recalcitrant Polysaccharides

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