ALBERT

Description: In this study, we aimed to investigate the ileum digesta of a large cohort of Japanese quail fed the same diet, with similar environmental conditions. We also address how P utilization (PU), Ca utilization (CaU), and bird performance (feed intake (FI), feed conversion (FC), and body weight gain (BWG)) modify intestinal microbiota of male and female quail. Despite the great number of samples analyzed (760), a core microbiome was composed of five bacteria. The Unc. Lactobacillus, Unc. Clostridaceae 1, Clostridium sensu stricto, Escherichia coli, and Streptococcus alactolyticus were detected in all samples and contributed to more than 70% of the total community. Depending on the bird predisposition for PU, CaU, FI, BWG, and FC, those species were present in higher or lower abundances. There was a significant gender effect on the ileal microbial community. While females had higher abundances of Lactobacillus, males were more colonized by Streptococcus alactolyticus. The entire cohort was highly colonized by Escherichia coli (8%–15%), an enteropathogenic bacteria. It remains unclear, if microbiota composition followed the mechanisms that caused different PU, CaU, FI, FC, and BWG or if the change in microbiota composition and function caused the differences in PU, CaU, and performance traits.

Description: Mangroves are highly productive ecosystems located at the transition between the terrestrial and marine environments. Mangroves play an important role in carbon storage, nutrient cycling and support for the marine food web. Mangrove soils are formed by fine particles rich in organic carbon and are subject to constant fluctuations in oxygen, salinity and nutrient availability due to fresh water flux and tidal variations. Microbes play an important role in nutrient cycling in mangrove soils; however, studies on the mangrove soil microbiome are scarce. Here we compare the microbiome of pristine mangrove soil located in an environmentally protected area in Guaratuba, Southern Brazil, with the microbiome of mangrove soil affected by the presence of carbonaceaous debris eroding from an archeological site known as Sambaqui. We show that although the Sambaqui site has a major effect on soil chemistry, increasing the soil pH by 2.6 units, only minor changes in the soil microbiome were detected indicating resilience of the microbial community to pH variations. The high alpha diversity indexes and predicted metabolic potential suggest that the mangrove soil microbiome not only provides important ecological services but also may host a broad range of microbes and genes of biotechnological interest.

Description: Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.

Description: Anaerobic digestion can produce biogas as an eco-friendly energy source, driven by a microbial community-dependent process and, as such, suffer influences from many biotic and abiotic factors. Understanding the players and how they interact, the mechanisms involved, what the factors are, and how they influence the biogas process and production is an important way to better control it and make it more efficient. Metagenomic approach is a powerful tool to assess microbial diversity and further, allow correlating changes in microbial communities with multiple factors in virtually all environments. In the present study, we used metagenomic approach to assess microbial community structure changes in two biodigesters, differing in their biogas production capacity, architecture, and feed. A total of 1,440,096 reads of the 16S rRNA gene V4 region were obtained and analyzed. The main bacterial phyla were Firmicutes and Bacteroidetes in both biodigesters, but the biodiversity was greater in the Upflow Anaerobic Sludge Blanket (UASB) reactor fed with bovine manure than in the Continuous Stirred Tank Reactor (CSTR) fed with swine manure, which also correlated with an increase in biogas or methane production. Microbial community structure associated with biodigesters changed seasonally and depended on animal growth stage. Random forest algorithm analysis revealed key microbial taxa for each biodigester. Candidatus Cloacomonas, Methanospirillum, and Methanosphaera were the marker taxa for UASB and the archaea groups Methanobrevibacter and Candidatus Methanoplasma were the marker taxa for CSTR. A high abundance of Candidatus Methanoplasma and Marinimicrobia SAR406 clade suggested lower increments in methane production. Network analysis pointed to negative and positive associations and specific key groups, essential in maintaining the anaerobic digestion (AD) process, as being uncultured Parcubacteria bacteria, Candidatus Cloacomonas, and Candidatus Methanoplasma groups, whose functions in AD require investigation.

Description: The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where 〈200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples appears to be the most important factor in regards to the collection and preservation of samples from glacial environments.